Literature DB >> 22244752

Computational design of membrane proteins.

Jose Manuel Perez-Aguilar1, Jeffery G Saven.   

Abstract

Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues, and this review discusses recent studies that tailor membrane proteins to display specific structures or functions and examines how redesigned membrane proteins are being used to facilitate structural and functional studies.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22244752      PMCID: PMC4108999          DOI: 10.1016/j.str.2011.12.003

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  85 in total

1.  Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

Authors:  H Kono; J G Saven
Journal:  J Mol Biol       Date:  2001-02-23       Impact factor: 5.469

2.  The Calpha ---H...O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions.

Authors:  A Senes; I Ubarretxena-Belandia; D M Engelman
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-31       Impact factor: 11.205

3.  Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.

Authors:  Beili Wu; Ellen Y T Chien; Clifford D Mol; Gustavo Fenalti; Wei Liu; Vsevolod Katritch; Ruben Abagyan; Alexei Brooun; Peter Wells; F Christopher Bi; Damon J Hamel; Peter Kuhn; Tracy M Handel; Vadim Cherezov; Raymond C Stevens
Journal:  Science       Date:  2010-10-07       Impact factor: 47.728

4.  Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.

Authors:  Matthew W Bowler; Matias Guijarro; Sebastien Petitdemange; Isabel Baker; Olof Svensson; Manfred Burghammer; Christoph Mueller-Dieckmann; Elspeth J Gordon; David Flot; Sean M McSweeney; Gordon A Leonard
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-07-09

5.  Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.

Authors:  Ellen Y T Chien; Wei Liu; Qiang Zhao; Vsevolod Katritch; Gye Won Han; Michael A Hanson; Lei Shi; Amy Hauck Newman; Jonathan A Javitch; Vadim Cherezov; Raymond C Stevens
Journal:  Science       Date:  2010-11-19       Impact factor: 47.728

Review 6.  New tools for membrane protein research.

Authors:  Yilmaz Alguel; James Leung; Shweta Singh; Rohini Rana; Laura Civiero; Claudia Alves; Bernadette Byrne
Journal:  Curr Protein Pept Sci       Date:  2010-03       Impact factor: 3.272

7.  X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel.

Authors:  Hugues Nury; Catherine Van Renterghem; Yun Weng; Alphonso Tran; Marc Baaden; Virginie Dufresne; Jean-Pierre Changeux; James M Sonner; Marc Delarue; Pierre-Jean Corringer
Journal:  Nature       Date:  2011-01-20       Impact factor: 49.962

Review 8.  Designing artificial enzymes by intuition and computation.

Authors:  Vikas Nanda; Ronald L Koder
Journal:  Nat Chem       Date:  2009-12-17       Impact factor: 24.427

9.  De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

Authors:  Ivan V Korendovych; Alessandro Senes; Yong Ho Kim; James D Lear; H Christopher Fry; Michael J Therien; J Kent Blasie; F Ann Walker; William F Degrado
Journal:  J Am Chem Soc       Date:  2010-11-10       Impact factor: 15.419

10.  Metal-binding dependent disruption of membranes by designed helices.

Authors:  Rachel S Signarvic; William F Degrado
Journal:  J Am Chem Soc       Date:  2009-03-11       Impact factor: 15.419

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  17 in total

1.  Naturally evolved G protein-coupled receptors adopt metastable conformations.

Authors:  Kuang-Yui Michael Chen; Fuguo Zhou; Bartlomiej G Fryszczyn; Patrick Barth
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-30       Impact factor: 11.205

2.  Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Authors:  J C Gaines; S Acebes; A Virrueta; M Butler; L Regan; C S O'Hern
Journal:  Proteins       Date:  2018-02-26

Review 3.  Outer membrane protein design.

Authors:  Joanna Sg Slusky
Journal:  Curr Opin Struct Biol       Date:  2016-11-26       Impact factor: 6.809

4.  Computational design of membrane proteins using RosettaMembrane.

Authors:  Amanda M Duran; Jens Meiler
Journal:  Protein Sci       Date:  2017-11-15       Impact factor: 6.725

5.  De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.

Authors:  Nathan H Joh; Tuo Wang; Manasi P Bhate; Rudresh Acharya; Yibing Wu; Michael Grabe; Mei Hong; Gevorg Grigoryan; William F DeGrado
Journal:  Science       Date:  2014-12-19       Impact factor: 47.728

6.  The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

Authors:  Shao-Qing Zhang; Daniel W Kulp; Chaim A Schramm; Marco Mravic; Ilan Samish; William F DeGrado
Journal:  Structure       Date:  2015-02-19       Impact factor: 5.006

Review 7.  Recent advances in automated protein design and its future challenges.

Authors:  Dani Setiawan; Jeffrey Brender; Yang Zhang
Journal:  Expert Opin Drug Discov       Date:  2018-04-25       Impact factor: 6.098

8.  Characterization of a computationally designed water-soluble human μ-opioid receptor variant using available structural information.

Authors:  Xuelian Zhao; Jose Manuel Perez-Aguilar; Felipe Matsunaga; Mitchell Lerner; Jin Xi; Bernard Selling; A T Charlie Johnson; Jeffery G Saven; Renyu Liu
Journal:  Anesthesiology       Date:  2014-10       Impact factor: 7.892

9.  A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor.

Authors:  Jose Manuel Perez-Aguilar; Jin Xi; Felipe Matsunaga; Xu Cui; Bernard Selling; Jeffery G Saven; Renyu Liu
Journal:  PLoS One       Date:  2013-06-14       Impact factor: 3.240

10.  TanCAR: A Novel Bispecific Chimeric Antigen Receptor for Cancer Immunotherapy.

Authors:  Zakaria Grada; Meenakshi Hegde; Tiara Byrd; Donald R Shaffer; Alexia Ghazi; Vita S Brawley; Amanda Corder; Kurt Schönfeld; Joachim Koch; Gianpietro Dotti; Helen E Heslop; Stephen Gottschalk; Winfried S Wels; Matthew L Baker; Nabil Ahmed
Journal:  Mol Ther Nucleic Acids       Date:  2013-07-09       Impact factor: 10.183

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