Literature DB >> 33973689

AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP.

Diego Del Alamo1, Cédric Govaerts2, Hassane S Mchaourab1.   

Abstract

As part of the CASP competition, the protein structure prediction algorithm AlphaFold2 generated multiple models of the proton/drug antiporter LmrP. Previous distance restraints from double electron-electron resonance spectroscopy, a technique which reports distance distributions between spin labels attached to proteins, suggest that one of the lower-ranked models may have captured a conformation that has so far eluded experimental structure determination.
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Year:  2021        PMID： 33973689      PMCID： PMC8522053          DOI： 10.1002/prot.26138

Source DB:  PubMed          Journal:  Proteins        ISSN： 0887-3585


  11 in total

Review 1.  Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.

Authors:  Hassane S McHaourab; P Ryan Steed; Kelli Kazmier
Journal:  Structure       Date:  2011-11-09       Impact factor: 5.006

2.  DEER distance measurements on proteins.

Authors:  Gunnar Jeschke
Journal:  Annu Rev Phys Chem       Date:  2012-01-30       Impact factor: 12.703

3.  Lipids modulate the conformational dynamics of a secondary multidrug transporter.

Authors:  Chloé Martens; Richard A Stein; Matthieu Masureel; Aurélie Roth; Smriti Mishra; Rosie Dawaliby; Albert Konijnenberg; Frank Sobott; Cédric Govaerts; Hassane S Mchaourab
Journal:  Nat Struct Mol Biol       Date:  2016-07-11       Impact factor: 15.369

4.  An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity.

Authors:  Vincent Debruycker; Andrew Hutchin; Matthieu Masureel; Emel Ficici; Chloé Martens; Pierre Legrand; Richard A Stein; Hassane S Mchaourab; José D Faraldo-Gómez; Han Remaut; Cédric Govaerts
Journal:  Nat Struct Mol Biol       Date:  2020-07-27       Impact factor: 15.369

5.  Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction.

Authors:  Diego Del Alamo; Maxx H Tessmer; Richard A Stein; Jimmy B Feix; Hassane S Mchaourab; Jens Meiler
Journal:  Biophys J       Date:  2019-12-18       Impact factor: 4.033

6.  Protonation drives the conformational switch in the multidrug transporter LmrP.

Authors:  Matthieu Masureel; Chloé Martens; Richard A Stein; Smriti Mishra; Jean-Marie Ruysschaert; Hassane S Mchaourab; Cédric Govaerts
Journal:  Nat Chem Biol       Date:  2013-12-08       Impact factor: 15.040

Review 7.  CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

Authors:  Sunhwan Jo; Xi Cheng; Shahidul M Islam; Lei Huang; Huan Rui; Allen Zhu; Hui Sun Lee; Yifei Qi; Wei Han; Kenno Vanommeslaeghe; Alexander D MacKerell; Benoît Roux; Wonpil Im
Journal:  Adv Protein Chem Struct Biol       Date:  2014-08-24       Impact factor: 3.507

8.  Mechanism of allosteric modulation of P-glycoprotein by transport substrates and inhibitors.

Authors:  Reza Dastvan; Smriti Mishra; Yelena B Peskova; Robert K Nakamoto; Hassane S Mchaourab
Journal:  Science       Date:  2019-05-17       Impact factor: 47.728

Review 9.  Applications of sequence coevolution in membrane protein biochemistry.

Authors:  John M Nicoludis; Rachelle Gaudet
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-10-07       Impact factor: 3.747

10.  Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.

Authors:  Benoît Roux; Shahidul M Islam
Journal:  J Phys Chem B       Date:  2013-04-11       Impact factor: 2.991
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  10 in total

1.  Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter.

Authors:  Diego Del Alamo; Lillian DeSousa; Rahul M Nair; Suhaila Rahman; Jens Meiler; Hassane S Mchaourab
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-15       Impact factor: 12.779

2.  Critical assessment of methods of protein structure prediction (CASP)-Round XIV.

Authors:  Andriy Kryshtafovych; Torsten Schwede; Maya Topf; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2021-10-07

3.  AlphaFold2 fails to predict protein fold switching.

Authors:  Devlina Chakravarty; Lauren L Porter
Journal:  Protein Sci       Date:  2022-06       Impact factor: 6.993

4.  Applying and improving AlphaFold at CASP14.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli; Demis Hassabis
Journal:  Proteins       Date:  2021-12

Review 5.  The AlphaFold Database of Protein Structures: A Biologist's Guide.

Authors:  Alessia David; Suhail Islam; Evgeny Tankhilevich; Michael J E Sternberg
Journal:  J Mol Biol       Date:  2021-10-29       Impact factor: 5.469

6.  Ins and outs of AlphaFold2 transmembrane protein structure predictions.

Authors:  Tamás Hegedűs; Markus Geisler; Gergely László Lukács; Bianka Farkas
Journal:  Cell Mol Life Sci       Date:  2022-01-15       Impact factor: 9.261

7.  Current structure predictors are not learning the physics of protein folding.

Authors:  Carlos Outeiral; Daniel A Nissley; Charlotte M Deane
Journal:  Bioinformatics       Date:  2022-01-31       Impact factor: 6.937

8.  Target highlights in CASP14: Analysis of models by structure providers.

Authors:  Leila T Alexander; Rosalba Lepore; Andriy Kryshtafovych; Athanassios Adamopoulos; Markus Alahuhta; Ann M Arvin; Yannick J Bomble; Bettina Böttcher; Cécile Breyton; Valerio Chiarini; Naga Babu Chinnam; Wah Chiu; Krzysztof Fidelis; Rhys Grinter; Gagan D Gupta; Marcus D Hartmann; Christopher S Hayes; Tatjana Heidebrecht; Andrea Ilari; Andrzej Joachimiak; Youngchang Kim; Romain Linares; Andrew L Lovering; Vladimir V Lunin; Andrei N Lupas; Cihan Makbul; Karolina Michalska; John Moult; Prasun K Mukherjee; William Sam Nutt; Stefan L Oliver; Anastassis Perrakis; Lucy Stols; John A Tainer; Maya Topf; Susan E Tsutakawa; Mauricio Valdivia-Delgado; Torsten Schwede
Journal:  Proteins       Date:  2021-10-10

9.  Sampling alternative conformational states of transporters and receptors with AlphaFold2.

Authors:  Diego Del Alamo; Davide Sala; Hassane S Mchaourab; Jens Meiler
Journal:  Elife       Date:  2022-03-03       Impact factor: 8.713

10.  Isolation, Purification, and Characterization of a Laccase-Degrading Aflatoxin B1 from Bacillus amyloliquefaciens B10.

Authors:  Dongwei Xiong; Jun Wen; Gen Lu; Tianxi Li; Miao Long
Journal:  Toxins (Basel)       Date:  2022-03-31       Impact factor: 5.075
  10 in total

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