Hot spots—A review of the protein–protein interface determinant amino‐acid residues

Irina S. Moreira; Pedro A. Fernandes; Maria J. Ramos

doi:10.1002/prot.21396

journal article Open Access Jun 01, 2007

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

Irina S. Moreira Pedro A. Fernandes

Maria J. Ramos

Proteins: Structure, Function, and Bioinformatics Vol. 68 No. 4 pp. 803-812 · Wiley

View at Publisher Save 10.1002/prot.21396

Abstract

AbstractProteins tendency to bind to one another in a highly specific manner forming stable complexes is fundamental to all biological processes. A better understanding of complex formation has many practical applications, which include the rational design of new therapeutic agents, and the analysis of metabolic and signal transduction networks. Alanine‐scanning mutagenesis made possible the detection of the functional epitopes, and demonstrated that most of the protein–protein binding energy is related only to a group of few amino acids at intermolecular protein interfaces: the hot spots. The scope of this review is to summarize all the available information regarding hot spots for a better atomic understanding of their structure and function. The ultimate objective is to improve the rational design of complexes of high affinity and specificity as well as that of small molecules, which can mimic the functional epitopes of the proteic complexes. Proteins 2007. © 2007 Wiley‐Liss, Inc.

Topics

No keywords indexed for this article. Browse by subject →

References

120

[1]

10.1002/prot.20433

[2]

10.1002/prot.340210105

[3]

10.1016/s0079-6107(96)00001-6

[4]

Principles of protein-protein interactions.

S Jones, J M Thornton

Proceedings of the National Academy of Sciences 10.1073/pnas.93.1.13

[5]

Anatomy of hot spots in protein interfaces

Andrew A Bogan, Kurt S Thorn

Journal of Molecular Biology 10.1006/jmbi.1998.1843

[6]

10.1093/protein/12.9.713

[7]

10.1006/jmbi.1996.0424

[8]

Hydrophobic folding units at protein‐protein interfaces: Implications to protein folding and to protein‐protein association

Chung‐Jung Tsai, Ruth Nussinov

Protein Science 10.1002/pro.5560060707

[9]

Folding funnels, binding funnels, and protein function

Chung‐Jung Tsai, Sandeep Kumar, Buyong Ma et al.

Protein Science 10.1110/ps.8.6.1181

[10]

Computational design of protein–protein interactions

Tanja Kortemme, David Baker

Current Opinion in Chemical Biology 10.1016/j.cbpa.2003.12.008

[11]

10.1016/j.sbi.2004.04.006

[12]

Small-molecule inhibitors of protein–protein interactions: progressing towards the dream

Michelle R. Arkin, James A. Wells

Nature Reviews Drug Discovery 10.1038/nrd1343

[13]

Principles of protein–protein recognition

Cyrus Chothia, Joël Janin

Nature 10.1038/256705a0

[14]

The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht

Loredana Lo Conte, Cyrus Chothia, Joël Janin

Journal of Molecular Biology 10.1006/jmbi.1998.2439

[15]

10.1016/j.jmb.2004.09.051

[16]

10.1016/s0959-440x(00)00154-8

[17]

10.1073/pnas.93.1.7

[18]

10.1002/prot.10139

[19]

10.1016/j.jmb.2005.01.040

[20]

10.1002/prot.10456

[21]

10.1021/ar010014p

[22]

Ofran Y "Analysing six types of protein–protein interfaces" J Mol Biol (2003)

[23]

Insufficiently dehydrated hydrogen bonds as determinants of protein interactions

Ariel Fernández, Harold A. Scheraga

Proceedings of the National Academy of Sciences 10.1073/pnas.0136888100

[24]

10.1016/s0022-2836(02)00811-2

[25]

10.1016/s0021-9258(17)46181-3

[26]

10.1002/pro.5560010117

[27]

10.1016/j.jmb.2004.10.077

[28]

10.1021/bi00437a034

[29]

Stability of Proteins Small Globular Proteins

P.L. Privalov

Advances in Protein Chemistry 10.1016/s0065-3233(08)60460-x

[30]

10.1002/pro.5560030501

[31]

10.1002/prot.340090106

[32]

Some Factors in the Interpretation of Protein Denaturation

W. Kauzmann

Advances in Protein Chemistry 10.1016/s0065-3233(08)60608-7

[33]

10.1002/(sici)1097-0134(199707)28:3<333::aid-prot4>3.0.co;2-d

[34]

Dominant forces in protein folding

Ken A. Dill

Biochemistry 10.1021/bi00483a001

[35]

10.1042/0264-6021:3470193

[36]

10.1016/s0959-440x(00)00065-8

[37]

10.1006/jmbi.1996.0712

[38]

10.1093/protein/10.9.999

[39]

10.1006/abbi.2001.2405

[40]

10.1006/jmbi.1998.1747

[41]

10.1016/s0006-3495(99)77281-4

[42]

Archakov AI (1999)

[43]

10.1073/pnas.95.11.5942

[44]

10.1002/(sici)1097-0134(19990201)34:2<255::aid-prot10>3.0.co;2-o

[45]

10.1002/(sici)1097-0134(20000601)39:4<331::aid-prot60>3.0.co;2-a

[46]

10.1006/jmbi.1997.1234

[47]

Prediction of protein-protein interaction sites using patch analysis 1 1Edited by G. von Heijne

Susan Jones, Janet M Thornton

Journal of Molecular Biology 10.1006/jmbi.1997.1233

[48]

Laskowski RA "Protein clefts in molecular recognition and function" Protein Sci (1996)

[49]

10.1006/jmbi.1998.2559

[50]

10.1073/pnas.93.1.7

Showing 50 of 120 references

Cited By

668

Global O-GlcNAcome Identifies O-GlcNAcylated Proteins Regulating Oligodendrocyte Precursor Cells Differentiation

Xinyue Jiang, Chi Zhang · 2026

Acta Biochimica et Biophysica Sinic...

New insights into protein–protein interaction modulators in drug discovery and therapeutic advance

Hossam Nada, Yongseok Choi · 2024

Signal Transduction and Targeted Th...

Trifluoromethylthiolation of Tryptophan and Tyrosine Derivatives: A Tool for Enhancing the Local Hydrophobicity of Peptides

Jure Gregorc, Nathalie Lensen · 2023

The Journal of Organic Chemistry

Drug discovery by targeting the protein–protein interactions involved in autophagy

Honggang Xiang, Mi Zhou · 2023

Acta Pharmaceutica Sinica B

The chemistry of snake venom and its medicinal potential

Ana L. Oliveira, Matilde F. Viegas · 2022

Nature Reviews Chemistry

Nonspecific Binding—Fundamental Concepts and Consequences for Biosensing Applications

Andreas Frutiger, Alexander Tanno · 2021

Chemical Reviews

Recent advances in the development of protein–protein interactions modulators: mechanisms and clinical trials

Haiying Lu, Qiaodan Zhou · 2020

Signal Transduction and Targeted Th...

Machine Learning Approaches for Protein–Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment

Siyu Liu, Chuyao Liu · 2018

Molecules

A peptidomimetic with a chiral switch is an inhibitor of epidermal growth factor receptor heterodimerization

Shanthi P. Kanthala, Yong-Yu Liu · 2017

Oncotarget

Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking

Daisuke Kuroda, Jeffrey J. Gray · 2016

Bioinformatics

Side-Chain Conformational Preferences Govern Protein–Protein Interactions

Andrew M. Watkins, Richard Bonneau · 2016

Journal of the American Chemical So...

State-of-the-art strategies for targeting protein–protein interactions by small-molecule inhibitors

Chunquan Sheng, Guoqiang Dong · 2015

Chemical Society Reviews

Hot spots in protein–protein interfaces: Towards drug discovery

Engin Cukuroglu, H. Billur Engin · 2014

Progress in Biophysics and Molecula...

Protein painting reveals solvent-excluded drug targets hidden within native protein–protein interfaces

Alessandra Luchini, Virginia Espina · 2014

Nature Communications

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin · 2013

Journal of The Royal Society Interf...

Structure of the protein core of the glypican Dally-like and localization of a region important for hedgehog signaling

Min-Sung Kim, Adam M. Saunders · 2011

Proceedings of the National Academy...

Assessing Helical Protein Interfaces for Inhibitor Design

Brooke N. Bullock, Andrea L. Jochim · 2011

Journal of the American Chemical So...

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

Nurcan Tuncbag, Attila Gursoy · 2009

Bioinformatics

Computational design of second‐site suppressor mutations at protein–protein interfaces

Deanne W. Sammond, Ziad M. Eletr · 2009

Proteins: Structure, Function, and...

Targeting Protein–Protein Interactions for Therapeutic Intervention: A Challenge for the Future

Giovanna Zinzalla, David E Thurston · 2009

Future Medicinal Chemistry

Metrics

668

Citations

120

References

Details

Published: Jun 01, 2007
Vol/Issue: 68(4)
Pages: 803-812
License: View

Authors

REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal

M

Maria J. Ramos

REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal

Cite This Article

Irina S. Moreira, Pedro A. Fernandes, Maria J. Ramos (2007). Hot spots—A review of the protein–protein interface determinant amino‐acid residues. Proteins: Structure, Function, and Bioinformatics, 68(4), 803-812. https://doi.org/10.1002/prot.21396

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

You May Also Like