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  - Malkov, Sasa N.
AU  - Živković, Miodrag V.
AU  - Beljanski, Milos V.
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2008
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/953
AB  - The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natural amino acids.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure
VL  - 14
IS  - 8
SP  - 769
EP  - 775
DO  - 10.1007/s00894-008-0313-0
ER  - 

@article{
author = "Malkov, Sasa N. and Živković, Miodrag V. and Beljanski, Milos V. and Hall, Michael B. and Zarić, Snežana D.",
year = "2008",
abstract = "The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natural amino acids.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure",
volume = "14",
number = "8",
pages = "769-775",
doi = "10.1007/s00894-008-0313-0"
}

Malkov, S. N., Živković, M. V., Beljanski, M. V., Hall, M. B.,& Zarić, S. D.. (2008). A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. in Journal of Molecular Modeling
Springer, New York., 14(8), 769-775.
https://doi.org/10.1007/s00894-008-0313-0

Malkov SN, Živković MV, Beljanski MV, Hall MB, Zarić SD. A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. in Journal of Molecular Modeling. 2008;14(8):769-775.
doi:10.1007/s00894-008-0313-0 .

Malkov, Sasa N., Živković, Miodrag V., Beljanski, Milos V., Hall, Michael B., Zarić, Snežana D., "A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure" in Journal of Molecular Modeling, 14, no. 8 (2008):769-775,
https://doi.org/10.1007/s00894-008-0313-0 . .

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 . .