[NMR paper] A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNA.
A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNA.
Related ArticlesA Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNA.
J Am Chem Soc. 2014 Feb 12;136(6):2204-7
Authors: Kannan A, Camilloni C, Sahakyan AB, Cavalli A, Vendruscolo M
Abstract
Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. Such advances also suggest the possibility of using chemical shifts to characterize the conformational fluctuations of these molecules. Here we describe a method of using methyl chemical shifts as restraints in replica-averaged molecular dynamics (MD) simulations, which enables us to determine the conformational ensemble of the HU dimer and characterize the range of motions accessible to its flexible ?-arms. Our analysis suggests that the bending action of HU on DNA is mediated by a mechanical clamping mechanism, in which metastable structural intermediates sampled during the hinge motions of the ?-arms in the free state are presculpted to bind DNA. These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms.
A ConformationalEnsemble Derived Using NMR MethylChemical Shifts Reveals a Mechanical Clamping Transition That Gatesthe Binding of the HU Protein to DNA
A ConformationalEnsemble Derived Using NMR MethylChemical Shifts Reveals a Mechanical Clamping Transition That Gatesthe Binding of the HU Protein to DNA
Arvind Kannan, Carlo Camilloni, Aleksandr B. Sahakyan, Andrea Cavalli and Michele Vendruscolo
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja4105396/aop/images/medium/ja-2013-105396_0006.gif
Journal of the American Chemical Society
DOI: 10.1021/ja4105396
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/I9LCRqDsIVA
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Authors: Kragelj J, Ozenne V, Blackledge M, Jensen MR
Abstract
The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review...
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Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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J Biomol NMR. 2005 May;32(1):71-81
Authors: Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
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BMC Struct Biol. 2010 Oct 29;10(1):39
Authors: Angyan AF, Szappanos B, Perczel A, Gaspari Z
ABSTRACT: BACKGROUND: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data -
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - 7thSpace Interactive (press release)
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
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These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill ...
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[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
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Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
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[NMR paper] Representing an ensemble of NMR-derived protein structures by a single structure.
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http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Representing an ensemble of NMR-derived protein structures by a single structure.
Protein Sci. 1993 Jun;2(6):936-44
Authors: Sutcliffe MJ
The usefulness of representing an ensemble of...
A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNA.
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