Predicting the types of J-proteins using clustered amino acids.

Pengmian Feng,Yongchun Zuo,Wei Chen,Hao Lin

doi:10.1155/2014/935719

Abstract

J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed.

Highlights

J-protein, known as Hsp40, is a molecular chaperone protein and is found ubiquitously in both prokaryotes and eukaryotes [1, 2]
In the present work, we proposed a model to predict the four functional types of J-proteins based on reduced amino acid alphabet compositions
Cell death is a common phenomenon in developmental processes or in normal physiological conditions and is induced by an array of extra- or intracellular stimuli [7]

Summary

Introduction

J-protein, known as Hsp (heat shock protein 40 kD), is a molecular chaperone protein and is found ubiquitously in both prokaryotes and eukaryotes [1, 2]. J-proteins represent a large family of molecular chaperones and have cooperative functions with Hsp. Most of the J-proteins contain a “J” domain through which they can interact with and stimulate Hsp. Type I J-proteins contain an N-terminal J-domain that is separated from the rest of the proteins by a linker “G/F” region (glycine/phenylalanine region) [3, 4]. Type II proteins possess all the domains in Type I except the zinc-finger domain [3]. Type III Jproteins contain a C-terminal J-domain but lack both G/F and zinc-finger domains [3]. Type IV, known as the Jlike protein [5], is a group of recently identified proteins that lacks histidine, proline, and aspartate signature motifs in their sequences [4]

Methods

Results

Conclusion