Strategies for modeling the interactions of transmembrane helices of G protein-coupled receptors by geometric complementarity using the GRAMM computer algorithm.

Publisher Summary The progress in comparative modeling of globular proteins is based on the large number of available structural templates. At the same time, the importance of GPCR modeling studies that are not based on structural templates comes from the fact that out of >1000 known GPCRs, only one such potential template exists (rhodopsin). The similarity between protein docking and helix–helix packing is used and the protein docking procedure GRAMM is applied to the matching of helices in the TM bundle. GRAMM is based on the search for the steric complementarity at variable resolution. It is shown in the chapter that the steric interactions between TM helices are correlated with the helix–helix interaction energy to the degree that the steric interactions alone, in general, can be used to predict helix packing. The ability of GRAMM to predict the low-resolution match between the helices based on the smoothing of the energy landscape is demonstrated in this chapter. The existence of large-scale structural recognition factors in TM helices that facilitate the low-resolution match have been determined.

[1]  G. Vriend,et al.  G protein-coupled receptors in silico , 1998, Journal of Molecular Medicine.

[2]  P. Conn.  Methods in neurosciences , 1991 .

[3]  T. Hirokawa,et al.  A Continuum theory for the prediction of lateral and rotational positioning of α‐helices in membrane proteins: Bacteriorhodopsin , 1995, Proteins.

[4]  Sung-Hou Kim,et al.  Electron transfer by domain movement in cytochrome bc1 , 1998, Nature.

[5]  I. Vakser,et al.  Side chains in transmembrane helices are shorter at helix‐helix interfaces , 2000, Proteins.

[6]  Jurgen Sygusch,et al.  High resolution fast quantitative docking using fourier domain correlation techniques , 1997, Proteins.

[7]  J. Cherfils,et al.  Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase , 1996, Nature Structural Biology.

[8]  K. Palczewski,et al.  Crystal Structure of Rhodopsin: A G‐Protein‐Coupled Receptor , 2002, Chembiochem : a European journal of chemical biology.

[9]  D. Ritchie,et al.  Protein docking using spherical polar Fourier correlations , 2000, Proteins.

[10]  G. Nikiforovich.  A novel, non-statistical method for predicting breaks in transmembrane helices. , 1998, Protein engineering.

[11]  Ettore Appella,et al.  Methods in Protein Structure Analysis , 1995, Springer US.

[12]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[13]  J U Bowie,et al.  Helix packing in membrane proteins. , 1997, Journal of molecular biology.

[14]  Jill E. Gready,et al.  Simple method for locating possible ligand binding sites on protein surfaces , 1999 .

[15]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[16]  I. Vakser,et al.  Main-chain complementarity in protein-protein recognition. , 1996, Protein engineering.

[17]  I. Vakser,et al.  Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex , 1997, Proteins.

[18]  A. Murzin.  Structure classification‐based assessment of CASP3 predictions for the fold recognition targets , 1999, Proteins.

[19]  K. Dill.  Polymer principles and protein folding , 1999, Protein science : a publication of the Protein Society.

[20]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[21]  I A Vakser.  Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. , 1996, Protein engineering.

[22]  P Herzyk,et al.  Automated method for modeling seven-helix transmembrane receptors from experimental data. , 1995, Biophysical journal.

[23]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[24]  I. Vakser.  Low-resolution docking: prediction of complexes for underdetermined structures. , 1998, Biopolymers.

[25]  I. Vakser.  Protein docking for low-resolution structures. , 1995, Protein engineering.

[26]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[27]  R Henderson,et al.  Electron-crystallographic refinement of the structure of bacteriorhodopsin. , 1996, Journal of molecular biology.

[28]  C. Orengo,et al.  Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts prediction , 1999, Proteins.

[29]  J Deisenhofer,et al.  Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. , 1989, Journal of molecular biology.

[30]  A. Lomize,et al.  The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. , 1997, Biophysical journal.

[31]  J M Friedman.  Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures. , 1997, Protein engineering.

[32]  T. Tomizaki,et al.  The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase at 2.8 Å , 1996, Science.

[33]  J. S. Dixon,et al.  Evaluation of the CASP2 docking section , 1997, Proteins.

[34]  Garland R. Marshall,et al.  A potential smoothing algorithm accurately predicts transmembrane helix packing , 1999, Nature Structural Biology.

[35]  R. Nussinov,et al.  Folding funnels, binding funnels, and protein function , 1999, Protein science : a publication of the Protein Society.

[36]  D. Schomburg,et al.  Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. , 1996, Journal of molecular biology.

[37]  L. C. Andrews,et al.  The Fourier-Green's function and the rapid evaluation of molecular potentials. , 1994, Protein engineering.