Predicting the Effect of a Point Mutation on a Protein Fold: The Villin and Advillin Headpieces and Their Pro62Ala Mutants
Abstract
Homology modeling of unknown proteins is based on the assumption that highly similar sequences are likely to share the same fold. However, this does not provide any information on the stability of a given fold, which is ultimately determined by the subtle interplay of enthalpic and entropic contributions. Herein it is shown that ab initio atomistic simulations can be used to predict the effect of point mutations on the stability of a protein fold. The calculations indicate that the fold stabilities of two proteins of similar sequence and identical fold, the villin and advillin C-terminal headpiece fragments, are different and that the same P62A point mutation has a dramatic effect on the fold of villin but a minor one on that of advillin. These predictions were subsequently validated by NMR and CD experiments.
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Metadynamics methods have been successfully applied to study free energy landscapes of flexible proteins, protein oligomers, peptide folding, ligand and selective ion permeation through membrane channels.
“These methods alone, or in combination with high-resolution experimental techniques such as x-ray crystallography and NMR, have been successfully applied to the study of the free energy landscape of flexible proteins and protein oligomers,36,388–389 peptide folding,390–392 ligand and selective ion permeation through cell membrane protein channels.393”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [391]
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- Authors
- Piana, S., Laio, A., Marinelli, F., Van Troys, M., Bourry, D., Ampe, C., & Martins, J. C.
- Affiliations
- Curtin University (AU)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- Ghent University (BE)
- Corresponding author
- Piana, Stefano
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2008-01
- Volume
- 375
- Issue
- 2
- Pages
- 460-470
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W1997147743
- Cited by
- 48
- References
- 45
- Citations by year
- 2019: 2 · 2018: 2 · 2016: 2 · 2015: 1 · 2014: 1 · 2013: 2 · 2012: 6
- FWCI
- 3.04
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- SDL (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- point mutations, villin, enthalpy-entropy compensation
- MeSH terms
- Alanine, Amino Acid Sequence, Circular Dichroism, Computer Simulation, Hot Temperature, Humans, Kinetics, Microfilament Proteins, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Denaturation, Thermodynamics, Cluster Analysis, Conserved Sequence, Point Mutation, Sequence Homology, Amino Acid, Protein Structure, Secondary, Protein Folding, Computational Biology, Nuclear Magnetic Resonance, Biomolecular, Amino Acid Motifs, Hydrophobic and Hydrophilic Interactions
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