On the packing density of the unbound protein-protein interaction interface and its implications in dynamics

BMC Bioinformatics

Proceedings

Zih-Lin Lin¹  Tsun-Tsao Huang¹  Jenn-Kang Hwang¹  Jau-Ji Lin² 

[1] Institute of Bioinformatics and Systems Biology, National Chiao Tung University, No.75, Bo-Ai St., East District, 300, HsinChu City, Taiwan;Institute of Bioinformatics and Systems Biology, National Chiao Tung University, No.75, Bo-Ai St., East District, 300, HsinChu City, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong St., Beitou District, 112, Taipei City, Taiwan;Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, No. 128, Academia Rd., Sec. 2, Nankang District, 115, Taipei City, Taiwan;

关键词: Packing Density;    Thermal Fluctuation;    Interface Residue;    Central Interface;    Transient Complex;   

DOI  :  10.1186/1471-2105-16-S1-S7

来源: Springer

【 摘 要 】

BackgroundCharacterizing the interface residues will help shed light on protein-protein interactions, which are involved in many important biological processes. Many studies focus on characterizing sequence or structure features of protein interfaces, but there are few studies characterizing the dynamics of interfaces. Therefore, we would like to know whether there is any specific dynamics pattern in the protein-protein interaction interfaces. Thermal fluctuation is an important dynamical property for a residue, and could be quickly estimated by local packing density without large computation since studies have showen closely relationship between these two properties. Therefore, we divided surface of an unbound subunit (free protein subunits before they are involved in forming the protein complexes) into several separate regions, and compared their average thermal fluctuations of different regions in order to characterize the dynamics pattern in unbound protein-protein interaction interfaces.ResultsWe used weighted contact numbers (WCN), a parameter-free method to quantify packing density, to estimate the thermal fluctuations of residues in the interfaces. By analyzing the WCN distributions of interfaces in unbound subunits from 1394 non-homologous protein complexes, we show that the residues in the central regions of interfaces have higher packing density (i.e. more rigid); on the other hand, residues surrounding the central regions have smaller packing density (i.e. more flexible). The distinct distributions of packing density, suggesting distinct thermal fluctuation, reveals specific dynamics pattern in the interface of unbound protein subunits.ConclusionsWe found general trend that the unbound protein-protein interaction interfaces consist of rigid residues in the central regions, which are surrounded by flexible residues. This finding suggests that the dynamics might be one of the important features for the formation of protein complexes.

【 授权许可】

Unknown   
© Lin et al.; licensee BioMed Central Ltd. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.