TY  - JOUR
AU  - Leong, Patrick P. T.
AU  - Mihajlović, Aleksandar
AU  - Bogdanović, Nadežda
AU  - Breberina, Luka M.
AU  - Xi, Larry
PY  - 2021
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4685
AB  - Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample’s ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome.
PB  - Nature Research
T2  - Scientific Reports
T1  - Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
VL  - 11
IS  - 1
SP  - 18907
DO  - 10.1038/s41598-021-97852-w
ER  - 

@article{
author = "Leong, Patrick P. T. and Mihajlović, Aleksandar and Bogdanović, Nadežda and Breberina, Luka M. and Xi, Larry",
year = "2021",
abstract = "Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample’s ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome.",
publisher = "Nature Research",
journal = "Scientific Reports",
title = "Reconstructing and counting genomic fragments through tagmentation-based haploid phasing",
volume = "11",
number = "1",
pages = "18907",
doi = "10.1038/s41598-021-97852-w"
}

Leong, P. P. T., Mihajlović, A., Bogdanović, N., Breberina, L. M.,& Xi, L.. (2021). Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. in Scientific Reports
Nature Research., 11(1), 18907.
https://doi.org/10.1038/s41598-021-97852-w

Leong PPT, Mihajlović A, Bogdanović N, Breberina LM, Xi L. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. in Scientific Reports. 2021;11(1):18907.
doi:10.1038/s41598-021-97852-w .

Leong, Patrick P. T., Mihajlović, Aleksandar, Bogdanović, Nadežda, Breberina, Luka M., Xi, Larry, "Reconstructing and counting genomic fragments through tagmentation-based haploid phasing" in Scientific Reports, 11, no. 1 (2021):18907,
https://doi.org/10.1038/s41598-021-97852-w . .

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  - 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  - CONF
AU  - Radosavljević, Jelena
AU  - Luka, M.
AU  - Karina, W.
AU  - Emilia, S.
AU  - Johanna, B.
AU  - Pieters, Raymond
AU  - Smit, Joost
AU  - Ćirković-Veličković, Tanja
PY  - 2010
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1470
PB  - Wiley-Blackwell, Hoboken
C3  - Allergy
T1  - Allergenic potential of cross-linked peanut proteins
VL  - 65
SP  - 403
EP  - 403
UR  - https://hdl.handle.net/21.15107/rcub_cherry_1470
ER  - 

@conference{
author = "Radosavljević, Jelena and Luka, M. and Karina, W. and Emilia, S. and Johanna, B. and Pieters, Raymond and Smit, Joost and Ćirković-Veličković, Tanja",
year = "2010",
publisher = "Wiley-Blackwell, Hoboken",
journal = "Allergy",
title = "Allergenic potential of cross-linked peanut proteins",
volume = "65",
pages = "403-403",
url = "https://hdl.handle.net/21.15107/rcub_cherry_1470"
}

Radosavljević, J., Luka, M., Karina, W., Emilia, S., Johanna, B., Pieters, R., Smit, J.,& Ćirković-Veličković, T.. (2010). Allergenic potential of cross-linked peanut proteins. in Allergy
Wiley-Blackwell, Hoboken., 65, 403-403.
https://hdl.handle.net/21.15107/rcub_cherry_1470

Radosavljević J, Luka M, Karina W, Emilia S, Johanna B, Pieters R, Smit J, Ćirković-Veličković T. Allergenic potential of cross-linked peanut proteins. in Allergy. 2010;65:403-403.
https://hdl.handle.net/21.15107/rcub_cherry_1470 .

Radosavljević, Jelena, Luka, M., Karina, W., Emilia, S., Johanna, B., Pieters, Raymond, Smit, Joost, Ćirković-Veličković, Tanja, "Allergenic potential of cross-linked peanut proteins" in Allergy, 65 (2010):403-403,
https://hdl.handle.net/21.15107/rcub_cherry_1470 .