Prediction of protein (domain) structural classes based on amino-acid index

被引:45
作者
Bu, WS
Feng, ZP
Zhang, ZD
Zhang, CT [1 ]
机构
[1] Tianjin Univ, Dept Phys, Tianjin 300072, Peoples R China
[2] Tianjin Univ, Chem Engn Res Ctr, Tianjin, Peoples R China
来源
EUROPEAN JOURNAL OF BIOCHEMISTRY | 1999年 / 266卷 / 03期
关键词
structural classes; prediction of structural class; component-coupled algorithm; amino-acid composition; amino-acid index;
D O I
10.1046/j.1432-1327.1999.00947.x
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A protein (domain) is usually classified into one of the following four structural classes: all-alpha, all-beta, alpha/beta and alpha + beta. In this paper, a new formulation is proposed to predict the structural class of a protein (domain) from its primary sequence. Instead of the amino-acid composition used widely in the previous structural class prediction work, the auto-correlation functions based on the profile of amino-acid index along the primary sequence of the query protein (domain) are used for the structural class prediction. Consequently, the overall predictive accuracy is remarkably improved. For the same training database consisting of 359 proteins (domains) and the same component-coupled algorithm [Chou, K.C. & Maggiora, G.M. (1998) Protein Eng. 11, 523-538], the overall predictive accuracy of the new method for the jackknife test is 5-7% higher than the accuracy based only on the amino-acid composition. The overall predictive accuracy finally obtained for the jackknife test is as high as 90.5%, implying that a significant improvement has been achieved by making full use of the information contained in the primary sequence for the class prediction. This improvement depends on the size of the training database, the auto-correlation functions selected and the amino-acid index used. We have found that the aminoacid index proposed by Oobatake and Ooi, i.e. the average nonbonded energy per residue, leads to the optimal predictive result in the case for the database sets studied in this paper. This study may be considered as an alternative step towards making the structural class prediction more practical.
引用
收藏
页码:1043 / 1049
页数:7
相关论文
共 45 条
[1]   PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].
ANFINSEN, CB .
SCIENCE, 1973, 181 (4096) :223-230
[2]  
BEGHIN F, 1975, ARCH INT PHYSIOL BIO, V83, P167
[3]   SECONDARY STRUCTURE PREDICTION - COMBINATION OF 3 DIFFERENT METHODS [J].
BIOU, V ;
GIBRAT, JF ;
LEVIN, JM ;
ROBSON, B ;
GARNIER, J .
PROTEIN ENGINEERING, 1988, 2 (03) :185-191
[4]   A HEURISTIC APPROACH TO PREDICTING THE TERTIARY STRUCTURE OF BOVINE SOMATOTROPIN [J].
CARLACCI, L ;
CHOU, KC ;
MAGGIORA, GM .
BIOCHEMISTRY, 1991, 30 (18) :4389-4398
[5]   PREDICTION OF PROTEIN STRUCTURAL CLASSES [J].
CHOU, KC ;
ZHANG, CT .
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 1995, 30 (04) :275-349
[6]   A NOVEL-APPROACH TO PREDICTING PROTEIN STRUCTURAL CLASSES IN A (20-1)-D AMINO-ACID-COMPOSITION SPACE [J].
CHOU, KC .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1995, 21 (04) :319-344
[7]  
Chou KC, 1998, PROTEINS, V31, P97, DOI 10.1002/(SICI)1097-0134(19980401)31:1<97::AID-PROT8>3.3.CO
[8]  
2-Y
[9]   Domain structural class prediction [J].
Chou, KC ;
Maggiora, GM .
PROTEIN ENGINEERING, 1998, 11 (07) :523-538
[10]  
CHOU KC, 1994, J BIOL CHEM, V269, P22014