Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
Abstract
Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a <r(-6)> ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.
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For bacterial phosphotriesterase, maltose binding protein, choline oxidase, cytochrome bc1 complex, and many lid-gated enzymes, closed and open conformations are in equilibrium prior to ligand binding, permitting conformational selection at different catalytic steps.
“Conformational sampling for bacterial phosphotriesterase,443 maltose binding protein,444 and choline oxidase,445 cytochrome bc1 complex,446 and many other lid-gated enzymes indicated that the closed and open conformations are in equilibrium prior to ligand binding, permitting a conformational selection pathway at different catalytic steps.447”
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 [444]
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- Authors
- Tang, C., Schwieters, C. D., & Clore, G. M.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Clore, G. Marius
- Venue
- Nature
- Published
- 2007-10
- Volume
- 449
- Issue
- 7165
- Pages
- 1078-1082
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2079064092
- Cited by
- 416
- References
- 41
- Citations by year
- 2026: 10 · 2025: 12 · 2024: 11 · 2023: 13 · 2022: 19 · 2021: 11 · 2020: 22 · 2019: 19 · 2018: 20 · 2017: 19 · 2016: 32 · 2015: 22 · 2014: 15 · 2013: 40 · 2012: 32
- FWCI
- 10.48
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- Office of Science
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- maltose-binding protein, apo state, open-to-closed transition, paramagnetic relaxation enhancement, ligand binding, protein conformational heterogeneity, periplasmic binding protein
- MeSH terms
- Apoproteins, Carrier Proteins, Models, Molecular, Protein Binding, Trisaccharides, Protein Structure, Tertiary, Crystallography, X-Ray, Nuclear Magnetic Resonance, Biomolecular, Maltose-Binding Proteins
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