Literature DB >> 24477919

New opportunities for tensor-free calculations of residual dipolar couplings for the study of protein dynamics.

Rinaldo Montalvao1, Carlo Camilloni, Alfonso De Simone, Michele Vendruscolo.   

Abstract

Residual dipolar couplings (RDCs) can provide exquisitely detailed information about the structure and dynamics of proteins. It is challenging, however, to extract such information from RDC measurements in conformationally heterogeneous states of proteins because of the complex relationship between RDCs and protein structures. To obtain new insights into this problem, we discuss methods of calculating the RDCs that do not require the definition of an alignment tensor. These methods can help in particular in the search of effective ways to use RDCs to characterise disordered or partially disordered states of proteins.

Entities:  

Mesh:

Substances:

Year:  2014        PMID: 24477919     DOI: 10.1007/s10858-013-9801-3

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  61 in total

1.  An easy way to include weak alignment constraints into NMR structure calculations.

Authors:  H J Sass; G Musco; S J Stahl; P T Wingfield; S Grzesiek
Journal:  J Biomol NMR       Date:  2001-11       Impact factor: 2.835

2.  Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

Authors:  Carlo Camilloni; Paul Robustelli; Alfonso De Simone; Andrea Cavalli; Michele Vendruscolo
Journal:  J Am Chem Soc       Date:  2012-02-22       Impact factor: 15.419

3.  Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain.

Authors:  Tsuyoshi Terakawa; Shoji Takada
Journal:  Biophys J       Date:  2011-09-20       Impact factor: 4.033

4.  On the Use of Experimental Observations to Bias Simulated Ensembles.

Authors:  Jed W Pitera; John D Chodera
Journal:  J Chem Theory Comput       Date:  2012-08-27       Impact factor: 6.006

5.  Conformational fluctuations affect protein alignment in dilute liquid crystal media.

Authors:  Martti Louhivuori; Renee Otten; Kresten Lindorff-Larsen; Arto Annila
Journal:  J Am Chem Soc       Date:  2006-04-05       Impact factor: 15.419

6.  A unifying probabilistic framework for analyzing residual dipolar couplings.

Authors:  Michael Habeck; Michael Nilges; Wolfgang Rieping
Journal:  J Biomol NMR       Date:  2007-12-20       Impact factor: 2.835

7.  Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin.

Authors:  Jie-rong Huang; Stephan Grzesiek
Journal:  J Am Chem Soc       Date:  2010-01-20       Impact factor: 15.419

8.  Defining conformational ensembles of intrinsically disordered and partially folded proteins directly from chemical shifts.

Authors:  Malene Ringkjøbing Jensen; Loïc Salmon; Gabrielle Nodet; Martin Blackledge
Journal:  J Am Chem Soc       Date:  2010-02-03       Impact factor: 15.419

9.  Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.

Authors:  Oliver F Lange; Nils-Alexander Lakomek; Christophe Farès; Gunnar F Schröder; Korvin F A Walter; Stefan Becker; Jens Meiler; Helmut Grubmüller; Christian Griesinger; Bert L de Groot
Journal:  Science       Date:  2008-06-13       Impact factor: 47.728

10.  Systematic validation of protein force fields against experimental data.

Authors:  Kresten Lindorff-Larsen; Paul Maragakis; Stefano Piana; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  PLoS One       Date:  2012-02-22       Impact factor: 3.240

View more
  2 in total

1.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

Authors:  Witold Andrałojć; Konstantin Berlin; David Fushman; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Luca Sgheri
Journal:  J Biomol NMR       Date:  2015-06-05       Impact factor: 2.835

Review 2.  Mechanisms of amyloid formation revealed by solution NMR.

Authors:  Theodoros K Karamanos; Arnout P Kalverda; Gary S Thompson; Sheena E Radford
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2015-05-27       Impact factor: 9.795

  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.