Role of the amino acid sequence in domain swapping of the B1 domain of protein G

Proteins
Fernanda L SirotaShoshana J Wodak

Abstract

Substitution of four amino acid residues (L5V,F30V, Y33F,A34F) in the B1 domain of the immunoglobulin G binding protein (GB1) leads to the formation of a swapped dimer, shown to be in equilibrium with a native-like monomeric state of the protein (Byeon et al., J Mol Biol 2003;333:141-152). In this study, we employ protein design calculations and molecular dynamics simulations to investigate the role of these substitutions in fostering the swapping reaction. DESIGNER, a fully automatic procedure for computing the amino acid sequences likely to stabilize a given backbone structure is used to investigate the effect of the four substitutions on the stability of the wild type native monomeric conformation. Results indicate that at least three of these substitutions (L5V,F30V, A34F) have a destabilizing effect. The L5V forms destabilizing interactions with surrounding residues, whereas F30V causes local strain due to unfavorable interactions with its own backbone. A dual role in the swapping reaction is played by A34F. It destabilizes the monomer conformation while stabilizing the swapped dimer. Our calculations find an energetically favorable conformation for the 34F side chain in the core of the monomer, but only at the expense of ...Continue Reading

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Citations

Apr 5, 2012·Journal of Clinical Bioinformatics·Khader Shameer, Ramanathan Sowdhamini
Jul 1, 2008·Journal of Molecular Biology·Anatoly MalevanetsShoshana J Wodak
Mar 1, 2016·Archives of Biochemistry and Biophysics·Ana Cámara-Artigas

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