GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.

Experimental structure determination remains difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average Cα root-mean-square deviation 2.4 Å in the TM regions. The new hybrid protocol was applied to model all 1,026 GPCRs in the human genome, where 923 have a high confidence score and are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin, and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of TM proteins.

[1]  Sitao Wu,et al.  LOMETS: A local meta-threading-server for protein structure prediction , 2007, Nucleic acids research.

[2]  R. Abagyan,et al.  Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists , 2010, Science.

[3]  Yang Zhang,et al.  BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions , 2012, Nucleic Acids Res..

[4]  W. Greenlee,et al.  Non-peptide Angiotensin Agonist , 1995, The Journal of Biological Chemistry.

[5]  Hongyi Zhou,et al.  Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments , 2004, Proteins.

[6]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[7]  J. Köhl,et al.  Site-directed mutagenesis of conserved charged residues in the helical region of the human C5a receptor. Arg2O6 determines high-affinity binding sites of C5a receptor. , 1996, European journal of biochemistry.

[8]  G A Petsko,et al.  Aromatic-aromatic interaction: a mechanism of protein structure stabilization. , 1985, Science.

[9]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.

[10]  Dong Xu,et al.  ThreaDom: extracting protein domain boundary information from multiple threading alignments , 2013, Bioinform..

[11]  S. Mitaku,et al.  Identification of G protein‐coupled receptor genes from the human genome sequence , 2002, FEBS letters.

[12]  R. Eglen,et al.  Emerging concepts of guanine nucleotide-binding protein-coupled receptor (GPCR) function and implications for high throughput screening. , 2007, Assay and drug development technologies.

[13]  S. Costagliola,et al.  G protein-coupled receptors: mutations and endocrine diseases , 2011, Nature Reviews Endocrinology.

[14]  Hongyi Zhou,et al.  Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition , 2004, Proteins.

[15]  Andrei L Lomize,et al.  Positioning of proteins in membranes: A computational approach , 2006, Protein science : a publication of the Protein Society.

[16]  Yang Zhang,et al.  Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. , 2011, Structure.

[17]  Maya Topf,et al.  PREDICT modeling and in‐silico screening for G‐protein coupled receptors , 2004, Proteins.

[18]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[19]  D Baker,et al.  Prediction of membrane protein structures with complex topologies using limited constraints , 2009, Proceedings of the National Academy of Sciences.

[20]  W. Greenlee,et al.  Dual agonistic and antagonistic property of nonpeptide angiotensin AT1 ligands: susceptibility to receptor mutations. , 1997, Molecular pharmacology.

[21]  Ruben Abagyan,et al.  Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. , 2011, Structure.

[22]  A. Godzik,et al.  Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.

[23]  Sitao Wu,et al.  MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information , 2008, Proteins.

[24]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[25]  T. Bártfai,et al.  Delineation of the peptide binding site of the human galanin receptor. , 1996, The EMBO journal.

[26]  O. Lichtarge,et al.  C5a Receptor Activation , 1999, The Journal of Biological Chemistry.

[27]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[28]  J. Köhl,et al.  Site-Directed Mutagenesis of Conserved Charged Residues in the Helical Region of the Human C5a Receptor , 1996 .

[29]  R. Genco,et al.  Recombinant expression and partial characterization of the human formyl peptide receptor. , 1993, Biochimica et biophysica acta.

[30]  Francesca Fanelli,et al.  Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. , 2011, Chemical reviews.

[31]  Yang Zhang,et al.  A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction , 2013, Scientific Reports.

[32]  Thomas A. Hopf,et al.  Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing , 2012, Cell.

[33]  Peter L. Freddolino,et al.  Prediction of structure and function of G protein-coupled receptors , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  G. Tusnády,et al.  Principles governing amino acid composition of integral membrane proteins: application to topology prediction. , 1998, Journal of molecular biology.

[35]  R. Breyer,et al.  Prostanoid receptors: subtypes and signaling. , 2001, Annual review of pharmacology and toxicology.

[36]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[37]  Terri L. Gilbert,et al.  Multiple activation steps of the N-formyl peptide receptor. , 1999, Biochemistry.

[38]  T. Schwartz,et al.  Mutations in transmembrane segment VIJ of the AT1 receptor differentiate between closely related insurmountable and competitive angiotensin antagonists , 1994, British journal of pharmacology.

[39]  L. Brouchon,et al.  Identification of the Major Phosphorylation Sites in Human C5a Anaphylatoxin Receptor in Vivo(*) , 1995, The Journal of Biological Chemistry.

[40]  L. F. Kolakowski,et al.  Probing the Message:Address Sites for Chemoattractant Binding to the C5a Receptor , 1995, The Journal of Biological Chemistry.

[41]  Timothy Nugent,et al.  Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis , 2012, Proceedings of the National Academy of Sciences.

[42]  R. Stevens,et al.  The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist , 2008, Science.

[43]  M. Burghammer,et al.  Crystal structure of the human β2 adrenergic G-protein-coupled receptor , 2007, Nature.

[44]  Ruben Abagyan,et al.  Structure of the human histamine H1 receptor complex with doxepin , 2011, Nature.

[45]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[46]  Jonathan A. Javitch,et al.  Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist , 2010, Science.

[47]  Bernard Maigret,et al.  Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? , 2003, Trends in pharmacological sciences.

[48]  J. Skolnick,et al.  TOUCHSTONE II: a new approach to ab initio protein structure prediction. , 2003, Biophysical journal.

[49]  Yang Zhang,et al.  I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.

[50]  E Uberbacher,et al.  Protein threading by PROSPECT: a prediction experiment in CASP3. , 1999, Protein engineering.

[51]  Adrian A Canutescu,et al.  Cyclic coordinate descent: A robotics algorithm for protein loop closure , 2003, Protein science : a publication of the Protein Society.

[52]  Yang Zhang,et al.  A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction , 2010, PloS one.

[53]  Yang Zhang.  Interplay of I‐TASSER and QUARK for template‐based and ab initio protein structure prediction in CASP10 , 2014, Proteins.

[54]  Richard Bonneau,et al.  Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.

[55]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[56]  J S Mills,et al.  Characterization of the Binding Site on the Formyl Peptide Receptor Using Three Receptor Mutants and Analogs of Met-Leu-Phe and Met-Met-Trp-Leu-Leu* , 2000, The Journal of Biological Chemistry.

[57]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[58]  Yang Zhang,et al.  High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling , 2013, Bioinform..

[59]  Lei Shi,et al.  The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. , 2002, Annual review of pharmacology and toxicology.

[60]  J. Prestegard,et al.  Optimal mutation sites for PRE data collection and membrane protein structure prediction. , 2011, Structure.

[61]  E. Vallender,et al.  Trace Amine Associated Receptor 1 Signaling in Activated Lymphocytes , 2011, Journal of Neuroimmune Pharmacology.

[62]  T. Bártfai,et al.  Mutagenesis and ligand modification studies on galanin binding to its GTP-binding-protein-coupled receptor GalR1. , 1997, European journal of biochemistry.

[63]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[64]  Nir Ben-Tal,et al.  Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications , 2010, Proceedings of the National Academy of Sciences.

[65]  David Eisenberg,et al.  The helical hydrophobic moment: a measure of the amphiphilicity of a helix , 1982, Nature.

[66]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[67]  Yang Zhang,et al.  GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation , 2010, Bioinform..

[68]  Claes Wahlestedt,et al.  Therapeutic potential of neuropeptide Y (NPY) receptor ligands , 2010, EMBO molecular medicine.

[69]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[70]  Yang Zhang,et al.  BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures , 2012, Proteins.

[71]  M. Gromiha.  Influence of cation-pi interactions in different folding types of membrane proteins. , 2003, Biophysical chemistry.

[72]  J. Skolnick,et al.  Automated structure prediction of weakly homologous proteins on a genomic scale. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Hualiang Jiang,et al.  Structural Basis for Molecular Recognition at Serotonin Receptors , 2013, Science.

[74]  T. Nett,et al.  Gonadotropin-releasing hormone and its receptor in normal and malignant cells. , 2004, Endocrine-related cancer.

[75]  Aashish Manglik,et al.  Structure of the δ-opioid receptor bound to naltrindole , 2012, Nature.

[76]  Yang Zhang,et al.  SPICKER: A clustering approach to identify near‐native protein folds , 2004, J. Comput. Chem..

[77]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[78]  J. Skolnick,et al.  Ab initio modeling of small proteins by iterative TASSER simulations , 2007, BMC Biology.

[79]  Yang Zhang,et al.  How significant is a protein structure similarity with TM-score = 0.5? , 2010, Bioinform..

[80]  Martin Madera,et al.  Profile Comparer: a program for scoring and aligning profile hidden Markov models , 2008, Bioinform..