Literature DB >> 27273630

Toward high-resolution computational design of the structure and function of helical membrane proteins.

Patrick Barth1,2,3, Alessandro Senes4.   

Abstract

The computational design of α-helical membrane proteins is still in its infancy but has already made great progress. De novo design allows stable, specific and active minimal oligomeric systems to be obtained. Computational reengineering can improve the stability and function of naturally occurring membrane proteins. Currently, the major hurdle for the field is the experimental characterization of the designs. The emergence of new structural methods for membrane proteins will accelerate progress.

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Year:  2016        PMID: 27273630      PMCID: PMC4962061          DOI: 10.1038/nsmb.3231

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN: 1545-9985            Impact factor:   15.369


  65 in total

1.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors:  A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal:  J Mol Biol       Date:  2001-01-19       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.  Multipass membrane protein structure prediction using Rosetta.

Authors:  Vladimir Yarov-Yarovoy; Jack Schonbrun; David Baker
Journal:  Proteins       Date:  2006-03-01

4.  Computational design of ligand-binding proteins with high affinity and selectivity.

Authors:  Christine E Tinberg; Sagar D Khare; Jiayi Dou; Lindsey Doyle; Jorgen W Nelson; Alberto Schena; Wojciech Jankowski; Charalampos G Kalodimos; Kai Johnsson; Barry L Stoddard; David Baker
Journal:  Nature       Date:  2013-09-04       Impact factor: 49.962

5.  Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.

Authors:  A Senes; M Gerstein; D M Engelman
Journal:  J Mol Biol       Date:  2000-02-25       Impact factor: 5.469

Review 6.  Structural Symmetry in Membrane Proteins.

Authors:  Lucy R Forrest
Journal:  Annu Rev Biophys       Date:  2015       Impact factor: 12.981

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

Authors:  Jian Zhang; Jianyi Yang; Richard Jang; Yang Zhang
Journal:  Structure       Date:  2015-07-16       Impact factor: 5.006

8.  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

Review 9.  Energy functions in de novo protein design: current challenges and future prospects.

Authors:  Zhixiu Li; Yuedong Yang; Jian Zhan; Liang Dai; Yaoqi Zhou
Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

10.  Activation and dynamic network of the M2 muscarinic receptor.

Authors:  Yinglong Miao; Sara E Nichols; Paul M Gasper; Vincent T Metzger; J Andrew McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-18       Impact factor: 11.205

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  15 in total

Review 1.  Reprogramming cellular functions with engineered membrane proteins.

Authors:  Caroline Arber; Melvin Young; Patrick Barth
Journal:  Curr Opin Biotechnol       Date:  2017-07-11       Impact factor: 9.740

2.  Cyclic oligomer design with de novo αβ-proteins.

Authors:  Yu-Ru Lin; Nobuyasu Koga; Sergey M Vorobiev; David Baker
Journal:  Protein Sci       Date:  2017-11       Impact factor: 6.725

Review 3.  Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport.

Authors:  Nathan H Joh; Gevorg Grigoryan; Yibing Wu; William F DeGrado
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

4.  Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.

Authors:  Rebecca F Alford; Patrick J Fleming; Karen G Fleming; Jeffrey J Gray
Journal:  Biophys J       Date:  2020-03-14       Impact factor: 4.033

Review 5.  Protein Design: From the Aspect of Water Solubility and Stability.

Authors:  Rui Qing; Shilei Hao; Eva Smorodina; David Jin; Arthur Zalevsky; Shuguang Zhang
Journal:  Chem Rev       Date:  2022-08-03       Impact factor: 72.087

Review 6.  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

7.  Membrane Protein Engineering with Rosetta.

Authors:  Rebecca F Alford; Jeffrey J Gray
Journal:  Methods Mol Biol       Date:  2021

8.  Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.

Authors:  Virginia Jiang; Sagar D Khare; Scott Banta
Journal:  Protein Sci       Date:  2021-05-25       Impact factor: 6.993

Review 9.  Computational protein design with backbone plasticity.

Authors:  James T MacDonald; Paul S Freemont
Journal:  Biochem Soc Trans       Date:  2016-10-19       Impact factor: 5.407

10.  Small-residue packing motifs modulate the structure and function of a minimal de novo membrane protein.

Authors:  Paul Curnow; Benjamin J Hardy; Virginie Dufour; Christopher J Arthur; Richard Stenner; Lorna R Hodgson; Paul Verkade; Christopher Williams; Deborah K Shoemark; Richard B Sessions; Matthew P Crump; Michael R Jones; J L Ross Anderson
Journal:  Sci Rep       Date:  2020-09-16       Impact factor: 4.379

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