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Fast Fourier Transform-based Support Vector Machine for Prediction of g-protein coupled receptor Subfamilies

Acta Biochimica et Biophysica Sinica 2005年第11期37卷 759-766页

作者： Yan-Zhi gUO Meng-Long LI Ke-Long WANg Zhi-Ning WEN Min-Chun LU Li-Xia LIU Lin JIANg College of Chemistry,Sichuan University,Chengdu 610064,China College of Chemistry Sichuan UniversityChengdu 610064 China

Although the sequence information on g-protein coupled receptors(gPCRs)continues togrow,many gPCRs remain orphaned(i.***.ligand specificity unknown)or poorly characterized with littlestructural information available,so an automated and reliable method is badly needed to facilitate the identifi-cation of novel receptors.In this study,a method of fast Fourier transform-based support vector machinehas been developed for predicting gPCR subfamilies according to protein’s hydrophobicity.In classifyingClass B,C,D and F subfamilies,the method achieved an overall Matthew’s correlation coefficient andaccuracy of 0.95 and 93.3%,respectively,when evaluated using the jackknife test.The method achieved anaccuracy of 100% on the Class B independent dataset.The results show that this method can classify gPCRsubfamilies as well as their functional classification with high accuracy.A web server implementing theprediction is available at http://***/blast/Pred-gPCR.

关键词： g-protein coupled receptor subfamily fast Fourier transform support vector machine prediction

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Identification of a key g-protein coupled receptor in mediating appressorium formation and fungal virulence against insects

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Science China(Life Sciences) 2021年第3期64卷 466-477页

作者： Junmei Shang Yanfang Shang guirong Tang Chengshu Wang Key Laboratory of Insect Developmental and Evolutionary Biology CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

Fungal g-protein coupled receptors(gPCRs)play essential roles in sensing environmental cues including host signals.The study of gPCR in mediating fungus-insect interactions is still limited.Here we report the evolution of gPCR genes encoded in the entomopathogenic Metarhizium species and found the expansion of Pth11-like gPCRs in the generalist species with a wide host range.By deletion of ten candidate genes Mrgpr1–Mrgpr10 selected from the six obtained subfamilies in the generalist M.robertsii,we found that each of them played a varied level of roles in mediating appressorium formation.In particular,deletion of Mrgpr8 resulted in the failure of appressorium formation on different substrates and the loss of virulence during topical infection of insects but not during injection assays when compared with the wild-type(WT)strain.Further analysis revealed that disruption of Mrgpr8 substantially impaired the nucleus translocation of the mitogen-activated protein kinase(MAPK)Mero-Fus3 but not the MAPK Mero-Slt2 during appressorium formation.We also found that the defect ofΔMrgpr8 could not be rescued with the addition of cyclic AMP for appressorium formation.Relative to the WT,differential expression of the selected genes have also been detected inΔMrgpr8.The results of this study may benefit the understanding of fungus-interactions mediated by gPCRs.

关键词： g-protein coupled receptor appressorium virulence signal pathway Metarhizium

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Comparative domain modeling of human EgF-like module EMR2 and study of interaction of the fourth domain of EgF with chondroitin 4-sulphate

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The Journal of Biomedical Research 2011年第2期25卷 100-110页

作者： Mukta Rani Manas R.Dikhit ganesh C Sahoo Pradeep Das Biomedical Informatics Division Rajendra Memorial Research Institute of Medical SciencesAgam KuanPatna 800007India

EMR2 is an EgF-like module containing mucin-like hormone receptor-2 precursor, a g-protein coupled receptor （g-PCR）. Mutation in EMR2 causes complicated disorders like polycystic kidney disease （PKD）. The structure of EMR2 shows that the fifth domain is comprised of EgF-TM7 helices. Functional assignment of EMR2 by support vector machine （SVM） revealed that along with transporter activity, several novel functions are predicted. A twenty amino acid sequence ＂MggRVFLVFLAFCVWLTLPg＂ acts as the signal peptide responsible for post- translational transport. Eight amino acids are involved in N-glycosylation sites and two cleavage sites are LeuS17 and SerS18 in EMR2. The residue Arg241 is responsible for interaction with glycosaminoglycan and chondroitin sulfate. On the basis of structure, function and ligand binding sites, competitive EMR2 inhibitors designed may decrease the rate of human diseases like Usher＇s syndrome, bilateral frontoparietal polymicrogyria and PKD.

关键词： EMR2 g-protein coupled receptor transmembrane homology modeling EgF-TM7

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Exploring the mechanism of the mutation-caused constitutive activity of gPCR by a computational study

Exploring the mechanism of the mutation-caused constitutive ...

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中国化学会第30届学术年会-第二十五分会：化学信息学与...

作者： Nan gao Tao Liang Xiuchan Xiao Yihuan Zhao Yanzhi guo Menglong Li Xuemei Pu College of Chemistry Sichuan University

g-protein-coupled receptors（gPCRs）are important drug targets,which are in general activated by ligands and deliver signal to cytosolic part.However,some experiments already indicated that gPCRs also give rise to constitutive activity through some mutations（viz.,CAM）,independent on the ligands,which are usually associated with different kinds of diseases.Nevertheless,the mechanisms of CAM and their roles in interactions with the drug-ligands have been unclear on experiments.Herein,we used microsecond time-scale molecular dynamics simulations to study the effect of an important F282L mutation onβ2AR in order to address the questions above.With aid of the principle component analysis and the correlation analysis,our results revealed that F282L mutation could increase instability of the overall structure,dramatic fluctuation of NPxxY and extracellular loops,and decrease restraining of helices through weakening the interhelical H-bonding,which should contribute to the constitutive activity reported by the experiments.In addition,we also utilized the protein structure network（PSN）method to explore the impact of F282L mutation on the structural communication pathways ofβ2AR.The result indicates that the mutant exhibits less information flows with respect to the wildβ2AR.Furthermore,the mutation weakens the role of TM6 in taking part in the signal transmission but enhances the impact of TM3.In addition,we also used virtual screening method to study the impact of the mutation on the interaction with the drug ligands.Similar to the active state ofβ2AR,the mutant exhibits higher enrichment factor for the agonists than the inverse agonists,in contrast to the result of the inactive state ofβ2AR（PDB ID:2RH1）,indicating that the F282L mutation advances the activation ofβ2AR.In a whole,our observations provide valuable information for understanding the mechanism of the mutation-caused constitutive activity of gPCR and related drug-design.

关键词： g-protein coupled receptor molecular dynamics simulations mutation constitutive activity protein structure network

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Study on mechanism of mutation-caused constitutive activity of gPCR via molecular dynamics simulation

Study on mechanism of mutation-caused constitutive activity ...

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第十三届全国量子化学会议

作者： Nan gao Tao Liang Yanzhi guo Menglong Li Anmin Tian Xuemei Pu College of Chemistry Sichuan University

g-protein-coupled receptors(gPCRs) are important drug targets, which are in general activated by ligands and deliver signal to cytosolic part. Nevertheless, the mechanisms of constitutively active mut

关键词： g-protein coupled receptor molecular dynamics simulations mutation constitutive activity protein structure network

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