Anatomy of hot spots in protein interfaces

doi:10.1006/jmbi.1998.1843

Journal of Molecular Biology

Volume 280, Issue 1, 3 July 1998, Pages 1-9

https://doi.org/10.1006/jmbi.1998.1843 Get rights and content

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.

Section snippets

Hot spots are protected from bulk solvent

Hot spots of binding energy located near the center of the interface are a general property of the interfaces we examined (Figure 2), as was previously shown for human growth hormone bound to its receptor (Clackson & Wells, 1995). The residues that make up each hot spot tend to cluster together near the center of the interface; very few residues that contribute a large amount of binding energy (>3.5 kcal/mol) are at the edge of an interface. There is no purely geometric reason that hot spot

Amino acid preferences in hot spots

The distribution of percentages of different amino acid types that occur in hot spots (contribute more than 2 kcal/mol to a binding interaction) in our database is strikingly non-random (Table 2). Only three amino acids appear in hot spots with a frequency of more than 10%; 21% of tryptophan, 13.3% of arginine and 12.3% of tyrosine residues are in hot spots. However, many amino acids are found in hot spots very rarely. Less than 3% of the leucine, methionine, serine, threonine and valine

Implications for drug design

In contrast to protein-protein targets, the design of small-molecule ligands for various enzymes has been quite successful. Unlike the reasonably large and flat interfaces seen in many protein heterodimers, most enzymes have deep pockets on their surface in which ligands can bind. The pocket is often the enzyme active site, so the rational design of inhibitors is possible without including an O-ring in the designed ligand, because the deep pocket that is provided by the enzyme presumably

Acknowledgements

A.A.B. is supported by a National Defense Science and Engineering Graduate Fellowship from the United States Department of Defense. K.S.T. is supported by a Howard Hughes Medical Institute Predoctoral Fellowship. We thank Fred Cohen, Wendell Lim and Jim Wells for helpful comments and discussion. We appreciate the comments of Warren DeLano, Marcin Joachimiak, Dave Miller and Dirk Walther. Also, we thank C. Schutt for pointing out the importance of tryptophan.

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¹: Edited by J. Wells

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Journal of Molecular Biology

CommunicationAnatomy of hot spots in protein interfaces1

Abstract

Section snippets

Hot spots are protected from bulk solvent

Amino acid preferences in hot spots

Implications for drug design

Acknowledgements

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Proc. Natl Acad. Sci. USA

Structural plasticity in a remodeled protein-protein interface

Science

A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor

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Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitoreffects on the kinetics and thermodynamics of binding to β-trypsin and α-chymotrypsin

Biochemistry

Mutational analysis of the interaction between staphylococcal protein A and human IgG1

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Recent successes and continuing limitations in computer-aided drug design

Site-specific mutagenesis reveals differences in the structural bases for tight binding of RNase inhibitor to angiogenin and RNase A

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Nature

A hot spot of binding energy in a hormone-receptor interface

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Science

Rational design of receptor-specific variants of human growth hormone

Proc. Natl Acad. Sci. USA

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A mutational analysis of the binding of two different proteins to the same antibody

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Identification of surface residues mediating tissue factor binding and catalytic function of the serine protease factor VIIa

Proc. Natl Acad. Sci. USA

Communication
Anatomy of hot spots in protein interfaces¹