Literature DB >> 22280745

Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations.

Yaroslav Ryabov1, G Marius Clore, Charles D Schwieters.   

Abstract

We present a general formalism for the computation of orientation correlation functions involving a molecular system undergoing rotational diffusion in the presence of transitions between discrete conformational states. In this formalism, there are no proscriptions on the time scales of conformational rearrangement relative to that for rotational diffusion, and the rotational diffusion tensors of the different states can be completely arbitrary. Although closed-form results are limited to the frequency domain, this is generally useful for many spectroscopic observables as the result allows the computation of the spectral density function. We specialize the results for the computation of the frequency-domain correlation function associated with the NMR relaxation.
© 2012 American Institute of Physics

Mesh:

Year:  2012        PMID: 22280745      PMCID: PMC3272066          DOI: 10.1063/1.3675602

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  11 in total

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2.  Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  J Phys Chem A       Date:  2006-07-13       Impact factor: 2.781

3.  An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.

Authors:  Yaroslav E Ryabov; Charles Geraghty; Amitabh Varshney; David Fushman
Journal:  J Am Chem Soc       Date:  2006-12-06       Impact factor: 15.419

4.  Influence of the coupling of interdomain and overall motions on NMR relaxation.

Authors:  Vance Wong; David A Case; Attila Szabo
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-18       Impact factor: 11.205

5.  Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy.

Authors:  G M Clore; P C Driscoll; P T Wingfield; A M Gronenborn
Journal:  Biochemistry       Date:  1990-08-14       Impact factor: 3.162

6.  Interdomain mobility in di-ubiquitin revealed by NMR.

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Journal:  Proteins       Date:  2006-06-01

7.  A model of interdomain mobility in a multidomain protein.

Authors:  Yaroslav E Ryabov; David Fushman
Journal:  J Am Chem Soc       Date:  2007-02-24       Impact factor: 15.419

8.  Slow exchange model of nonrigid rotational motion in RNA for combined solid-state and solution NMR studies.

Authors:  Prashant S Emani; Gregory L Olsen; Dorothy C Echodu; Gabriele Varani; Gary P Drobny
Journal:  J Phys Chem B       Date:  2010-11-10       Impact factor: 2.991

9.  Structure and dynamics of KH domains from FBP bound to single-stranded DNA.

Authors:  Demetrios T Braddock; John M Louis; James L Baber; David Levens; G Marius Clore
Journal:  Nature       Date:  2002-02-28       Impact factor: 49.962

10.  Extended model free approach to analyze correlation functions of multidomain proteins in the presence of motional coupling.

Authors:  Kang Chen; Nico Tjandra
Journal:  J Am Chem Soc       Date:  2008-08-30       Impact factor: 15.419

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  11 in total

1.  Correction to "Theory of nonrigid rotational motion applied to NMR relaxation in RNA".

Authors:  Prashant S Emani; Gregory L Olsen; Gabriele Varani; Gary P Drobny
Journal:  J Phys Chem A       Date:  2012-06-22       Impact factor: 2.781

2.  Accurate determination of rates from non-uniformly sampled relaxation data.

Authors:  Matthew A Stetz; A Joshua Wand
Journal:  J Biomol NMR       Date:  2016-07-08       Impact factor: 2.835

Review 3.  NMR studies of dynamic biomolecular conformational ensembles.

Authors:  Dennis A Torchia
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-11-28       Impact factor: 9.795

4.  Determining interdomain structure and dynamics of a retroviral capsid protein in the presence of oligomerization: implication for structural transition in capsid assembly.

Authors:  Kang Chen; Nico Tjandra
Journal:  Biochemistry       Date:  2013-08-01       Impact factor: 3.162

5.  Exposing the Moving Parts of Proteins with NMR Spectroscopy.

Authors:  J W Peng
Journal:  J Phys Chem Lett       Date:  2012-04-02       Impact factor: 6.475

6.  Decoding the components of dynamics in three-domain proteins.

Authors:  Mateusz Maciejewski; Paul N Barlow; Nico Tjandra
Journal:  J Comput Chem       Date:  2013-12-09       Impact factor: 3.376

7.  NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.

Authors:  Junchao Xia; Nan-jie Deng; Ronald M Levy
Journal:  J Phys Chem B       Date:  2013-05-28       Impact factor: 2.991

8.  Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry.

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9.  Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles.

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Journal:  J Phys Chem B       Date:  2014-02-11       Impact factor: 2.991

10.  Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation.

Authors:  Michelle L Gill; Arthur G Palmer
Journal:  J Phys Chem B       Date:  2014-09-11       Impact factor: 2.991

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