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Protein Science (2006), 15:1858-1872. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Energetics of aliphatic deletions in protein cores

Marta Bueno, Luis A. Campos, Jorge Estrada and Javier Sancho

Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias & Biocomputation, and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, 50009-Zaragoza, Spain

(RECEIVED April 7, 2006; FINAL REVISION May 3, 2006; ACCEPTED May 3, 2006)

Although core residues can sometimes be replaced by shorter ones without introducing significant changes in protein structure, the energetic consequences are typically large and destabilizing. Many efforts have been devoted to understand and predict changes in stability from analysis of the environment of mutated residues, but the relationships proposed for individual proteins have often failed to describe additional data. We report here 17 apoflavodoxin large-to-small mutations that cause overall protein destabilizations of 0.6–3.9 kcal.mol–1. By comparing two-state urea and three-state thermal unfolding data, the overall destabilizations observed are partitioned into effects on the N-to-I and on the I-to-U equilibria. In all cases, the equilibrium intermediate exerts a "buffering" effect that reduces the impact of the overall destabilization on the N-to-I equilibrium. The performance of several structure-energetics relationships, proposed to explain the energetics of hydrophobic shortening mutations, has been evaluated by using an apoflavodoxin data set consisting of 14 mutations involving branching-conservative aliphatic side-chain shortenings and a larger data set, including similar mutations implemented in seven model proteins. Our analysis shows that the stability changes observed for any of the different types of mutations (LA, IA, IV, and VA) in either data set are best explained by a combination of differential hydrophobicity and of the calculated volume of the modeled cavity (as previously observed for LA and IA mutations in lysozyme T4). In contrast, sequence conservation within the flavodoxin family, which is a good predictor for charge-reversal stabilizing mutations, does not perform so well for aliphatic shortening ones.

Keywords: protein stability; hydrophobic interaction; protein intermediate; protein folding; protein cavity


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