title: Stability of halophilic proteins: from dipeptide attributes to discrimination classifier.
abstract: To investigate the molecular features responsible for protein halophilicity is of great significance for understanding the structure basis of protein halo-stability and would help to develop a practical strategy for designing halophilic proteins. In this work, we have systematically analyzed the dipeptide composition of the halophilic and non-halophilic protein sequences. We observed the halophilic proteins contained more DA, RA, AD, RR, AP, DD, PD, EA, VG and DV at the expense of LK, IL, II, IA, KK, IS, KA, GK, RK and AI. We identified some macromolecular signatures of halo-adaptation, and thought the dipeptide composition might contain more information than amino acid composition. Based on the dipeptide composition, we have developed a machine learning method for classifying halophilic and non-halophilic proteins for the first time. The accuracy of our method for the training dataset was 100.0%, and for the 10-fold cross-validation was 93.1%. We also discussed the influence of some specific dipeptides on prediction accuracy.
authors.affiliation: Department of Biotechnology and Bioengineering, Huaqiao University, Xiamen 361021, Fujian, PR China. zhgyghh@hqu.edu.cn
authors.forename: Guangya
authors.initials: G
authors.lastname: Zhang
authors.forename: Ge
authors.initials: G
authors.lastname: Huihua
authors.forename: Lin
authors.initials: L
authors.lastname: Yi
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019540:Area Under Curve; D001426:Bacterial Proteins / Q000737:chemistry*; D041963:Bacteroidetes / Q000737:chemistry; D041883:Chlorobium / Q000737:chemistry; D019295:Computational Biology; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D004151:Dipeptides / Q000737:chemistry*; D008956:Models, Chemical; D016571:Neural Networks, Computer; D055550:Protein Stability; D012372:ROC Curve; D055049:Salt Tolerance; D020539:Sequence Analysis, Protein; D060388:Support Vector Machine
chemical_list: D001426:Bacterial Proteins; D004151:Dipeptides