ArticleProtein science : a publication of the Protein Society2012
The dynamical response of hen egg white lysozyme to the binding of a carbohydrate ligand.
Article in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
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- Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.Nature chemistry · 2023Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.European biophysics journal : EBJ · 2022Article
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- Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.Physical chemistry chemical physics : PCCP · 2022Article
- Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study.JACS Au · 2021Article
- On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.Chembiochem : a European journal of chemical biology · 2021Article
- On the use ofJournal of biomolecular NMR · 2021Article
- Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics.ACS omega · 2020Article
- Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation.Methods in enzymology · 2019Article
- Moving in the Right Direction: Protein Vibrations Steering Function.Biophysical journal · 2017Article
- On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.Protein science : a publication of the Protein Society · 2016Article
- Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities.Journal of the American Society for Mass Spectrometry · 2016Article
- The unusual internal motion of the villin headpiece subdomain.Protein science : a publication of the Protein Society · 2016Article
- Microscopic insights into the NMR relaxation-based protein conformational entropy meter.Journal of the American Chemical Society · 2013Article
- A surprising role for conformational entropy in protein function.Topics in current chemistry · 2013Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
It has become clear that the binding of small and large ligands to proteins can invoke significant changes in side chain and main chain motion in the fast picosecond to nanosecond timescale. Recently, the use of a "dynamical proxy" has indicated that changes in these motions often reflect significant changes in conformational entropy. These entropic contributions are sometimes of the same order as the total entropy of binding. Thus, it is important to understand the connections amongst motion between the manifold of states accessible to the native state of proteins, the corresponding entropy, and how this impacts the overall energetics of protein function. The interaction of proteins with carbohydrate ligands is central to a range of biological functions. Here, we examine a classic carbohydrate interaction with an enzyme: the binding of wild-type hen egg white lysozyme (HEWL) to the natural, competitive inhibitor chitotriose. Using NMR relaxation experiments, backbone amide and side chain methyl axial order parameters were obtained across apo and chitotriose-bound HEWL. Upon binding, changes in the apparent amplitude of picosecond to nanosecond main chain and side chain motions are seen across the protein. Indeed, binding of chitotriose renders a large contiguous fraction of HEWL effectively completely rigid. Changes in methyl flexibility are most pronounced closest to the binding site, but average to only a small overall change in the dynamics across the protein. The corresponding change in conformational entropy is unfavorable and estimated to be a significant fraction of the total binding entropy.
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