TY  - JOUR
AU  - Stojanović, Srđan Đ.
AU  - Petrović, Zoran Z.
AU  - Zlatović, Mario
PY  - 2021
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4754
AB  - In this work, the influence of amide–π interactions on stability and properties of superoxide dismutase (SOD) active centres was analysed. In the data set of 43 proteins, 5017 amide–π interactions were observed, and every active centre formed averagely about 117 interactions. Most of the interactions belonged to the backbone of proteins. The analysis of the geometry of the amide–π interactions revealed two preferred structures, parallel-displaced and T-shaped structure. The aim of this study was to investigate the energy contribution resulting the from amide–π interactions, which were in the lower range of strong hydrogen bonds. The conservation patterns in the present study indicate that more than half of the residues involved in these interactions are evolutionarily conserved. The stabilization centres for these proteins showed that all residues involved in amide–π interactions were of use in locating one or more of such centres. The results presented in this work can be very useful for the understanding of contribution of amide–π interaction to the stability of SOD active centres.
PB  - Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - Amide-π interactions in active centers of superoxide dismutase
VL  - 86
IS  - 9
SP  - 781
EP  - 793
DO  - 10.2298/JSC210321042S
ER  - 

@article{
author = "Stojanović, Srđan Đ. and Petrović, Zoran Z. and Zlatović, Mario",
year = "2021",
abstract = "In this work, the influence of amide–π interactions on stability and properties of superoxide dismutase (SOD) active centres was analysed. In the data set of 43 proteins, 5017 amide–π interactions were observed, and every active centre formed averagely about 117 interactions. Most of the interactions belonged to the backbone of proteins. The analysis of the geometry of the amide–π interactions revealed two preferred structures, parallel-displaced and T-shaped structure. The aim of this study was to investigate the energy contribution resulting the from amide–π interactions, which were in the lower range of strong hydrogen bonds. The conservation patterns in the present study indicate that more than half of the residues involved in these interactions are evolutionarily conserved. The stabilization centres for these proteins showed that all residues involved in amide–π interactions were of use in locating one or more of such centres. The results presented in this work can be very useful for the understanding of contribution of amide–π interaction to the stability of SOD active centres.",
publisher = "Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "Amide-π interactions in active centers of superoxide dismutase",
volume = "86",
number = "9",
pages = "781-793",
doi = "10.2298/JSC210321042S"
}

Stojanović, S. Đ., Petrović, Z. Z.,& Zlatović, M.. (2021). Amide-π interactions in active centers of superoxide dismutase. in Journal of the Serbian Chemical Society
Serbian Chemical Society., 86(9), 781-793.
https://doi.org/10.2298/JSC210321042S

Stojanović SĐ, Petrović ZZ, Zlatović M. Amide-π interactions in active centers of superoxide dismutase. in Journal of the Serbian Chemical Society. 2021;86(9):781-793.
doi:10.2298/JSC210321042S .

Stojanović, Srđan Đ., Petrović, Zoran Z., Zlatović, Mario, "Amide-π interactions in active centers of superoxide dismutase" in Journal of the Serbian Chemical Society, 86, no. 9 (2021):781-793,
https://doi.org/10.2298/JSC210321042S . .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Zlatović, Mario
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2019
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3790
AB  - Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard-size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.
PB  - Willey
T2  - Molecular Informatics
T1  - Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces
VL  - 38
IS  - 11-12
SP  - 1800145
DO  - 10.1002/minf.201800145
ER  - 

@article{
author = "Breberina, Luka M. and Zlatović, Mario and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2019",
abstract = "Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard-size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.",
publisher = "Willey",
journal = "Molecular Informatics",
title = "Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces",
volume = "38",
number = "11-12",
pages = "1800145",
doi = "10.1002/minf.201800145"
}

Breberina, L. M., Zlatović, M., Nikolić, M.,& Stojanović, S. Đ.. (2019). Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics
Willey., 38(11-12), 1800145.
https://doi.org/10.1002/minf.201800145

Breberina LM, Zlatović M, Nikolić M, Stojanović SĐ. Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics. 2019;38(11-12):1800145.
doi:10.1002/minf.201800145 .

Breberina, Luka M., Zlatović, Mario, Nikolić, Milan, Stojanović, Srđan Đ., "Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces" in Molecular Informatics, 38, no. 11-12 (2019):1800145,
https://doi.org/10.1002/minf.201800145 . .

TY  - DATA
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3152
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3152
ER  - 

@misc{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3152"
}

Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam..
https://hdl.handle.net/21.15107/rcub_cherry_3152

Ribić VR, Stojanović SĐ, Zlatović M. Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050. in International Journal of Biological Macromolecules. 2018;.
https://hdl.handle.net/21.15107/rcub_cherry_3152 .

Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050" in International Journal of Biological Macromolecules (2018),
https://hdl.handle.net/21.15107/rcub_cherry_3152 .

TY  - JOUR
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3151
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 

@article{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}

Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050

Ribić VR, Stojanović SĐ, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .

Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .

TY  - JOUR
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/2564
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 

@article{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}

Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050

Ribić VR, Stojanović SĐ, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .

Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .

TY  - DATA
AU  - Borozan, Sunčica
AU  - Zlatović, Mario
AU  - Stojanović, Srđan Đ.
PY  - 2016
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3344
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - Supplementary data for the article: Borozan, S. Z.; Zlatović, M. V.; Stojanović, S. Đ. Anion–π Interactions in Complexes of Proteins and Halogen-Containing Amino Acids. Journal of Biological Inorganic Chemistry 2016, 21 (3), 357–368. https://doi.org/10.1007/s00775-016-1346-y
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3344
ER  - 

@misc{
author = "Borozan, Sunčica and Zlatović, Mario and Stojanović, Srđan Đ.",
year = "2016",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "Supplementary data for the article: Borozan, S. Z.; Zlatović, M. V.; Stojanović, S. Đ. Anion–π Interactions in Complexes of Proteins and Halogen-Containing Amino Acids. Journal of Biological Inorganic Chemistry 2016, 21 (3), 357–368. https://doi.org/10.1007/s00775-016-1346-y",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3344"
}

Borozan, S., Zlatović, M.,& Stojanović, S. Đ.. (2016). Supplementary data for the article: Borozan, S. Z.; Zlatović, M. V.; Stojanović, S. Đ. Anion–π Interactions in Complexes of Proteins and Halogen-Containing Amino Acids. Journal of Biological Inorganic Chemistry 2016, 21 (3), 357–368. https://doi.org/10.1007/s00775-016-1346-y. in Journal of Biological Inorganic Chemistry
Springer, New York..
https://hdl.handle.net/21.15107/rcub_cherry_3344

Borozan S, Zlatović M, Stojanović SĐ. Supplementary data for the article: Borozan, S. Z.; Zlatović, M. V.; Stojanović, S. Đ. Anion–π Interactions in Complexes of Proteins and Halogen-Containing Amino Acids. Journal of Biological Inorganic Chemistry 2016, 21 (3), 357–368. https://doi.org/10.1007/s00775-016-1346-y. in Journal of Biological Inorganic Chemistry. 2016;.
https://hdl.handle.net/21.15107/rcub_cherry_3344 .

Borozan, Sunčica, Zlatović, Mario, Stojanović, Srđan Đ., "Supplementary data for the article: Borozan, S. Z.; Zlatović, M. V.; Stojanović, S. Đ. Anion–π Interactions in Complexes of Proteins and Halogen-Containing Amino Acids. Journal of Biological Inorganic Chemistry 2016, 21 (3), 357–368. https://doi.org/10.1007/s00775-016-1346-y" in Journal of Biological Inorganic Chemistry (2016),
https://hdl.handle.net/21.15107/rcub_cherry_3344 .

TY  - JOUR
AU  - Borozan, Sunčica
AU  - Zlatović, Mario
AU  - Stojanović, Srđan Đ.
PY  - 2016
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1930
AB  - We analyzed the potential influence of anion-pi interactions on the stability of complexes of proteins and halogen-containing non-natural amino acids. Anion-pi interactions are distance and orientation dependent and our ab initio calculations showed that their energy can be lower than -8 kcal mol(-1), while most of their interaction energies lie in the range from -1 to -4 kcal mol(-1). About 20 % of these interactions were found to be repulsive. We have observed that Tyr has the highest occurrence among the aromatic residues involved in anion-pi interactions, while His made the least contribution. Furthermore, our study showed that 67 % of total interactions in the dataset are multiple anion-pi interactions. Most of the amino acid residues involved in anion-pi interactions tend to be buried in the solvent-excluded environment. The majority of the anion-pi interacting residues are located in regions with helical secondary structure. Analysis of stabilization centers for these complexes showed that all of the six residues capable of anion-pi interactions are important in locating one or more of such centers. We found that anion-pi interacting residues are sometimes involved in simultaneous interactions with halogens as well. With all that in mind, we can conclude that the anion-pi interactions can show significant influence on molecular organization and on the structural stability of the complexes of proteins and halogen-containing non-natural amino acids. Their influence should not be neglected in supramolecular chemistry and crystal engineering fields as well.
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - Anion-pi interactions in complexes of proteins and halogen-containing amino acids
VL  - 21
IS  - 3
SP  - 357
EP  - 368
DO  - 10.1007/s00775-016-1346-y
ER  - 

@article{
author = "Borozan, Sunčica and Zlatović, Mario and Stojanović, Srđan Đ.",
year = "2016",
abstract = "We analyzed the potential influence of anion-pi interactions on the stability of complexes of proteins and halogen-containing non-natural amino acids. Anion-pi interactions are distance and orientation dependent and our ab initio calculations showed that their energy can be lower than -8 kcal mol(-1), while most of their interaction energies lie in the range from -1 to -4 kcal mol(-1). About 20 % of these interactions were found to be repulsive. We have observed that Tyr has the highest occurrence among the aromatic residues involved in anion-pi interactions, while His made the least contribution. Furthermore, our study showed that 67 % of total interactions in the dataset are multiple anion-pi interactions. Most of the amino acid residues involved in anion-pi interactions tend to be buried in the solvent-excluded environment. The majority of the anion-pi interacting residues are located in regions with helical secondary structure. Analysis of stabilization centers for these complexes showed that all of the six residues capable of anion-pi interactions are important in locating one or more of such centers. We found that anion-pi interacting residues are sometimes involved in simultaneous interactions with halogens as well. With all that in mind, we can conclude that the anion-pi interactions can show significant influence on molecular organization and on the structural stability of the complexes of proteins and halogen-containing non-natural amino acids. Their influence should not be neglected in supramolecular chemistry and crystal engineering fields as well.",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "Anion-pi interactions in complexes of proteins and halogen-containing amino acids",
volume = "21",
number = "3",
pages = "357-368",
doi = "10.1007/s00775-016-1346-y"
}

Borozan, S., Zlatović, M.,& Stojanović, S. Đ.. (2016). Anion-pi interactions in complexes of proteins and halogen-containing amino acids. in Journal of Biological Inorganic Chemistry
Springer, New York., 21(3), 357-368.
https://doi.org/10.1007/s00775-016-1346-y

Borozan S, Zlatović M, Stojanović SĐ. Anion-pi interactions in complexes of proteins and halogen-containing amino acids. in Journal of Biological Inorganic Chemistry. 2016;21(3):357-368.
doi:10.1007/s00775-016-1346-y .

Borozan, Sunčica, Zlatović, Mario, Stojanović, Srđan Đ., "Anion-pi interactions in complexes of proteins and halogen-containing amino acids" in Journal of Biological Inorganic Chemistry, 21, no. 3 (2016):357-368,
https://doi.org/10.1007/s00775-016-1346-y . .

TY  - JOUR
AU  - Mucic, Ivana D.
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2015
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1732
AB  - In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation-pi residues shows that Arg and Lys preferred to be in strand. Among the pi residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. More than 50 % of the cation-pi interacting residues are highly conserved. It is likely that the cation-pi interactions contribute significantly to the overall stability of Sm/LSm proteins.
PB  - Springer Wien, Wien
T2  - Protoplasma
T1  - Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies
VL  - 252
IS  - 4
SP  - 947
EP  - 958
DO  - 10.1007/s00709-014-0727-8
ER  - 

@article{
author = "Mucic, Ivana D. and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2015",
abstract = "In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation-pi residues shows that Arg and Lys preferred to be in strand. Among the pi residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. More than 50 % of the cation-pi interacting residues are highly conserved. It is likely that the cation-pi interactions contribute significantly to the overall stability of Sm/LSm proteins.",
publisher = "Springer Wien, Wien",
journal = "Protoplasma",
title = "Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies",
volume = "252",
number = "4",
pages = "947-958",
doi = "10.1007/s00709-014-0727-8"
}

Mucic, I. D., Nikolić, M.,& Stojanović, S. Đ.. (2015). Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies. in Protoplasma
Springer Wien, Wien., 252(4), 947-958.
https://doi.org/10.1007/s00709-014-0727-8

Mucic ID, Nikolić M, Stojanović SĐ. Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies. in Protoplasma. 2015;252(4):947-958.
doi:10.1007/s00709-014-0727-8 .

Mucic, Ivana D., Nikolić, Milan, Stojanović, Srđan Đ., "Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies" in Protoplasma, 252, no. 4 (2015):947-958,
https://doi.org/10.1007/s00709-014-0727-8 . .

TY  - JOUR
AU  - Zlatović, Mario
AU  - Borozan, Sunčica
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2015
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1705
AB  - In this work, we have analyzed the influence of anion-pi interactions on the stability of high resolution protein-porphyrin complex crystal structures. The anion-pi interactions are distance and orientation dependent. Results of ab initio calculations of stabilization energies showed that they lie mostly in the range from -2 to -4 kcal mol(-1) with some of the anion-pi interactions having stabilization energies of up to -16 kcal mol(-1). In the anionic group, the numbers of anion-pi interactions involving Asp and Glu are similar, while His is more often involved in these interactions than other aromatic residues. Furthermore, our study showed that in the dataset used about 70% of the investigated anion-pi interactions are in fact multiple anion-pi interactions. Our results suggest that interacting residues are predominantly located in buried and partially buried regions. The secondary structure of the anion-pi interaction involving residues shows that most of the interacting residues preferred to be in helix conformations. Significant numbers of aromatic residues involved in anion-pi interactions have one or more stabilization centers, providing additional stability to the protein-porphyrin complexes. The conservation patterns indicate that more than half of the residues involved in these interactions are evolutionarily conserved, indicating that the contribution of the anion-pi interaction is an important factor for the structural stability of the investigated protein-porphyrin complexes.
PB  - Royal Soc Chemistry, Cambridge
T2  - RSC Advances
T1  - Anion-pi interactions in protein-porphyrin complexes
VL  - 5
IS  - 48
SP  - 38361
EP  - 38372
DO  - 10.1039/c5ra03373j
ER  - 

@article{
author = "Zlatović, Mario and Borozan, Sunčica and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2015",
abstract = "In this work, we have analyzed the influence of anion-pi interactions on the stability of high resolution protein-porphyrin complex crystal structures. The anion-pi interactions are distance and orientation dependent. Results of ab initio calculations of stabilization energies showed that they lie mostly in the range from -2 to -4 kcal mol(-1) with some of the anion-pi interactions having stabilization energies of up to -16 kcal mol(-1). In the anionic group, the numbers of anion-pi interactions involving Asp and Glu are similar, while His is more often involved in these interactions than other aromatic residues. Furthermore, our study showed that in the dataset used about 70% of the investigated anion-pi interactions are in fact multiple anion-pi interactions. Our results suggest that interacting residues are predominantly located in buried and partially buried regions. The secondary structure of the anion-pi interaction involving residues shows that most of the interacting residues preferred to be in helix conformations. Significant numbers of aromatic residues involved in anion-pi interactions have one or more stabilization centers, providing additional stability to the protein-porphyrin complexes. The conservation patterns indicate that more than half of the residues involved in these interactions are evolutionarily conserved, indicating that the contribution of the anion-pi interaction is an important factor for the structural stability of the investigated protein-porphyrin complexes.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "RSC Advances",
title = "Anion-pi interactions in protein-porphyrin complexes",
volume = "5",
number = "48",
pages = "38361-38372",
doi = "10.1039/c5ra03373j"
}

Zlatović, M., Borozan, S., Nikolić, M.,& Stojanović, S. Đ.. (2015). Anion-pi interactions in protein-porphyrin complexes. in RSC Advances
Royal Soc Chemistry, Cambridge., 5(48), 38361-38372.
https://doi.org/10.1039/c5ra03373j

Zlatović M, Borozan S, Nikolić M, Stojanović SĐ. Anion-pi interactions in protein-porphyrin complexes. in RSC Advances. 2015;5(48):38361-38372.
doi:10.1039/c5ra03373j .

Zlatović, Mario, Borozan, Sunčica, Nikolić, Milan, Stojanović, Srđan Đ., "Anion-pi interactions in protein-porphyrin complexes" in RSC Advances, 5, no. 48 (2015):38361-38372,
https://doi.org/10.1039/c5ra03373j . .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Milčić, Miloš K.
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2015
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1481
AB  - We have analyzed the influence of anion-pi interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-pi interactions than Asp. Phe has the highest occurrence in these interactions than the other two pi residues. Among the anion-pi residue pairs, Glu-Phe residue pair showed the maximum number of anion-pi. We have found hot-spot residues forming anion-pi interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-pi interacting residues identified in the dataset were involved in the formation of multiple anion-pi interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-pi interaction energies are distance and orientation dependent. It was found that anion-pi interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-pi interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same pi-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-pi interaction to the stability of Sm/LSm proteins.
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - Contribution of anion-pi interactions to the stability of Sm/LSm proteins
VL  - 20
IS  - 3
SP  - 475
EP  - 485
DO  - 10.1007/s00775-014-1227-1
ER  - 

@article{
author = "Breberina, Luka M. and Milčić, Miloš K. and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2015",
abstract = "We have analyzed the influence of anion-pi interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-pi interactions than Asp. Phe has the highest occurrence in these interactions than the other two pi residues. Among the anion-pi residue pairs, Glu-Phe residue pair showed the maximum number of anion-pi. We have found hot-spot residues forming anion-pi interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-pi interacting residues identified in the dataset were involved in the formation of multiple anion-pi interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-pi interaction energies are distance and orientation dependent. It was found that anion-pi interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-pi interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same pi-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-pi interaction to the stability of Sm/LSm proteins.",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "Contribution of anion-pi interactions to the stability of Sm/LSm proteins",
volume = "20",
number = "3",
pages = "475-485",
doi = "10.1007/s00775-014-1227-1"
}

Breberina, L. M., Milčić, M. K., Nikolić, M.,& Stojanović, S. Đ.. (2015). Contribution of anion-pi interactions to the stability of Sm/LSm proteins. in Journal of Biological Inorganic Chemistry
Springer, New York., 20(3), 475-485.
https://doi.org/10.1007/s00775-014-1227-1

Breberina LM, Milčić MK, Nikolić M, Stojanović SĐ. Contribution of anion-pi interactions to the stability of Sm/LSm proteins. in Journal of Biological Inorganic Chemistry. 2015;20(3):475-485.
doi:10.1007/s00775-014-1227-1 .

Breberina, Luka M., Milčić, Miloš K., Nikolić, Milan, Stojanović, Srđan Đ., "Contribution of anion-pi interactions to the stability of Sm/LSm proteins" in Journal of Biological Inorganic Chemistry, 20, no. 3 (2015):475-485,
https://doi.org/10.1007/s00775-014-1227-1 . .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Nikolić, Milan
AU  - Stojanović, Srđan Đ.
PY  - 2014
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/82
AB  - In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins.
AB  - U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.
T2  - Facta Universitatis: Series Physics, Chemistry and Technology
T1  - Aromatic π-networks in Sm/LSm protein interfaces
T1  - Aromatična π-mreža u interfejsima Sm/LSm proteina
VL  - 12
IS  - 1
SP  - 27
EP  - 39
DO  - 10.2298/FUPCT1401027B
ER  - 

@article{
author = "Breberina, Luka M. and Nikolić, Milan and Stojanović, Srđan Đ.",
year = "2014",
abstract = "In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins., U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.",
journal = "Facta Universitatis: Series Physics, Chemistry and Technology",
title = "Aromatic π-networks in Sm/LSm protein interfaces, Aromatična π-mreža u interfejsima Sm/LSm proteina",
volume = "12",
number = "1",
pages = "27-39",
doi = "10.2298/FUPCT1401027B"
}

Breberina, L. M., Nikolić, M.,& Stojanović, S. Đ.. (2014). Aromatic π-networks in Sm/LSm protein interfaces. in Facta Universitatis: Series Physics, Chemistry and Technology, 12(1), 27-39.
https://doi.org/10.2298/FUPCT1401027B

Breberina LM, Nikolić M, Stojanović SĐ. Aromatic π-networks in Sm/LSm protein interfaces. in Facta Universitatis: Series Physics, Chemistry and Technology. 2014;12(1):27-39.
doi:10.2298/FUPCT1401027B .

Breberina, Luka M., Nikolić, Milan, Stojanović, Srđan Đ., "Aromatic π-networks in Sm/LSm protein interfaces" in Facta Universitatis: Series Physics, Chemistry and Technology, 12, no. 1 (2014):27-39,
https://doi.org/10.2298/FUPCT1401027B . .

TY  - JOUR
AU  - Zarić, Božidarka L.
AU  - Jovanović, Vesna B.
AU  - Stojanović, Srđan Đ.
PY  - 2011
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1140
AB  - The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures. (C) 2010 Elsevier Ltd. All rights reserved.
PB  - Academic Press Ltd- Elsevier Science Ltd, London
T2  - Journal of Theoretical Biology
T1  - Non-covalent interactions across subunit interfaces in Sm proteins
VL  - 271
IS  - 1
SP  - 18
EP  - 26
DO  - 10.1016/j.jtbi.2010.11.025
ER  - 

@article{
author = "Zarić, Božidarka L. and Jovanović, Vesna B. and Stojanović, Srđan Đ.",
year = "2011",
abstract = "The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures. (C) 2010 Elsevier Ltd. All rights reserved.",
publisher = "Academic Press Ltd- Elsevier Science Ltd, London",
journal = "Journal of Theoretical Biology",
title = "Non-covalent interactions across subunit interfaces in Sm proteins",
volume = "271",
number = "1",
pages = "18-26",
doi = "10.1016/j.jtbi.2010.11.025"
}

Zarić, B. L., Jovanović, V. B.,& Stojanović, S. Đ.. (2011). Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology
Academic Press Ltd- Elsevier Science Ltd, London., 271(1), 18-26.
https://doi.org/10.1016/j.jtbi.2010.11.025

Zarić BL, Jovanović VB, Stojanović SĐ. Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology. 2011;271(1):18-26.
doi:10.1016/j.jtbi.2010.11.025 .

Zarić, Božidarka L., Jovanović, Vesna B., Stojanović, Srđan Đ., "Non-covalent interactions across subunit interfaces in Sm proteins" in Journal of Theoretical Biology, 271, no. 1 (2011):18-26,
https://doi.org/10.1016/j.jtbi.2010.11.025 . .

TY  - JOUR
AU  - Stojanović, Srđan Đ.
AU  - Zarić, Božidarka L.
AU  - Zarić, Snežana D.
PY  - 2010
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1123
AB  - The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between the interfaces of Sm proteins and those of the BID set are the content of charged residues, the coordination numbers of the residues, knowledge-based pair potentials, and the conservation scores of hot spots. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surfaces, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Hot spots are residues that make up a small fraction of the interfaces, but they contribute most of the binding energy. These residues are critical to protein-protein interactions. Analyses of knowledge-based pair potentials of hot spot and non-hot spot residues in Sm proteins show that they are significantly different; their mean values are 31.5 and 11.3, respectively. In the BID set, this difference is smaller; in this case, the mean values for hot spot and non-hot spot residues are 20.7 and 12.4, respectively. Hence, the pair potentials of hot spots differ significantly for the Sm and BID data sets. In the interfaces of Sm proteins, the amino acids are tightly packed, and the coordination numbers are larger in Sm proteins than in the BID set for both hot spots and non-hot spots. At the same time, the coordination numbers are higher for hot spots; the average coordination number of the hot spot residues in Sm proteins is 7.7, while it is 6.1 for the non-hot spot residues. The difference in the calculated average conservation score for hot spots and non-hot spots in Sm proteins is significantly larger than it is in the BID set. In Sm proteins, the average conservation score for the hot spots is 7.4. Hot spots are surrounded by residues that are moderately conserved (5.9). The average conservation score for the other interface residues is 5.6. The conservation scores in the BID set do not show a significant distinction between hot and non-hot spots: the mean values for hot and non-hot spot residues are 5.5 and 5.2, respectively. These data show that structurally conserved residues and hot spots are significantly correlated in Sm proteins.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins
VL  - 16
IS  - 11
SP  - 1743
EP  - 1751
DO  - 10.1007/s00894-010-0787-4
ER  - 

@article{
author = "Stojanović, Srđan Đ. and Zarić, Božidarka L. and Zarić, Snežana D.",
year = "2010",
abstract = "The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between the interfaces of Sm proteins and those of the BID set are the content of charged residues, the coordination numbers of the residues, knowledge-based pair potentials, and the conservation scores of hot spots. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surfaces, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Hot spots are residues that make up a small fraction of the interfaces, but they contribute most of the binding energy. These residues are critical to protein-protein interactions. Analyses of knowledge-based pair potentials of hot spot and non-hot spot residues in Sm proteins show that they are significantly different; their mean values are 31.5 and 11.3, respectively. In the BID set, this difference is smaller; in this case, the mean values for hot spot and non-hot spot residues are 20.7 and 12.4, respectively. Hence, the pair potentials of hot spots differ significantly for the Sm and BID data sets. In the interfaces of Sm proteins, the amino acids are tightly packed, and the coordination numbers are larger in Sm proteins than in the BID set for both hot spots and non-hot spots. At the same time, the coordination numbers are higher for hot spots; the average coordination number of the hot spot residues in Sm proteins is 7.7, while it is 6.1 for the non-hot spot residues. The difference in the calculated average conservation score for hot spots and non-hot spots in Sm proteins is significantly larger than it is in the BID set. In Sm proteins, the average conservation score for the hot spots is 7.4. Hot spots are surrounded by residues that are moderately conserved (5.9). The average conservation score for the other interface residues is 5.6. The conservation scores in the BID set do not show a significant distinction between hot and non-hot spots: the mean values for hot and non-hot spot residues are 5.5 and 5.2, respectively. These data show that structurally conserved residues and hot spots are significantly correlated in Sm proteins.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins",
volume = "16",
number = "11",
pages = "1743-1751",
doi = "10.1007/s00894-010-0787-4"
}

Stojanović, S. Đ., Zarić, B. L.,& Zarić, S. D.. (2010). Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins. in Journal of Molecular Modeling
Springer, New York., 16(11), 1743-1751.
https://doi.org/10.1007/s00894-010-0787-4

Stojanović SĐ, Zarić BL, Zarić SD. Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins. in Journal of Molecular Modeling. 2010;16(11):1743-1751.
doi:10.1007/s00894-010-0787-4 .

Stojanović, Srđan Đ., Zarić, Božidarka L., Zarić, Snežana D., "Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins" in Journal of Molecular Modeling, 16, no. 11 (2010):1743-1751,
https://doi.org/10.1007/s00894-010-0787-4 . .

TY  - JOUR
AU  - Malkov, Saga N.
AU  - Živković, Miodrag V.
AU  - Beljanski, Milos V.
AU  - Stojanović, Srđan Đ.
AU  - Zarić, Snežana D.
PY  - 2009
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/991
AB  - Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.
PB  - Springer, New York
T2  - Protein Journal
T1  - A Reexamination of Correlations of Amino Acids with Particular Secondary Structures
VL  - 28
IS  - 2
SP  - 74
EP  - 86
DO  - 10.1007/s10930-009-9166-3
ER  - 

@article{
author = "Malkov, Saga N. and Živković, Miodrag V. and Beljanski, Milos V. and Stojanović, Srđan Đ. and Zarić, Snežana D.",
year = "2009",
abstract = "Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.",
publisher = "Springer, New York",
journal = "Protein Journal",
title = "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures",
volume = "28",
number = "2",
pages = "74-86",
doi = "10.1007/s10930-009-9166-3"
}

Malkov, S. N., Živković, M. V., Beljanski, M. V., Stojanović, S. Đ.,& Zarić, S. D.. (2009). A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal
Springer, New York., 28(2), 74-86.
https://doi.org/10.1007/s10930-009-9166-3

Malkov SN, Živković MV, Beljanski MV, Stojanović SĐ, Zarić SD. A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal. 2009;28(2):74-86.
doi:10.1007/s10930-009-9166-3 .

Malkov, Saga N., Živković, Miodrag V., Beljanski, Milos V., Stojanović, Srđan Đ., Zarić, Snežana D., "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures" in Protein Journal, 28, no. 2 (2009):74-86,
https://doi.org/10.1007/s10930-009-9166-3 . .

TY  - JOUR
AU  - Stojanović, Srđan Đ.
AU  - Medaković, Vesna
AU  - Predovic, Goran
AU  - Beljanski, Milos
AU  - Zarić, Snežana D.
PY  - 2007
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/863
AB  - Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins
VL  - 12
IS  - 7
SP  - 1063
EP  - 1071
DO  - 10.1007/s00775-007-0276-0
ER  - 

@article{
author = "Stojanović, Srđan Đ. and Medaković, Vesna and Predovic, Goran and Beljanski, Milos and Zarić, Snežana D.",
year = "2007",
abstract = "Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins",
volume = "12",
number = "7",
pages = "1063-1071",
doi = "10.1007/s00775-007-0276-0"
}

Stojanović, S. Đ., Medaković, V., Predovic, G., Beljanski, M.,& Zarić, S. D.. (2007). XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry
Springer, New York., 12(7), 1063-1071.
https://doi.org/10.1007/s00775-007-0276-0

Stojanović SĐ, Medaković V, Predovic G, Beljanski M, Zarić SD. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry. 2007;12(7):1063-1071.
doi:10.1007/s00775-007-0276-0 .

Stojanović, Srđan Đ., Medaković, Vesna, Predovic, Goran, Beljanski, Milos, Zarić, Snežana D., "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins" in Journal of Biological Inorganic Chemistry, 12, no. 7 (2007):1063-1071,
https://doi.org/10.1007/s00775-007-0276-0 . .

TY  - THES
AU  - Stojanović, Srđan Đ.
PY  - 2004
UR  - http://eteze.bg.ac.rs/application/showtheses?thesesId=968
UR  - https://fedorabg.bg.ac.rs/fedora/get/o:7550/bdef:Content/download
UR  - http://vbs.rs/scripts/cobiss?command=DISPLAY&base=70036&RID=29155087
UR  - http://nardus.mpn.gov.rs/123456789/3483
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/2630
AB  - Sisаri su izlоžеni еndоgеnim i еgzоgеnim izvоrimа аzоt mоnоksidа (NO). U biоlоškој srеdini NO pоdlеžе kоmplеksnim rеаkciјаmа u kојimа nаstајu vrstе rеаktivniје оd sаmоg аzоt mоnоksidа (RNOC), kоје su uklјučеnе u mnоgе fiziоlоškе i (nаrоčitо) pаtоfiziоlоškе prоcеsе. Оvе rеаkciје оbuhvаtајu i kоnvеrziјu NO u njеgоvе rеаktivnе srоdnikе, nitrоzоniјum јоn (NO+) i nitrоksilni (HNO/NO-) аnјоn, kојi mоgu rеаgоvаti sа rаznim cilјnim mоlеkulimа u biоlоškim sistеmimа štо imа vаžnu ulоgu u NO pоsrеdоvаnim prоcеsimа. Prеdlоžеnо је dа u biоlоškim sistеmimа NO prеlаzi u NO+ ili  HNO/NO- vrstе оksidаciјоm оdnоsnо rеdukciјоm NO pоmоću mеtаlnih јоnа. Мi smо pоstаvili hipоtеzu dа kаtаlizоm pоmоću SOD i "slоbоdnоg" gvоžđа NO mоžе dа dismutuје (2NO → NO+ + HNO/NO-) dајući оbе vrstе. U prvоm dеlu rаdа ispitivаn је еfеkаt NO nа аktivnоst svе tri klаsе SOD: gоvеđu Cu/ZnSOD, MnSOD (E.coli), FeSOD (E.coli) i FeSOD (P.leiognathi), а dеtаlјnо su ispitаnе mоdifikаciје MnSOD nаkоn trеtirаnjа sа NO. Nаđеnо је dа је Cu/ZnSOD stаbilnа pri inkubirаnju sа NO: čаk i pri prоdužеnоm inkubirаnju niје dоšlо dо znаčајnih prоmеnа u strukturi i аktivnоsti еnzimа. Inkubirаnjе FeSOD i MnSOD sа NO dоvоdi dо brzе i znаtnе inаktivаciје еnzimа. Pоkаzаnо је dа inаktivаciја MnSOD nаstаје kао pоslеdicа еkstеnzivnih mоdifikаciја mоlеkulа еnzimа: frаgmеntаciје pоlipеptidnоg nizа nа оstаcimа histidinа u аktivnоm cеntru, mоdifikаciја аminо grupа, nitrоvаnjа i оksidаciје оstаtаkа tirоzinа. Dоkumеntоvаnо је dа FeSOD i MnSOD kаtаlizuјu dismutаciјu NO u NO+ i NO- vrstе kоје izаzivајu mоdifikаciјu i inаktivаciјu еnzimа. U drugоm dеlu rаdа ispitivаnа је spоsоbnоst trаgоvа јоnа gvоžđа nа dismutаciјu NO. Nаstајаnjе NO+ vrstа rеzultuје u sintеzi S-nitrоzоtiоlа (RSNO) i nitritа, а HNO/NO- u nаstајаnju hidrоksilаminа. Hidrоksilаmin је dеtеktоvаn u rаstvоrimа јоnа gvоžđа inkubirаnim sа NO u prisustvu cistеinа, аli nе i glutаtiоnа (GSH). Pоkаzаnо је dа dоdаtаk urаtа, dоminаntnоg аgеnsа zа vеzivаnjе "slоbоdnоg" gvоžđа, u rаstvоr glutаtiоnа i јоnа gvоžđа prе njihоvоg inkubirаnjа sа NO, dоvоdi dо pоvеćаnе sintеzе GSNO i nаstајаnjа hidrоksilаminа, uz gubitаk urаtа kојi prеlаzi u nitrоzо/nitrо prоizvоdе kојi nisu zа sаdа idеntifikоvаni. Utvrđеnо је dа GSH štiti urаt оd rаspаdаnjа; еfеkаt zаvisi оd оdnоsа GSH:urаt. U nеutrаlnim rаstvоrimа prоtеinа i јоnа gvоžđа inkubirаnih sа NO u prisustvu (аli nе i u оdsustvu) urаtа dеtеktоvаn је hidrоksilаmin i S-nitrоzоvаnjе prоtеinа. RNOS gеnеrisаnе kао pоslеdicа dismutаciје NO u rаstvоrimа tirоzinа i јоnа gvоžđа izаzivајu nitrоvаnjе i оksidаciјu tirоzinа. U trеćеm dеlu је u in vitro еkspеrimеntimа ispitivаnа dismutаciја NO kаtаlizоvаnа "slоbоdnim" gvоžđеm u cеrеbrоspinаlnој tеčnоsti (CSF) zdrаvih оsоbа i оsоbа оbоlеlih оd аmiоtrоfičnе lаtеrаlnе sklеrоzе (SALS). Nivо аntiоksidаnаtа,  prоtеinskih SH grupа, аskоrbаtа i urаtа, kојi prеdstаvlјајu ligаndе zа dinitrоzil-gvоžđе kоmplеksе (DNIC) sа "slоbоdnim" gvоžđеm  i/ili hvаtаčе NO+ i HNO/NO- vrstа је prоmеnjеn kоd SALS pаciјеnаtа. Dа "slоbоdnо" gvоžđе kаtаlizuје dismutаciјu NO је dоkаzаnо nаstајаnjеm RSNO i hidrоksilаminа u CSF uzоrcimа inkubirаnim sа NO in vitro, оdnоsnо pоtpunоm inhibiciјоm оvih rеаkciја pоmоću о-fеnаntrоlinа, hеlаtоrа zа јоnе gvоžđа. Pоkаzаnо је dа RNOS gеnеrisаnе dismutаciјоm NO rеаguјu sа аskоrbаtоm i urаtоm, štо dоvоdi dо njihоvоg gubitkа, dа prisustvо urаtа pоvеćаvа kаpаcitеt "slоbоdnоg" gvоžđа dа kаtаlizuје NO dismutаciјu, dоk је аskоrbаt bоlјi hvаtаč оd urаtа zа gеnеrisаnе RNOS. Vеći prinоs RSNO, nitritа, hidrоksilаminа i 3-nitrоtirоzinа u CSF uzоrcimа SALS pаciјеnаtа inkubirаnih sа NO u оdnоsu nа kоličinе nаđеnе u kоntrоlnim CSF uzоrcimа mоžе dа sе оbјаsni pоvеćаnim nivооm urаtа i smаnjеnim nivооm аskоrbаtа u CSF uzоrcimа SALS pаciјеnаtа. Rеzultаti prеzеntirаni u оvоm rаdu ubеdlјivо pоkаzuјu dа mеtаl-pоsrеdоvаnа dismutаciја NO u biоlоškim uslоvimа nе sаmо dа је mоgućа nеgо је i fiziоlоški rеlеvаntnа. Zbоg tоgа fiziоlоški znаčај mеtаl pоsrеdоvаnе dismutаciје NO zаslužuје dаlја istrаživаnjа.
AB  - Mammalian systems are exposed to nitric oxide (NO) through both exogenous and endogenous sources. Once formed, NO undergoes a complex series of reactions which lead to formation of several species more reactive than NO itself. Reactive nitrogen species (RNOS) derived from NO have been implicated in numerous physiological and (particularly) pathophysiological processes. These include NO conversion into its reactive congeners, nitrosonium (NO+) and nitroxyl (HNO/NO-) species, which both could react with various target molecules in biological systems with important consequences for NO mediated processes. It was suggested that in a biological system NO may be converted either to NO+ or HNO/NO- species by metal-catalyzed oxidation or reduction of NO, respectively. We hypothesized that the conversion of NO into both NO+ and HNO/NO- species may occur through the metal assisted NO dismutation (2NO → NO+ + HNO/NO-) catalyzed by SODs and "free" iron. The effect of NO treatment in vitro on structural and functional alterations of Cu/Zn, Mn, and Fe type of SODs was studied. Significant difference in response to NO of Cu/ZnSOD compared to the Mn and Fe types was demonstrated. Cu/ZnSOD was shown to be stable with respect to NO: even on prolonged exposure, NO produced negligible effect on its structure and activity. In contrast, exposure to NO led to fast and extensive inactivation of both Mn and Fe types. Inactivation of MnSOD was demonstrated to be due to the extensive structural alterations, including the cleavage of enzyme polypeptide chains, presumably at His residues of the enzyme metal binding sites, amino groups modifications, tyrosine residue nitration and oxidation. The generation of nitrosonium and nitroxyl ions in NO treated Mn and FeSODs, which produce enzyme modifications and inactivation, was demonstrated. Dinitrosyl iron complex (DNIC) initiated iron ion catalyzed NO dismutation into NO+, resulting in the synthesis of S-nitrosothiols (RSNO) and nitrite, and into HNO/NO- to produce hydroxylamine was demonstrated. Hydroxylamine was detected in NO treated solutions of iron ions in the presence of cysteine, but not glutathione. The addition of urate, a major "free" iron-binding agent in humans, to solutions of GSH and iron ions and the subsequent treatment of these solutions with NO increased the synthesis of GSNO and resulted in the formation of hydroxylamine. This caused a loss of urate and yielded a novel nitrosative/nitration product. GSH attenuated the urate decomposition to such a degree that it could be reflected as the function of GSH:urate. NO treatment of a neutral solution containing proteins and iron ions in the presence of urate, but not in its absence, resulted in hydroxylamine formation and protein S-nitrosation. The consequences of NO exposure in vitro were tested on cerebrospinal fluid (CSF), system containing "free" iron and constituents such as protein-SH groups, ascorbate and urate which represent ligands and/or scavengers of both NO+ and HNO/NO- species. The results demonstrate that "free" iron in CSF can catalyze NO dismutation as evidenced from the formation of both RSNO and hydroxylamine in CSF exposed to NO in vitro which was inhibited upon addition of iron ion chelator o-phenanthroline. NO treatment caused loss of CSF ascorbate and urate. Urate and ascorbate levels were found to affect both "free" iron ion catalyzed NO dismutation as well as the reactions of protein -SH groups with NO+ and HNO/NO- species. Results described in this work suggest that metal/assisted NO dismutation into NO+ and HNO/NO- species in biological systems may be feasible and possibly physiologically relevant.
PB  - Универзитет у Београду, Хемијски факултет
T2  - Универзитет у Београду
T1  - Dismutacija azot monoksida u biološkim i model sistemima : in vitro ispitivanja
T1  - Dismutation of nitric oxide in biological and model systems: in vitro study
UR  - https://hdl.handle.net/21.15107/rcub_nardus_3483
ER  - 

@phdthesis{
author = "Stojanović, Srđan Đ.",
year = "2004",
abstract = "Sisаri su izlоžеni еndоgеnim i еgzоgеnim izvоrimа аzоt mоnоksidа (NO). U biоlоškој srеdini NO pоdlеžе kоmplеksnim rеаkciјаmа u kојimа nаstајu vrstе rеаktivniје оd sаmоg аzоt mоnоksidа (RNOC), kоје su uklјučеnе u mnоgе fiziоlоškе i (nаrоčitо) pаtоfiziоlоškе prоcеsе. Оvе rеаkciје оbuhvаtајu i kоnvеrziјu NO u njеgоvе rеаktivnе srоdnikе, nitrоzоniјum јоn (NO+) i nitrоksilni (HNO/NO-) аnјоn, kојi mоgu rеаgоvаti sа rаznim cilјnim mоlеkulimа u biоlоškim sistеmimа štо imа vаžnu ulоgu u NO pоsrеdоvаnim prоcеsimа. Prеdlоžеnо је dа u biоlоškim sistеmimа NO prеlаzi u NO+ ili  HNO/NO- vrstе оksidаciјоm оdnоsnо rеdukciјоm NO pоmоću mеtаlnih јоnа. Мi smо pоstаvili hipоtеzu dа kаtаlizоm pоmоću SOD i "slоbоdnоg" gvоžđа NO mоžе dа dismutuје (2NO → NO+ + HNO/NO-) dајući оbе vrstе. U prvоm dеlu rаdа ispitivаn је еfеkаt NO nа аktivnоst svе tri klаsе SOD: gоvеđu Cu/ZnSOD, MnSOD (E.coli), FeSOD (E.coli) i FeSOD (P.leiognathi), а dеtаlјnо su ispitаnе mоdifikаciје MnSOD nаkоn trеtirаnjа sа NO. Nаđеnо је dа је Cu/ZnSOD stаbilnа pri inkubirаnju sа NO: čаk i pri prоdužеnоm inkubirаnju niје dоšlо dо znаčајnih prоmеnа u strukturi i аktivnоsti еnzimа. Inkubirаnjе FeSOD i MnSOD sа NO dоvоdi dо brzе i znаtnе inаktivаciје еnzimа. Pоkаzаnо је dа inаktivаciја MnSOD nаstаје kао pоslеdicа еkstеnzivnih mоdifikаciја mоlеkulа еnzimа: frаgmеntаciје pоlipеptidnоg nizа nа оstаcimа histidinа u аktivnоm cеntru, mоdifikаciја аminо grupа, nitrоvаnjа i оksidаciје оstаtаkа tirоzinа. Dоkumеntоvаnо је dа FeSOD i MnSOD kаtаlizuјu dismutаciјu NO u NO+ i NO- vrstе kоје izаzivајu mоdifikаciјu i inаktivаciјu еnzimа. U drugоm dеlu rаdа ispitivаnа је spоsоbnоst trаgоvа јоnа gvоžđа nа dismutаciјu NO. Nаstајаnjе NO+ vrstа rеzultuје u sintеzi S-nitrоzоtiоlа (RSNO) i nitritа, а HNO/NO- u nаstајаnju hidrоksilаminа. Hidrоksilаmin је dеtеktоvаn u rаstvоrimа јоnа gvоžđа inkubirаnim sа NO u prisustvu cistеinа, аli nе i glutаtiоnа (GSH). Pоkаzаnо је dа dоdаtаk urаtа, dоminаntnоg аgеnsа zа vеzivаnjе "slоbоdnоg" gvоžđа, u rаstvоr glutаtiоnа i јоnа gvоžđа prе njihоvоg inkubirаnjа sа NO, dоvоdi dо pоvеćаnе sintеzе GSNO i nаstајаnjа hidrоksilаminа, uz gubitаk urаtа kојi prеlаzi u nitrоzо/nitrо prоizvоdе kојi nisu zа sаdа idеntifikоvаni. Utvrđеnо је dа GSH štiti urаt оd rаspаdаnjа; еfеkаt zаvisi оd оdnоsа GSH:urаt. U nеutrаlnim rаstvоrimа prоtеinа i јоnа gvоžđа inkubirаnih sа NO u prisustvu (аli nе i u оdsustvu) urаtа dеtеktоvаn је hidrоksilаmin i S-nitrоzоvаnjе prоtеinа. RNOS gеnеrisаnе kао pоslеdicа dismutаciје NO u rаstvоrimа tirоzinа i јоnа gvоžđа izаzivајu nitrоvаnjе i оksidаciјu tirоzinа. U trеćеm dеlu је u in vitro еkspеrimеntimа ispitivаnа dismutаciја NO kаtаlizоvаnа "slоbоdnim" gvоžđеm u cеrеbrоspinаlnој tеčnоsti (CSF) zdrаvih оsоbа i оsоbа оbоlеlih оd аmiоtrоfičnе lаtеrаlnе sklеrоzе (SALS). Nivо аntiоksidаnаtа,  prоtеinskih SH grupа, аskоrbаtа i urаtа, kојi prеdstаvlјајu ligаndе zа dinitrоzil-gvоžđе kоmplеksе (DNIC) sа "slоbоdnim" gvоžđеm  i/ili hvаtаčе NO+ i HNO/NO- vrstа је prоmеnjеn kоd SALS pаciјеnаtа. Dа "slоbоdnо" gvоžđе kаtаlizuје dismutаciјu NO је dоkаzаnо nаstајаnjеm RSNO i hidrоksilаminа u CSF uzоrcimа inkubirаnim sа NO in vitro, оdnоsnо pоtpunоm inhibiciјоm оvih rеаkciја pоmоću о-fеnаntrоlinа, hеlаtоrа zа јоnе gvоžđа. Pоkаzаnо је dа RNOS gеnеrisаnе dismutаciјоm NO rеаguјu sа аskоrbаtоm i urаtоm, štо dоvоdi dо njihоvоg gubitkа, dа prisustvо urаtа pоvеćаvа kаpаcitеt "slоbоdnоg" gvоžđа dа kаtаlizuје NO dismutаciјu, dоk је аskоrbаt bоlјi hvаtаč оd urаtа zа gеnеrisаnе RNOS. Vеći prinоs RSNO, nitritа, hidrоksilаminа i 3-nitrоtirоzinа u CSF uzоrcimа SALS pаciјеnаtа inkubirаnih sа NO u оdnоsu nа kоličinе nаđеnе u kоntrоlnim CSF uzоrcimа mоžе dа sе оbјаsni pоvеćаnim nivооm urаtа i smаnjеnim nivооm аskоrbаtа u CSF uzоrcimа SALS pаciјеnаtа. Rеzultаti prеzеntirаni u оvоm rаdu ubеdlјivо pоkаzuјu dа mеtаl-pоsrеdоvаnа dismutаciја NO u biоlоškim uslоvimа nе sаmо dа је mоgućа nеgо је i fiziоlоški rеlеvаntnа. Zbоg tоgа fiziоlоški znаčај mеtаl pоsrеdоvаnе dismutаciје NO zаslužuје dаlја istrаživаnjа., Mammalian systems are exposed to nitric oxide (NO) through both exogenous and endogenous sources. Once formed, NO undergoes a complex series of reactions which lead to formation of several species more reactive than NO itself. Reactive nitrogen species (RNOS) derived from NO have been implicated in numerous physiological and (particularly) pathophysiological processes. These include NO conversion into its reactive congeners, nitrosonium (NO+) and nitroxyl (HNO/NO-) species, which both could react with various target molecules in biological systems with important consequences for NO mediated processes. It was suggested that in a biological system NO may be converted either to NO+ or HNO/NO- species by metal-catalyzed oxidation or reduction of NO, respectively. We hypothesized that the conversion of NO into both NO+ and HNO/NO- species may occur through the metal assisted NO dismutation (2NO → NO+ + HNO/NO-) catalyzed by SODs and "free" iron. The effect of NO treatment in vitro on structural and functional alterations of Cu/Zn, Mn, and Fe type of SODs was studied. Significant difference in response to NO of Cu/ZnSOD compared to the Mn and Fe types was demonstrated. Cu/ZnSOD was shown to be stable with respect to NO: even on prolonged exposure, NO produced negligible effect on its structure and activity. In contrast, exposure to NO led to fast and extensive inactivation of both Mn and Fe types. Inactivation of MnSOD was demonstrated to be due to the extensive structural alterations, including the cleavage of enzyme polypeptide chains, presumably at His residues of the enzyme metal binding sites, amino groups modifications, tyrosine residue nitration and oxidation. The generation of nitrosonium and nitroxyl ions in NO treated Mn and FeSODs, which produce enzyme modifications and inactivation, was demonstrated. Dinitrosyl iron complex (DNIC) initiated iron ion catalyzed NO dismutation into NO+, resulting in the synthesis of S-nitrosothiols (RSNO) and nitrite, and into HNO/NO- to produce hydroxylamine was demonstrated. Hydroxylamine was detected in NO treated solutions of iron ions in the presence of cysteine, but not glutathione. The addition of urate, a major "free" iron-binding agent in humans, to solutions of GSH and iron ions and the subsequent treatment of these solutions with NO increased the synthesis of GSNO and resulted in the formation of hydroxylamine. This caused a loss of urate and yielded a novel nitrosative/nitration product. GSH attenuated the urate decomposition to such a degree that it could be reflected as the function of GSH:urate. NO treatment of a neutral solution containing proteins and iron ions in the presence of urate, but not in its absence, resulted in hydroxylamine formation and protein S-nitrosation. The consequences of NO exposure in vitro were tested on cerebrospinal fluid (CSF), system containing "free" iron and constituents such as protein-SH groups, ascorbate and urate which represent ligands and/or scavengers of both NO+ and HNO/NO- species. The results demonstrate that "free" iron in CSF can catalyze NO dismutation as evidenced from the formation of both RSNO and hydroxylamine in CSF exposed to NO in vitro which was inhibited upon addition of iron ion chelator o-phenanthroline. NO treatment caused loss of CSF ascorbate and urate. Urate and ascorbate levels were found to affect both "free" iron ion catalyzed NO dismutation as well as the reactions of protein -SH groups with NO+ and HNO/NO- species. Results described in this work suggest that metal/assisted NO dismutation into NO+ and HNO/NO- species in biological systems may be feasible and possibly physiologically relevant.",
publisher = "Универзитет у Београду, Хемијски факултет",
journal = "Универзитет у Београду",
title = "Dismutacija azot monoksida u biološkim i model sistemima : in vitro ispitivanja, Dismutation of nitric oxide in biological and model systems: in vitro study",
url = "https://hdl.handle.net/21.15107/rcub_nardus_3483"
}

Stojanović, S. Đ.. (2004). Dismutacija azot monoksida u biološkim i model sistemima : in vitro ispitivanja. in Универзитет у Београду
Универзитет у Београду, Хемијски факултет..
https://hdl.handle.net/21.15107/rcub_nardus_3483

Stojanović SĐ. Dismutacija azot monoksida u biološkim i model sistemima : in vitro ispitivanja. in Универзитет у Београду. 2004;.
https://hdl.handle.net/21.15107/rcub_nardus_3483 .

Stojanović, Srđan Đ., "Dismutacija azot monoksida u biološkim i model sistemima : in vitro ispitivanja" in Универзитет у Београду (2004),
https://hdl.handle.net/21.15107/rcub_nardus_3483 .