ArticleBiophysical journal2012
Partial least-squares functional mode analysis: application to the membrane proteins AQP1, Aqy1, and CLC-ec1.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease.Computational and structural biotechnology journal · 2022Article
- Lipid-protein forces predict conformational changes in a mechanosensitive channel.European biophysics journal : EBJ · 2021Article
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Microtubule instability driven by longitudinal and lateral strain propagation.PLoS computational biology · 2020Article
- Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors.Retrovirology · 2020Article
- Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling.Nature communications · 2019Article
- Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes.Journal of chemical theory and computation · 2019Article
- Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer's Disease Mutant of APP.Scientific reports · 2019Article
- A molecular mechanism for transthyretin amyloidogenesis.Nature communications · 2019Article
- Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit.eLife · 2018Article
- Dissecting conformational changes in APP's transmembrane domain linked to ε-efficiency in familial Alzheimer's disease.PloS one · 2018Article
- Two Cl Ions and a Glu Compete for a Helix Cage in the CLC Proton/ClBiophysical journal · 2017Article
- Temperature dependence of protein-water interactions in a gated yeast aquaporin.Scientific reports · 2017Article
- Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0.Biophysical journal · 2017Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics that maximally correlate to an external order parameter of functional interest. Input structural data can be either experimentally determined structure ensembles or simulated ensembles, such as molecular dynamics trajectories. Partial least-squares regression is shown to yield a robust solution to the multidimensional optimization problem, with a minimal and controllable risk of overfitting, as shown by extensive cross-validation. Several examples illustrate that the partial least-squares-based functional mode analysis successfully reveals the collective dynamics underlying the fluctuations in selected functional order parameters. Applications to T4 lysozyme, the Trp-cage, the aquaporin channels Aqy1 and hAQP1, and the CLC-ec1 chloride antiporter are presented in which the active site geometry, the hydrophobic solvent-accessible surface, channel gating dynamics, water permeability (p(f)), and a dihedral angle are defined as functional order parameters. The Aqy1 case reveals a gating mechanism that connects the inner channel gating residues with the protein surface, thereby providing an explanation of how the membrane may affect the channel. hAQP1 shows how the p(f) correlates with structural changes around the aromatic/arginine region of the pore. The CLC-ec1 application shows how local motions of the gating Glu(148) couple to a collective motion that affects ion affinity in the pore.
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