Small protein–protein interfaces rich in electrostatic are often linked to regulatory function

References

• Bahadur, R. P., Chakrabarti, P., Rodier, F., & Janin, J. (2004). A dissection of specific and non-specific protein–protein interfaces. Journal of Molecular Biology, 336(4), 943–955. doi:10.1016/j.jmb.2003.12.073
   PubMed Web of Science ®Google Scholar
• Bendell, C. J., Liu, S., Aumentado-Armstrong, T., Istrate, B., Cernek, P. T., Khan, S., … Murgita, R. A. (2014). Transient protein–protein interface prediction: Datasets, features, algorithms, and the RAD-T predictor. BMC Bioinformatics, 15(1), 82. doi:10.1186/1471-2105-15-82
   PubMedGoogle Scholar
• Caffrey, D. R., Somaroo, S., Hughes, J. D., Mintseris, J., & Huang, E. S. (2004). Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science, 13(1), 190–202. doi:10.1110/ps.03323604
   PubMed Web of Science ®Google Scholar
• Chakrabarti, P., & Janin, J. (2002). Dissecting protein–protein recognition sites. Proteins: Structure, Function, and Genetics, 47(3), 334–343. doi:10.1002/prot.10085
   PubMed Web of Science ®Google Scholar
• Chothia, C., & Janin, J. (1975). Principles of protein–protein recognition. Nature, 256(5520), 705–708. doi:10.1038/256705a0
   PubMed Web of Science ®Google Scholar
• Chothia, C., Wodak, S., & Janin, J. (1976). Role of subunit interfaces in the allosteric mechanism of hemoglobin. Proceedings of the National Academy of Sciences of the United States of America, 73(11), 3793–3797. doi:10.1073/pnas.73.11.3793
   PubMed Web of Science ®Google Scholar
• Correa Marrero, M., Immink, R. G. H., de Ridder, D., & van Dijk, A. D. J. (2019). Improved inference of intermolecular contacts through protein–protein interaction prediction using co-evolutionary analysis. Bioinformatics, 35, 2036–2042. doi:10.1093/bioinformatics/bty924
   PubMed Web of Science ®Google Scholar
• Dai, W., Wu, A., Ma, L., Li, Y. X., Jiang, T., & Li, Y. Y. (2016). A novel index of protein–protein interface propensity improves interface residue recognition. BMC Systems Biology, 10(S4), 112. doi:10.1186/s12918-016-0351-7
   PubMedGoogle Scholar
• Daberdaku, S., & Ferrari, C. (2018). Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. BMC Bioinformatics, 19(1), 35. doi:10.1186/s12859-018-2043-3
   PubMedGoogle Scholar
• Dauzhenka, T., Kundrotas, P. J., & Vakser, I. A. (2018). Computational feasibility of an exhaustive search of side-chain conformations in protein–protein docking. Journal of Computational Chemistry, 39(24), 2012–2021. doi:10.1002/jcc.25381
   PubMed Web of Science ®Google Scholar
• Garcia-Garcia, J., Valls-Comamala, V., Guney, E., Andreu, D., Muñoz, F. J., Fernandez-Fuentes, N., … Oliva, B. (2017). iFrag: A protein–protein interface prediction server based on sequence fragments. Journal of Molecular Biology, 429(3), 382–389. doi:10.1016/j.jmb.2016.11.034
   PubMed Web of Science ®Google Scholar
• Gromiha, M. M., Yokota, K., & Fukui, K. (2009). Energy based approach for understanding the recognition mechanism in protein–protein complexes. Molecular Biosystems, 5, 1779–1786. doi:10.1039/b904161n
   PubMed Web of Science ®Google Scholar
• Guharoy, M., & Chakrabarti, P. (2005). Conservation and relative importance of residues across protein-protein interfaces. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15447–15452. doi:10.1073/pnas.0505425102
   PubMed Web of Science ®Google Scholar
• Guharoy, M., & Chakrabarti, P. (2010). Conserved residue clusters at protein–protein interfaces and their use in binding site identification. BMC Bioinformatics, 11(1), 286. doi:10.1186/1471-2105-11-286
   PubMedGoogle Scholar
• Guo, F., Ding, Y., Li, S. C., Shen, C., & Wang, L. (2016). Protein–protein interface prediction based on hexagon structure similarity. Computational Biology and Chemistry, 63, 83–88. doi:10.1016/j.compbiolchem.2016.02.008
   PubMed Web of Science ®Google Scholar
• Hubbard, S., & Thornton, J. (1993). NACCESS, computer program. London: Department of Biochemistry Molecular Biology, University College.
   Google Scholar
• Humphris, E. L., & Kortemme, T. (2008). Prediction of protein–protein interface sequence diversity using flexible backbone computational protein design. Structure, 16(12), 1777–1788. doi:10.1016/j.str.2008.09.012
   PubMed Web of Science ®Google Scholar
• Hwang, H., Petrey, D., & Honig, B. (2016). A hybrid method for protein–protein interface prediction. Protein Science, 25(1), 159–165. doi:10.1002/pro.2744
   PubMed Web of Science ®Google Scholar
• Janin, J., & Chothia, C. (1990). The structure of protein–protein recognition sites. The Journal of Biological Chemistry, 265(27), 16027–16030.
   PubMed Web of Science ®Google Scholar
• Jones, S. (2012). Computational and structural characterisation of protein associations. Advances in Experimental Medicine and Biology, 747, 42–54. doi:10.1007/978-1-4614-3229-6_3
   PubMed Web of Science ®Google Scholar
• Jones, S., & Thornton, J. M. (1995). Protein–protein interactions: A review of protein dimer structures. Progress in Biophysics and Molecular Biology, 63(1), 31–65. doi:10.1016/0079-6107(94)00008-W
   PubMed Web of Science ®Google Scholar
• Jones, S., & Thornton, J. M. (1996). Principles of protein–protein interactions. Proceedings of the National Academy of Sciences of the United States of America, 93(1), 13–20. doi:10.1073/pnas.93.1.13
   PubMed Web of Science ®Google Scholar
• Jones, S., & Thornton, J. M. (1997a). Analysis of protein–protein interaction sites using surface patches. Journal of Molecular Biology, 272(1), 121–132. doi:10.1006/jmbi.1997.1234
   PubMed Web of Science ®Google Scholar
• Jones, S., & Thornton, J. M. (1997b). Prediction of protein–protein interaction sites using patch analysis. Journal of Molecular Biology, 272(1), 133–143. doi:10.1006/jmbi.1997.1233
   PubMed Web of Science ®Google Scholar
• Jordan, R. A., El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2012). Predicting protein–protein interface residues using local surface structural similarity. BMC Bioinformatics, 13(1), 41. doi:10.1186/1471-2105-13-41
   PubMedGoogle Scholar
• Korn, A. P., & Burnett, R. M. (1991). Distribution and complementarity of hydropathy in multisubunit proteins. Proteins, 9(1), 37–55. doi:10.1002/prot.340090106
   PubMed Web of Science ®Google Scholar
• Lee, B., & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55(3), 379–400. doi:10.1016/0022-2836(71)90324-x
   PubMed Web of Science ®Google Scholar
• Li, B., & Kihara, D. (2012). Protein docking prediction using predicted protein–protein interface. BMC Bioinformatics, 13(1), 7.doi:10.1186/1471-2105-13-7
   PubMedGoogle Scholar
• Li, L., Gunasekaran, K., Gan, J. G.-K., Zhanhua, C., Shapshak, P., Sakharkar, M. K., … Kangueane, P. (2005). Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers. Bioinformation, 1(2), 42–49. doi:10.6026/97320630001042
   PubMedGoogle Scholar
• Li, L., Zhao, B., Cui, Z., Gan, J., Sakharkar, M. K., & Kangueane, P. (2006). Identification of hot spot residues at protein–protein interface. Bioinformation, 1(4), 121–126. doi:10.6026/97320630001121
   PubMedGoogle Scholar
• Li, M., He, Q., Ma, J., He, F., Zhu, Y., Chang, C., … Chen, T. (2019). PPICurator: A tool for extracting comprehensive protein–protein interaction information. Proteomics, 19(4), 1800291.
   Web of Science ®Google Scholar
• Lo Conte, L., Chothia, C., & Janin, J. (1999). The atomic structure of protein–protein recognition sites. Journal of Molecular Biology, 285(5), 2177–2198. doi:10.1006/jmbi.1998.2439
   PubMed Web of Science ®Google Scholar
• Lulu, S., Suresh, A., Karthikraja, V., Arumugam, M., Kayathri, R., & Kangueane, P. (2009). Structural features for homodimer folding mechanism. Journal of Molecular Graphics and Modelling, 28(2), 88–94. doi:10.1016/j.jmgm.2009.04.002
   PubMed Web of Science ®Google Scholar
• Marchetti, F., Capelli, R., Rizzato, F., Laio, A., & Colombo, G. (2019). The subtle trade-off between evolutionary and energetic constraints in protein–protein interactions. The Journal of Physical Chemistry Letters, 10(7), 1489–1497. doi:10.1021/acs.jpclett.9b00191
   PubMed Web of Science ®Google Scholar
• Martin, J. (2014). Benchmarking protein–protein interface predictions: Why you should care about protein size. Proteins: Structure, Function, and Bioinformatics, 82(7), 1444–1452. doi:10.1002/prot.24512
   PubMed Web of Science ®Google Scholar
• Miller, S., Lesk, A. M., Janin, J., & Chothia, C. (1987). The accessible surface area and stability of oligomeric proteins. Nature, 328(6133), 834–836. doi:10.1038/328834a0
   PubMed Web of Science ®Google Scholar
• Moreira, I. S., Koukos, P. I., Melo, R., Almeida, J. G., Preto, A. J., Schaarschmidt, J., … Bonvin, A. M. J. J. (2017). SpotOn: High accuracy identification of protein–protein interface hot-spots. Scientific Reports, 7(1), 8007. doi:10.1038/s41598-017-08321-2
   PubMedGoogle Scholar
• Murakami, Y., & Jones, S. (2006). SHARP2: Protein–protein interaction predictions using patch analysis. Bioinformatics, 22(14), 1794–1795. doi:10.1093/bioinformatics/btl171
   PubMed Web of Science ®Google Scholar
• Nilofer, C., Sukhwal, A., Mohanapriya, A., & Kangueane, P. (2017). Protein–protein interfaces are vdW dominant with selective H-bonds and (or) electrostatic towards broad functional specificity. Bioinformation, 13(6), 164–173. doi:10.6026/97320630013164
   PubMed Web of Science ®Google Scholar
• Pal, A., Chakrabarti, P., Bahadur, R., Rodier, F., & Janin, J. (2007). Peptide segments in protein–protein interfaces. Journal of Biosciences, 32(1), 101–111.
   PubMed Web of Science ®Google Scholar
• Petras, J. K., & Emil, A. (2006). Electrostatic properties of protein–protein complexes. Biophysical Journal, 91, 1724–1736. doi:10.1529/biophysj.106.086025
   PubMed Web of Science ®Google Scholar
• Porter, K. A., Desta, I., Kozakov, D., & Vajda, S. (2019). What method to use for protein-protein docking? Current Opinion in Structural Biology, 55, 1–7. doi:10.1016/j.sbi.2018.12.010
   PubMed Web of Science ®Google Scholar
• Qiao, Y., Xiong, Y., Gao, H., Zhu, X., & Chen, P. (2018). Protein–protein interface hot spots prediction based on a hybrid feature selection strategy. BMC Bioinformatics, 19(1), 14. doi:10.1186/s12859-018-2009-5
   PubMedGoogle Scholar
• Robert, C. H., & Janin, J. (1998). A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. Journal of Molecular Biology, 283(5), 1037–1047. doi:10.1006/jmbi.1998.2152
   PubMed Web of Science ®Google Scholar
• Sowmya, G., Anita, S., & Kangueane, P. (2011). Insights from the structural analysis of protein heterodimer interfaces. Bioinformation, 6(4), 137–143. doi:10.6026/97320630006137
   PubMedGoogle Scholar
• Sowmya, G., Breen, E. J., & Ranganathan, S. (2015). Linking structural features of protein complexes and biological function. Protein Science, 24(9), 1486–1494. doi:10.1002/pro.2736
   PubMed Web of Science ®Google Scholar
• Sowmya, G., & Ranganathan, S. (2015). Discrete structural features among interface residue-level classes. BMC Bioinformatics, 16(S18), S8. doi:10.1186/1471-2105-16-S18-S8
   PubMedGoogle Scholar
• Sukhwal, A., & Sowdhamini, R. (2013). Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies. Molecular Biosystems, 9(7), 1652–1661. doi:10.1039/c3mb25484d
   PubMedGoogle Scholar
• Sukhwal, A., & Sowdhamini, R. (2015). PPCheck: A webserver for the quantitative analysis of protein–protein interfaces and prediction of residue hotspot. Bioinformatics and Biology Insights, 9, 141–151. doi:10.4137/BBI.S25928
   PubMed Web of Science ®Google Scholar
• Taechalertpaisarn, J., Lyu, R.-L., Arancillo, M., Lin, C.-M., Perez, L. M., Ioerger, T. R., & Burgess, K. (2019). Correlations between secondary structure- and protein–protein interface-mimicry: The interface mimicry hypothesis. Organic & Biomolecular Chemistry, 17(12), 3267–3274. doi:10.1039/C9OB00204A
   PubMed Web of Science ®Google Scholar
• Tsai, C. J., Lin, S. L., Wolfson, H. J., & Nussinov, R. (2008). Studies of protein–protein interfaces: A statistical analysis of the hydrophobic effect. Protein Science, 6(1), 53–64. doi:10.1002/pro.5560060106
   Google Scholar
• Vaishnavi, A., Sowmya, G., Kalaivanii, J., Ilakya, S., Kangueane, U., & Kangueane, P. (2010). Interaction modes at protein hetero-dimer interfaces. Bioinformation, 4(7), 310–319. doi:10.6026/97320630004310
   PubMedGoogle Scholar
• Wang, W., Yang, Y., Yin, J., & Gong, X. (2017). Different protein–protein interface patterns predicted by different machine learning methods. Scientific Reports, 7(1), 16023. doi:10.1038/s41598-017-16397-z
   PubMedGoogle Scholar
• Xu, D., Tsai, C. J., & Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering Design and Selection, 10(9), 999–1012. doi:10.1093/protein/10.9.999
   Google Scholar
• Xue, L. C., Dobbs, D., & Honavar, V. (2011). HomPPI: A class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics, 12(1), 244. doi:10.1186/1471-2105-12-244
   PubMedGoogle Scholar
• Yang, Y., & Gong, X. (2018). A new probability method to understand protein–protein interface formation mechanism at amino acid level. Journal of Theoretical Biology, 436, 18–25. doi:10.1016/j.jtbi.2017.09.026
   PubMed Web of Science ®Google Scholar
• Zhanhua, C., Gan, J. G., Lei, L., Mathura, V. S., Sakharkar, M. K., & Kangueane, P. (2005). Protein subunit interfaces: Heterodimers versus homodimers. Bioinformation, 1(2), 28–39. doi:10.6026/97320630001028
   PubMedGoogle Scholar