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Anatomy of hot spots in protein interfaces
Abstract
Binding of one protein to another is involved in nearly all biological functions, yet the principles governing the interaction of proteins are not fully understood. To analyze the contributions of individual amino acid residues in protein-protein binding we have compiled a database of 2325 alanine mutants for which the change in free energy of binding upon mutation to alanine has been measured (available at http://motorhead. ucsf.edu/thorn/hotspot). Our analysis shows that at the level of side-chains there is little correlation between buried surface area and free energy of binding. We find that the free energy of binding is not evenly distributed across interfaces; instead, there are hot spots of binding energy made up of a small subset of residues in the dimer interface. These hot spots are enriched in tryptophan, tyrosine and arginine, and are surrounded by energetically less important residues that most likely serve to occlude bulk solvent from the hot spot. Occlusion of solvent is found to be a necessary condition for highly energetic interactions.
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“Protein-protein interfaces are characterized by the existence of hot spots or ‘hot regions’ in interacting regions instead of an even contribution across all contact areas.371,476,487,492–495”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [495]
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“The latter two are experimental hot‐spots41 (Supporting Information Tables S2 and S8) and the third one is a candidate for experimental verification.”
From iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations (2019) · cites this paper as [41]
Citations
Cites
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
Principles of protein-protein interactions
Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684
Raster3D Version 2.0. A program for photorealistic molecular graphics
Merritt, E. A., & Murphy, M. E. P. (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994006396 · Cited by 2,493
Stability of Proteins Small Globular Proteins
Privalov, P. L. (1979) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60460-x · Cited by 2,163
A Hot Spot of Binding Energy in a Hormone-Receptor Interface
Clackson, T., & Wells, J. A. (1995) · Science · doi:10.1126/science.7529940 · Cited by 1,987
High-Resolution Epitope Mapping of hGH-Receptor Interactions by Alanine-Scanning Mutagenesis
Cunningham, B. C., & Wells, J. A. (1989) · Science · doi:10.1126/science.2471267 · Cited by 1,361
Shape Complementarity at Protein/Protein Interfaces
Lawrence, M. C., & Colman, P. M. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1648 · Cited by 1,224
Shape complementarity at protein–protein interfaces
Norel, R., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1994) · Biopolymers · doi:10.1002/bip.360340711 · Cited by 1,208
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families
Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0167 · Cited by 1,196
Flagged first, then by citations
2 of the 71 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- Judice, 1997, Small molecule inhibitors of human growth hormone/receptor binding, FASEB J., 11, A839
- Schreiber, 1995, Energetics of protein-protein interactions, J. Mol. Biol., 248, 478, 10.1006/jmbi.1995.0235 · DOI
Cited by
Sorted by citations
Items 601–700 of 1,003
Deng, L., Guan, J., Wei, X., Yi, Y., Zhang, Q. C., & Zhou, S. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2013.0083 · Cited by 49
Urick, A. K., Calle, L. P., Espinosa, J. F., Hu, H., & Pomerantz, W. C. K. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.6b00730 · Cited by 47
Cell-penetrating TIR BB loop decoy peptides
Toshchakov, V. Y., & Vogel, S. N. (2007) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.7.7.1035 · Cited by 47
Inal, J. M., & Schifferli, J. A. (2002) · The Journal of Immunology · doi:10.4049/jimmunol.168.10.5213 · Cited by 47
Johansson, H., Jensen, M. R., Gesmar, H., Meier, S., Vinther, J. M., Keeler, C., Hodsdon, M. E., & Led, J. J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja503546j · Cited by 47
Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors
Martins, J. N., Lima, J. C., & Basílio, N. (2020) · Molecules · doi:10.3390/molecules26010106 · Cited by 46
Probing binding hot spots at protein–RNA recognition sites
Barik, A., Nithin, C., Karampudi, N. B. R., Mukherjee, S., & Bahadur, R. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv876 · Cited by 47
Weininger, U., Respondek, M., & Akke, M. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9656-z · Cited by 46
Eidam, O., Dworkowski, F., Glockshuber, R., Grütter, M. G., & Capitani, G. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.01.030 · Cited by 46
High‐throughput analysis of peptide‐binding modules
Liu, B. A., Engelmann, B. W., & Nash, P. (2012) · PROTEOMICS · doi:10.1002/pmic.201100599 · Cited by 46
Wu, X., Wang, Y., Zhuo, Z., Jiang, F., & Wu, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043005 · Cited by 49
dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions
Liu, L., Xiong, Y., Gao, H., Wei, D., Mitchell, J. C., & Zhu, X. (2018) · Database · doi:10.1093/database/bay034 · Cited by 46
Machner, M. P., Frese, S., Schubert, W., Orian‐Rousseau, V., Gherardi, E., Wehland, J., Niemann, H. H., & Heinz, D. W. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03532.x · Cited by 46
Handelsman, T., Barak, Y., Nakar, D., Mechaly, A., Lamed, R., Shoham, Y., & Bayer, E. A. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.07.040 · Cited by 46
Cho, S., Swaminathan, C. P., Yang, J., Kerzic, M. C., Guan, R., Kieke, M. C., Kranz, D. M., Mariuzza, R. A., & Sundberg, E. J. (2005) · Structure · doi:10.1016/j.str.2005.08.015 · Cited by 46
MolSurfer: a macromolecular interface navigator
Gabdoulline, R. R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg588 · Cited by 46
Druggable Orthosteric and Allosteric Hot Spots to Target Protein-protein Interactions
Ma, B., & Nussinov, R. (2014) · Current Pharmaceutical Design · doi:10.2174/13816128113199990073 · Cited by 45
Differences between High- and Low-Affinity Complexes of Enzymes and Nonenzymes
Carlson, H. A., Smith, R. D., Khazanov, N. A., Kirchhoff, P. D., Dunbar, J. B., & Benson, M. L. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm8006504 · Cited by 46
Understanding the importance of the aromatic amino-acid residues as hot-spots
Moreira, I. S., Martins, J. M. D. S., Ramos, R. M., Fernandes, P. A., & Ramos, M. J. (2012) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2012.07.005 · Cited by 45
The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures
Davis, F. P., & Šali, A. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000668 · Cited by 47
Keeble, A. H., Joachimiak, Ł. A., Maté, M. J., Meenan, N. A. G., Kirkpatrick, N., Baker, D. A., & Kleanthous, C. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.03.055 · Cited by 46
Bouvier, B., Grünberg, R., Nilges, M., & Cazals, F. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22381 · Cited by 45
Laine, É., & Carbone, A. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004580 · Cited by 44
Side-Chain Conformational Preferences Govern Protein–Protein Interactions
Watkins, A. M., Bonneau, R., & Arora, P. S. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b04892 · Cited by 45
Lee, M. M., & Peterson, B. R. (2016) · ACS Omega · doi:10.1021/acsomega.6b00356 · Cited by 45
Basu, S., & Mukharjee, D. (2017) · Journal of Molecular Modeling · doi:10.1007/s00894-017-3376-y · Cited by 44
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Kunig, V. B. K., Potowski, M., Škopić, M. K., & Brunschweiger, A. (2020) · ChemMedChem · doi:10.1002/cmdc.202000869 · Cited by 44
Yang, J., Swaminathan, C. P., Huang, Y., Guan, R., Cho, S., Kieke, M. C., Kranz, D. M., Mariuzza, R. A., & Sundberg, E. J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m306848200 · Cited by 46
Simeonov, A. M., Yasgar, A., Jadhav, A., Lokesh, G. L.-R., Klumpp-Thomas, C. A., Michael, S., Austin, C. P., Natarajan, A., & Inglese, J. (2007) · Analytical Biochemistry · doi:10.1016/j.ab.2007.11.039 · Cited by 45
Leonhardt, R. M., Vigneron, N., Hee, J. S., Graham, M. M., & Cresswell, P. (2013) · Molecular Biology of the Cell · doi:10.1091/mbc.e12-10-0742 · Cited by 44
Mazor, R., Onda, M., Park, D., Addissie, S., Xiang, L., Zhang, J., Hassan, R., & Pastan, I. H. (2016) · Oncotarget · doi:10.18632/oncotarget.9171 · Cited by 44
Computational and Artificial Intelligence Techniques for Drug Discovery and Administration
Balasubramanian, K. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820472-6.00015-3 · Cited by 44
Huth, J. R., Yu, L. P., Collins, I. J., Mack, J. C., Mendoza, R. R., Isaac, B., Braddock, D. T., Muchmore, S. W., Comess, K. M., Fesik, S. W., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0497803 · Cited by 44
Assessing the role of tryptophan residues in the binding site
Samanta, U., & Chakrabarti, P. (2001) · Protein Engineering Design and Selection · doi:10.1093/protein/14.1.7 · Cited by 44
Kamal, J. K. A., Benchaar, S. A., Takamoto, K., Reisler, E., & Chance, M. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611283104 · Cited by 44
Corrada, D., Soshilov, A. A., Denison, M. S., & Bonati, L. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004981 · Cited by 43
Taghizadeh, M. S., Taherishirazi, M., Niazi, A., Afsharifar, A., & Moghadam, A. A. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2024.1327820 · Cited by 43
Evolution of protein structures and interactions from the perspective of residue contact networks
Zhang, X., Perica, T., & Teichmann, S. A. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.07.004 · Cited by 43
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Synthetic peptide arrays for investigating protein interaction domains
Volkmer, R., Tapia, V., & Landgraf, C. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.04.028 · Cited by 43
Cortines, J. R., Weigele, P., Gilcrease, E. B., Casjens, S., & Teschke, C. M. (2011) · Virology · doi:10.1016/j.virol.2011.09.005 · Cited by 43
Wang, Y., Yao, H., Cheng, Y., Lovell, S., Battaile, K. P., Middaugh, C. R., & Rivera, M. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00937 · Cited by 42
Wilhelm, A., Lopez-Garcia, L. A., Busschots, K., Fröhner, W., Maurer, F., Boettcher, S., Zhang, H., Schulze, J. O., Biondi, R. M., & Engel, M. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm3010477 · Cited by 43
Culver, H. R., Steichen, S. D., & Peppas, N. A. (2016) · Biomacromolecules · doi:10.1021/acs.biomac.6b01482 · Cited by 43
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Livesey, B., & Marsh, J. A. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009858 · Cited by 46
Duquesnoy, R. J., Marrari, M., Mulder, A., Claas, F. H. J., Mostecki, J. W., & Balazs, I. (2011) · Human Immunology · doi:10.1016/j.humimm.2011.11.011 · Cited by 43
Kim, M., Sun, Z.-Y. J., Byron, O., Campbell, G., Wagner, G., Wang, J., & Reinherz, E. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4980 · Cited by 43
Rodenburg, K. W., Vallée, F., Juge, N., Aghajari, N., Guo, X., Haser, R., & Svensson, B. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01094.x · Cited by 43
Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., & Zhang, J. Z. H. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00241 · Cited by 40
Parmar, A. S., James, J. K., Grisham, D. R., Pike, D. H., & Nanda, V. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.5b10304 · Cited by 42
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Borroto‐Escuela, D. O., Tarakanov, A. O., Brito, I., & Fuxé, K. (2018) · Pharmacological Reports · doi:10.1016/j.pharep.2018.04.002 · Cited by 43
Korasick, D. A., Chatterjee, S., Tonelli, M., Dashti, H., Lee, S. G., Westfall, C. S., Fulton, D. B., Andreotti, A. H., Amarasinghe, G. K., Strader, L. C., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.648253 · Cited by 42
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Li, X., & Liang, J. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20438 · Cited by 42
Lichtenecker, R. J., Weinhäupl, K., Schmid, W., & Konrat, R. (2013) · Journal of Biomolecular NMR · doi:10.1007/s10858-013-9796-9 · Cited by 42
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Nemoto, W., & Toh, H. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20332 · Cited by 42
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Bailey, L. J., Sheehy, K. M., Hoey, R. J., Schaefer, Z. P., Ura, M., & Kossiakoff, A. A. (2014) · Journal of Immunological Methods · doi:10.1016/j.jim.2014.10.003 · Cited by 41
Goncearenco, A., Li, M., Simonetti, F. L., Shoemaker, B. A., & Panchenko, A. R. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7201-2_15 · Cited by 44
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Sulimov, V. B., Kutov, D. C., Taschilova, A. S., Ilin, I. S., Tyrtyshnikov, E. E., & Sulimov, A. V. (2020) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026620666201207095626 · Cited by 43
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Pletneva, E. V., Sundd, M., Fulton, D. B., & Andreotti, A. H. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.12.073 · Cited by 41
Wilkinson, K. D., Laleli-Sahin, E., Urbauer, J. L., Larsen, C. N., Shih, G. H., Haas, A. L., Walsh, S. T. R., & Wand, A. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3038 · Cited by 41
Shiroishi, M., Yokota, A., Tsumoto, K., Kondo, H., Nishimiya, Y., Horii, K., Matsushima, M., Ogasahara, K., Yutani, K., & Kumagai, I. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m100480200 · Cited by 41
Mapping arm-DNA-binding domain interactions in AraC 1 1Edited by J. A. Wells
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Säll, A., Walle, M., Wingren, C., Müller, S., Nyman, T., Vala, A., Ohlin, M., Borrebaeck, C. A. K., & Persson, H. (2016) · Protein Engineering Design and Selection · doi:10.1093/protein/gzw042 · Cited by 40
Yan, G., Wang, K., Shao, Z., Luo, L., Song, Z., Chen, J., Jin, R., Deng, X., Wang, H., Cao, Z., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1713526115 · Cited by 40
Zhong, M., Lynch, A. J., Muellers, S. N., Jehle, S., Luo, L., Hall, D. R., Iwase, R., Carolan, J. P., Egbert, M. E., Wakefield, A., et al. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00943 · Cited by 40
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Mangel, W. F., Baniecki, M. L., & McGrath, W. J. (2003) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-003-2318-2 · Cited by 40
Modulation von Protein‐Protein‐Wechselwirkungen mit niedermolekularen organischen Molekülen
Berg, T. (2003) · Angewandte Chemie · doi:10.1002/ange.200200558 · Cited by 41
Dubaquié, Y., & Lowman, H. B. (1999) · Biochemistry · doi:10.1021/bi990089p · Cited by 40
Peptide segments in protein-protein interfaces
Pal, A., Chakrabarti, P., Bahadur, R. P., Rodier, F., & Janin, J. (2007) · Journal of Biosciences · doi:10.1007/s12038-007-0010-7 · Cited by 39
Protein–protein interactions as a tool for site‐specific labeling of proteins
Jäger, M., Michalet, X., & Weiss, S. (2005) · Protein Science · doi:10.1110/ps.051384705 · Cited by 40
Mapping epitopes and antigenicity by site-directed masking
Paus, D., & Winter, G. P. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600263103 · Cited by 38
Lorenzo, D. D. (2024) · ChemMedChem · doi:10.1002/cmdc.202400180 · Cited by 46
Hot Spots in a Network of Functional Sites
Özbek, P., Soner, S., & Haliloǧlu, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074320 · Cited by 39
Fornili, A., Pandini, A., Lu, H., & Fraternali, F. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400486p · Cited by 38
Roles of residues in the interface of transient protein-protein complexes before complexation
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Metadata
- Authors
- Bogan, A. A., & Thorn, K. S.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Bogan, Andrew A
- ORCID
- Thorn, Kurt S
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1998-07
- Volume
- 280
- Issue
- 1
- Pages
- 1-9
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2051710717
- Cited by
- 1,988
- References
- 71
- Citations by year
- 2026: 62 · 2025: 52 · 2024: 68 · 2023: 40 · 2022: 51 · 2021: 75 · 2020: 69 · 2019: 65 · 2018: 77 · 2017: 75 · 2016: 94 · 2015: 105 · 2014: 88 · 2013: 110 · 2012: 112
- FWCI
- 11.85
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein-protein binding, binding hot spots, alanine scanning, binding free energy, protein interfaces, buried surface area, tryptophan, tyrosine, L-arginine, dimer interface, binding energy distribution
- MeSH terms
- Alanine, Amino Acids, Binding Sites, Humans, Protein Binding, Proteins, Structure-Activity Relationship
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