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Arm–domain interactions can provide high binding cooperativity
Author(s) -
Schleif Robert,
Wolberger Cynthia
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.04908404
Subject(s) - allosteric regulation , cooperativity , cooperative binding , allosteric enzyme , biophysics , plasma protein binding , chemistry , conformational change , protein–protein interaction , binding domain , protein structure , binding site , crystallography , biochemistry , stereochemistry , biology , enzyme
Peptidyl arms extending from one protein domain to another protein domain mediate many important interactions in biology. A well‐studied example of this type of protein–protein interaction occurs between the yeast homeodomain proteins, MAT α2 and MAT a 1, which form a high‐affinity heterodimer on DNA. The carboxyl‐terminal arm extending from MAT α2 to MAT a 1 has been proposed to produce an allosteric conformational change in the a 1 protein that generates a very large increase in the DNA binding affinity of a 1. Although early studies lent some support to this model, a more recent crystal structure determination of the free a 1 protein argues against any allosteric change. This note presents a thermodynamic argument that accounts for the proteins' binding behavior, so that allosteric conformational changes are not required to explain the large affinity increase. The analysis presented here should be useful in analyzing binding behavior in other systems involving arm interactions.