[NMR paper] Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
Related ArticlesCorrelation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
J Biomol Struct Dyn. 2013 Jun 3;
Authors: Mahajan S, de Brevern AG, Offmann B, Srinivasan N
Abstract
Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and ?-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.
PMID: 23730714 [PubMed - as supplied by publisher]
[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
J Phys Chem B. 2013 Feb 1;
Authors: Camilloni C, Cavalli A, Vendruscolo M
Abstract
It has been recently...
Interaction Tensors and Local Dynamics in Common Structural Motifs of Nitrogen: A Solid-State 14N NMR and DFT Study
Interaction Tensors and Local Dynamics in Common Structural Motifs of Nitrogen: A Solid-State 14N NMR and DFT Study
Luke A. O’Dell, Robert W. Schurko, Kristopher J. Harris, Jochen Autschbach and Christopher I. Ratcliffe
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja108181y/aop/images/medium/ja-2010-08181y_0020.gif
Journal of the American Chemical Society
DOI: 10.1021/ja108181y
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/RPRAYPgAJxo
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[NMR paper] Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics
Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics.
Related Articles Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics.
Biochemistry. 2001 Mar 6;40(9):2743-53
Authors: Viles JH, Donne D, Kroon G, Prusiner SB, Cohen FE, Dyson HJ, Wright PE
A template-assisted conformational change of the cellular prion protein (PrP(C)) from a predominantly helical structure to an amyloid-type structure with a higher proportion of beta-sheet is thought to be the causative factor in prion...
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[NMR paper] Essential spaces defined by NMR structure ensembles and molecular dynamics simulation
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
Related Articles Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
Proteins. 1998 Jun 1;31(4):370-82
Authors: Abseher R, Horstink L, Hilbers CW, Nilges M
Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation...
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Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure
Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.
Related Articles Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.
Prog Nucl Magn Reson Spectrosc. 2010 May;56(4):360-405
Authors: Meirovitch E, Shapiro YE, Polimeno A, Freed JH
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[NMR paper] Investigation of the local structure and dynamics of the H subunit of the mitochondri
Investigation of the local structure and dynamics of the H subunit of the mitochondrial glycine decarboxylase using heteronuclear NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Investigation of the local structure and dynamics of the H subunit of the mitochondrial glycine decarboxylase using heteronuclear NMR spectroscopy.
Biochemistry. 1999 Jun 29;38(26):8334-46
Authors: Guilhaudis L, Simorre JP, Blackledge M, Neuburger M, Bourguignon J, Douce R, Marion D, Gans P
The...
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Structural Dynamics of Bio-Macromolecules by NMR: The Slowly Relaxing Local Structure
Structural Dynamics of Bio-Macromolecules by NMR: The Slowly Relaxing Local Structure Approach
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 27 March 2010</br>
Eva, Meirovitch , Yury E., Shapiro , Antonino, Polimeno , Jack H., Freed</br>
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Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
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