AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP
Open accessAbstract
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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There is at least one example in CASP14 of flexibility between domains being reproduced (T1024).
“There is also at least one example in CASP14 of flexibility between domains being reproduced (T1024)47.”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [47]
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Self-citationIslam, S. M., Stein, R., Mchaourab, H., & Roux, B. (2013) · Journal of Physical Chemistry B · doi:10.1021/jp311723a · Cited by 93 · see citing works
Self-citationProtonation drives the conformational switch in the multidrug transporter LmrP
Masureel, M., Martens, C., Stein, R. A., Mishra, S., Ruysschaert, J., Mchaourab, H. S., & Govaerts, C. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1408 · Cited by 73 · see citing works
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An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity
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Self-citationApplications of sequence coevolution in membrane protein biochemistry
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Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · see citing works
“…we found that AF2 modeled the multidrug transporter LmrP (target T1024) in multiple conformations, two of which were individually consistent with published experimental data ( Jumper et al., 2021b ; Del Alamo et al., 2021a ; Debruycker et al., 2020 ; Martens et al., 2016 ; Masureel et al., 2014 ).”
ResultSelf-citationCritical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp>
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26237 · Cited by 503 · see citing works
The AlphaFold Database of Protein Structures: A Biologist’s Guide
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Ins and outs of AlphaFold2 transmembrane protein structure predictions
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Current structure predictors are not learning the physics of protein folding
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Novel machine learning approaches revolutionize protein knowledge
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Integrative Structural Biology in the Era of Accurate Structure Prediction
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Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2
Gulsevin, A., Han, B., Porta, J. C., Mchaourab, H. S., Meiler, J., & Kenworthy, A. K. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2022.11.011 · Cited by 16 · see citing works
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- Authors
- del Alamo, D., Govaerts, C., & Mchaourab, H. S.
- Affiliations
- Department of Molecular Physiology and Biophysics Vanderbilt University Nashville Tennessee USA
- Université Libre de Bruxelles (BE)
- Vanderbilt University (US)
- Corresponding author
- Mchaourab, Hassane S.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2021-05-18
- Volume
- 89
- Issue
- 9
- Pages
- 1226-1228
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC8522053
- OpenAlex
- W3162141586
- Cited by
- 29
- References
- 12
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 2 · 2023: 5 · 2022: 12 · 2021: 7
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
- Funders
- National Institutes of Health (GM077659)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- multidrug transporter, inward-facing conformation, protein structure prediction, AlphaFold2, double electron-electron resonance, distance restraints, protein conformation
- MeSH terms
- Protein Conformation, alpha-Helical, Algorithms, Bacterial Proteins, Binding Sites, Biological Transport, Cell Membrane, Models, Molecular, Protein Binding, Protons, Software, Lactococcus lactis, Gene Expression, Membrane Transport Proteins, Protein Interaction Domains and Motifs
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