Literature DB >> 23868852

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

Ashok Sekhar1, Lewis E Kay.   

Abstract

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

Keywords:  energy landscape; invisible states; structure–function paradigm; transiently and sparsely populated biomolecular states

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Year:  2013        PMID: 23868852      PMCID: PMC3740838          DOI: 10.1073/pnas.1305688110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  89 in total

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3.  Accessing protein conformational ensembles using room-temperature X-ray crystallography.

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4.  Characterization of a transient unfolding intermediate in a core mutant of γS-crystallin.

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5.  Chemical exchange saturation transfer (CEST): what is in a name and what isn't?

Authors:  Peter C M van Zijl; Nirbhay N Yadav
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6.  Transient, sparsely populated compact states of apo and calcium-loaded calmodulin probed by paramagnetic relaxation enhancement: interplay of conformational selection and induced fit.

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7.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

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8.  Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.

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9.  Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study.

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Journal:  J Am Chem Soc       Date:  2011-06-28       Impact factor: 15.419

10.  Transient Hoogsteen base pairs in canonical duplex DNA.

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  100 in total

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2.  pH-dependent transient conformational states control optical properties in cyan fluorescent protein.

Authors:  Elena N Laricheva; Garrett B Goh; Alex Dickson; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2015-02-18       Impact factor: 15.419

3.  Accelerating physical simulations of proteins by leveraging external knowledge.

Authors:  Alberto Perez; Joseph A Morrone; Ken A Dill
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Review 5.  The nature of protein folding pathways.

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Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-17       Impact factor: 11.205

6.  Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

Authors:  Nur Alia Oktaviani; Michael W Risør; Young-Ho Lee; Rik P Megens; Djurre H de Jong; Renee Otten; Ruud M Scheek; Jan J Enghild; Niels Chr Nielsen; Takahisa Ikegami; Frans A A Mulder
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7.  Intrinsically disordered chromatin protein NUPR1 binds to the C-terminal region of Polycomb RING1B.

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Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-18       Impact factor: 11.205

8.  A methyl 1H double quantum CPMG experiment to study protein conformational exchange.

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9.  Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange.

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Review 10.  Characterizing excited conformational states of RNA by NMR spectroscopy.

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Journal:  Curr Opin Struct Biol       Date:  2015-03-10       Impact factor: 6.809

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