Extensive conformational heterogeneity within protein cores
Open accessAbstract
Basic principles of statistical mechanics require that proteins sample an ensemble of conformations at any nonzero temperature. However, it is still common to treat the crystallographic structure of a protein as the structure of its native state, largely because high-resolution structural characterization of protein flexibility remains a profound challenge. To assess the typical degree of conformational heterogeneity within folded proteins, we construct Markov state models describing the thermodynamics and kinetics of proteins ranging from 72 to 263 residues in length. Each of these models is built from hundreds of microseconds of atomically detailed molecular dynamics simulations. Examination of the side-chain degrees of freedom reveals that almost every residue visits at least two rotameric states over this time frame, with rotamer transition rates spanning a wide range of time scales (from nanoseconds to tens of microseconds). We also report substantial backbone dynamics on time scales longer than are typically addressed by experimental measures of protein flexibility, such as NMR order parameters. Finally, we demonstrate that these extensive rearrangements are consistent with NMR and crystallographic data, which supports the validity of our models. Altogether, these results depict the interior of proteins not as well-ordered solids, as is often imagined, but instead as dense fluids, which undergo substantial structural fluctuations despite their high packing fraction.
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Sidechains of residues within the cores of folded proteins appear to show some degree of liquid-like behavior.
“In fact, sidechains of residues within the cores of folded proteins appear to show some degree of liquid-like behavior [53].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [53]
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- Authors
- Bowman, G. R., & Geissler, P. L.
- Affiliations
- University of California System (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Bowman, Gregory R.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-02-24
- Volume
- 118
- Issue
- 24
- Pages
- 6417-6423
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- PMC
- PMC4065209
- OpenAlex
- W2027676182
- Cited by
- 38
- References
- 46
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 1 · 2023: 2 · 2022: 3 · 2021: 4 · 2020: 1 · 2019: 3 · 2018: 4 · 2017: 4 · 2016: 6 · 2015: 4 · 2014: 1
- FWCI
- 2.05
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- The Journal of Physical Chemistry B (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (CHE-1048789)
- National Institutes of Health (R01-GM062868)
- Burroughs Wellcome Fund (NA)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- protein conformational heterogeneity, protein core, protein flexibility, Markov state models, backbone dynamics, protein folding kinetics, protein thermodynamics, structural fluctuations
- MeSH terms
- beta-Lactamases, Kinetics, Markov Chains, Magnetic Resonance Spectroscopy, Proteins, Thermodynamics, Ribonuclease H, Ubiquitin, Molecular Dynamics Simulation
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