Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics

Amino Acids
T Kikuchi

Abstract

It is well-known that the IgG-binding domain from staphylococcal protein A folds into a 3 alpha helix bundle structure, while the IgG-binding domain of streptococcal protein G forms an (alpha + beta) structure. Recently, He et al. (Biochemistry 44:14055-14061, 2005) made mutants of these proteins from the wild types of protein A and protein G strains. These mutants are referred to as protein A219 and protein G311, and it was showed that these two mutants have different 3D structures, i.e., the 3 alpha helix bundle structure and the (alpha + beta) structure, respectively, despite the high sequence identity (59%). The purpose of our study was to clarify how such 3D structural differences are coded in the sequences with high homology. To address this problem, we introduce a predicted contact map constructed based on the interresidue average-distance statistics for prediction of folding properties of a protein. We refer to this map as an average distance map (ADM). Furthermore, the statistics of interresidue distances can be converted to an effective interresidue potential. We calculated the contact frequency of each residue of a protein in random conformations with this effective interresidue potential, and then we obtained values...Continue Reading

References

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May 2, 2006·Biochemical and Biophysical Research Communications·Dong-Qing WeiKuo-Chen Chou
May 23, 2006·Amino Acids·D-Q WeiK-C Chou
Jun 20, 2006·Journal of Molecular Biology·Satoshi SatoAlan R Fersht
Sep 5, 2006·Medicinal Chemistry·Rui ZhangKuo-Chen Chou
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Feb 1, 2008·Nature·Jason R Schnell, James J Chou

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Citations

Jun 3, 2014·BMC Structural Biology·Masanari Matsuoka, Takeshi Kikuchi
Aug 2, 2011·Biosensors & Bioelectronics·Bo FengYouzhi Dai
Jun 10, 2014·Biochemical and Biophysical Research Communications·Bo FengZhijian Cao
May 9, 2013·Statistics in Medicine·D J LowskyS A Zenios

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