Influence of the g- conformation of Ser and Thr on the structure of transmembrane helices.

In order to study the influence of Ser and Thr on the structure of transmembrane helices we have analyzed a database of helix stretches extracted from crystal structures of membrane proteins and an ensemble of model helices generated by molecular dynamics simulations. Both complementary analyses show that Ser and Thr in the g- conformation induce and/or stabilize a structural distortion in the helix backbone. Using quantum mechanical calculations, we have attributed this effect to the electrostatic repulsion between the side chain Ogamma atom of Ser and Thr and the backbone carbonyl oxygen at position i-3. In order to minimize the repulsive force between these negatively charged oxygens, there is a modest increase of the helix bend angle as well as a local opening of the helix turn preceding Ser/Thr. This small distortion can be amplified through the helix, resulting in a significant displacement of the residues located at the other side of the helix. The crystal structures of aquaporin Z and the beta(2)-adrenergic receptor are used to illustrate these effects. Ser/Thr-induced structural distortions can be implicated in processes as diverse as ligand recognition, protein function and protein folding.

[1]  B. Matthews,et al.  Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins. , 1984, Journal of molecular biology.

[2]  Wei Liu,et al.  Comparison of helix interactions in membrane and soluble alpha-bundle proteins. , 2002, Biophysical journal.

[3]  Tom Lenaerts,et al.  Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments , 2008, PLoS Comput. Biol..

[4]  M. Sternberg,et al.  Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. , 1987, Journal of molecular biology.

[5]  Andrei L. Lomize,et al.  OPM: Orientations of Proteins in Membranes database , 2006, Bioinform..

[6]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[7]  Jacopo Tomasi,et al.  Quantum Mechanical Continuum Solvation Models , 2005 .

[8]  Leonardo Pardo,et al.  Ser and Thr Residues Modulate the Conformation of Pro-Kinked Transmembrane α-Helices , 2004 .

[9]  L. Pardo,et al.  Ser and Thr residues modulate the conformation of pro-kinked transmembrane alpha-helices. , 2004, Biophysical journal.

[10]  Duan Yang,et al.  The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Leonardo Pardo,et al.  Structural models of class a G protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity. , 2007, Current topics in medicinal chemistry.

[12]  P. Kollman,et al.  Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .

[13]  I. Rigoutsos,et al.  Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. , 2003, Nucleic acids research.

[14]  T. Allen.  Modeling Charged Protein Side Chains in Lipid Membranes , 2007, The Journal of general physiology.

[15]  Leonardo Pardo,et al.  Influence of the environment in the conformation of alpha-helices studied by protein database search and molecular dynamics simulations. , 2002, Biophysical journal.

[16]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[17]  Hutchinson Ge.  THE INFLUENCE OF THE ENVIRONMENT , 1964 .

[18]  F. Cordes,et al.  Proline-induced distortions of transmembrane helices. , 2002, Journal of molecular biology.

[19]  J. Bowie.  Solving the membrane protein folding problem , 2005, Nature.

[20]  Kuo-Chen Chou,et al.  Energetic approach to the packing of α-helices. II: General treatment of nonequivalent and nonregular helices , 1984 .

[21]  Thomas M Frimurer,et al.  Ligand binding and micro-switches in 7TM receptor structures. , 2009, Trends in pharmacological sciences.

[22]  Zsuzsanna Dosztányi,et al.  PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank , 2004, Nucleic Acids Res..

[23]  Shoshana J. Wodak,et al.  The TXP Motif in the Second Transmembrane Helix of CCR5 , 2001, The Journal of Biological Chemistry.

[24]  S. Rasmussen,et al.  The structure and function of G-protein-coupled receptors , 2009, Nature.

[25]  Rob Leurs,et al.  Pharmacogenomic and structural analysis of constitutive g protein-coupled receptor activity. , 2007, Annual review of pharmacology and toxicology.

[26]  C. Deber,et al.  Missense mutations in transmembrane domains of proteins: Phenotypic propensity of polar residues for human disease , 2004, Proteins.

[27]  G von Heijne,et al.  A turn propensity scale for transmembrane helices. , 1999, Journal of molecular biology.

[28]  I. Pogozheva,et al.  Highly conserved serine in the third transmembrane helix of the luteinizing hormone/human chorionic gonadotropin receptor regulates receptor activation. , 2003, Biochemistry.

[29]  Markus Eilers,et al.  Comparison of Helix Interactions in Membrane and Soluble α-Bundle Proteins , 2002 .

[30]  J. Bowie,et al.  Analysis of side-chain rotamers in transmembrane proteins. , 2004, Biophysical journal.

[31]  D. Engelman,et al.  Motifs of serine and threonine can drive association of transmembrane helices. , 2002, Journal of molecular biology.

[32]  Leonardo Pardo,et al.  Serine and Threonine Residues Bend α-Helices in the χ1 = g− Conformation , 2000 .

[33]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[34]  L. Kelley,et al.  An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. , 1996, Protein engineering.

[35]  Virgil L. Woods,et al.  Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins , 2008, Nature.

[36]  M. Gerstein,et al.  Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. , 2000, Journal of molecular biology.

[37]  J Novotny,et al.  Non-alpha-helical elements modulate polytopic membrane protein architecture. , 2001, Journal of molecular biology.

[38]  Jessica Sallander,et al.  Conformational Toggle Switches Implicated in Basal Constitutive and Agonist-Induced Activated States of 5-Hydroxytryptamine-4 Receptors , 2009, Molecular Pharmacology.

[39]  M. Bansal,et al.  HELANAL: A Program to Characterize Helix Geometry in Proteins , 2000, Journal of biomolecular structure & dynamics.

[40]  Sarel J Fleishman,et al.  Transmembrane protein structures without X-rays. , 2006, Trends in biochemical sciences.

[41]  Mark S.P. Sansom,et al.  Hinges, swivels and switches: the role of prolines in signalling via transmembrane α-helices , 2000 .

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

[43]  L. Pardo,et al.  Design, synthesis and pharmacological evaluation of 5-hydroxytryptamine(1a) receptor ligands to explore the three-dimensional structure of the receptor. , 2002, Molecular pharmacology.

[44]  L. Pardo,et al.  Serine and Threonine Residues Bend a-Helices in the x 1 5 g 2 Conformation , 2000 .

[45]  Robert M. Graham,et al.  Non-α-helical elements modulate polytopic membrane protein architecture , 2001 .