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Biochim Biophys Acta Proteins Proteom. 2018 Feb;1866(2):379-386. doi: 10.1016/j.bbapap.2017.09.003. Epub 2017 Sep 11.

Relationships between residue Voronoi volume and sequence conservation in proteins.

Author information

1
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: jwliu.nctu@gmail.com.
2
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: mikun800527@gmail.com.
3
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: claire.bi99g@nctu.edu.tw.
4
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: evelynchen.bi04g@nctu.edu.tw.
5
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C; Center for Bioinformatics Research, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: jkhwang@faculty.nctu.edu.tw.
6
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C. Electronic address: nebula.bi97g@nctu.edu.tw.

Abstract

BACKGROUND:

Functional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure. Herein, we present a simple structural determinant termed the relative space of Voronoi volume (RSV); it uses the Voronoi volume and the van der Waals volume of particular residues to quantify the local structural environment.

METHODS:

RSV (range, 0-1) is defined as (Voronoi volume-van der Waals volume)/Voronoi volume of the target residue. The concept of RSV describes the extent of available space for every protein residue.

RESULTS:

RSV and Voronoi profiles with and without water molecules (RSVw, RSV, VOw, and VO) were compared for 554 non-homologous proteins. RSV (without water) showed better Pearson's correlations with CS than did RSVw, VO, or VOw values. The mean correlation coefficient between RSV and CS was 0.51, which is comparable to the correlation between RSA and CS (0.49) and that between WCN and CS (0.56).

CONCLUSIONS:

RSV is a robust structural descriptor with and without water molecules and can quantitatively reflect evolutionary information in a single protein structure. Therefore, it may represent a practical structural determinant to study protein sequence, structure, and function relationships.

KEYWORDS:

Free space; Local structural environments; Packing density; RSV; Sequence conservation; Voronoi volume

PMID:
28911812
DOI:
10.1016/j.bbapap.2017.09.003
[Indexed for MEDLINE]

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