4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
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01-09-2011 12:46 PM
[NMR paper] Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Related Articles Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
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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11-25-2010 08:21 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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11-24-2010 10:03 PM
[NMR paper] Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR
Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
Related Articles Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
Biochemistry. 2001 Mar 27;40(12):3439-48
Authors: Inman KG, Baldisseri DM, Miller KE, Weber DJ
Backbone dynamics of homodimeric apo-S100B were studied by (15)N nuclear magnetic resonance relaxation at 9.4 and 14.1 T. Longitudinal relaxation (T(1)), transverse relaxation (T(2)), and the (15)N- NOE were measured for 80 of 91 backbone...
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11-19-2010 08:32 PM
Linking Local Environments and Hyperfine Shifts: A Combined Experimental and Theoreti
Linking Local Environments and Hyperfine Shifts: A Combined Experimental and Theoretical 31P and 7Li Solid-State NMR Study of Paramagnetic Fe(III) Phosphates
Jongsik Kim, Derek S. Middlemiss, Natasha A. Chernova, Ben Y. X. Zhu, Christian Masquelier and Clare P. Grey
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja102678r/aop/images/medium/ja-2010-02678r_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja102678r
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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11-17-2010 06:08 PM
[NMR paper] Application of 1H NMR chemical shifts to measure the quality of protein structures.
Application of 1H NMR chemical shifts to measure the quality of protein structures.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Application of 1H NMR chemical shifts to measure the quality of protein structures.
J Mol Biol. 1995 Apr 7;247(4):541-6
Authors: Williamson MP, Kikuchi J, Asakura T
We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When...
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08-22-2010 03:41 AM
Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...