Delaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition.
As an important transmembrane protein family in eukaryon, G-protein coupled receptors (GPCRs) play a significant role in cellular signal transduction and are important targets for drug design. However, it is very difficult to resolve their tertiary structure by X-ray crystallography. In this study, we have developed a Delaunay model, which constructs a series of simplexes with latent variables to classify the families of GPCRs and projects unknown sequences to principle component space (PC-space) to predict their topology. Computational results show that, for the classification of GPCRs, the method achieves the accuracy of 91.0 and 87.6% for Class A, more than 80% for the other three classes in differentiating GPCRs from non-GPCRs and 70% for discriminating between four major classes of GPCR, respectively. When recognizing the structure of GPCRs, all the N-terminals of sequences can be determined correctly. The maximum accuracy of predicting transmembrane segments is achieved in the 7th transmembrane segment of Rhodopsin, which is 99.4%, and the average error is 2.1 amino acids, which is the lowest in all of the segments prediction. This method could provide structural information of a novel GPCR as a tool for experiments and other algorithms of structure prediction of GPCRs. Academic users should send their request for the MATLAB program for classifying GPCRs and predicting the topology of them at liml@scu.edu.cn .
Wen
Z
Z
College of Chemistry, Sichuan University, Chengdu, Sichuan, China.
Li
M
M
Li
Y
Y
Guo
Y
Y
Wang
K
K
D000465:Algorithms; D000818:Animals; D002138:Calibration; D002417:Cattle; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006801:Humans; D008956:Models, Chemical; D008962:Models, Theoretical; D025341:Principal Component Analysis; D017434:Protein Structure, Tertiary; D018340:Receptors, Adrenergic, alpha-1 / Q000378:metabolism; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry*; D012243:Rhodopsin / Q000378:metabolism
C547716:ADRA1B protein, human; D018340:Receptors, Adrenergic, alpha-1; D043562:Receptors, G-Protein-Coupled; D012243:Rhodopsin