[NMR paper] Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Related ArticlesInterpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Chemistry. 2017 May 15;:
Authors: Smith LJ, Athill R, van Gunsteren WF, Hansen N
Abstract
At low pH human growth hormone (hGH) adopts a partially folded state in which the native helices are maintained but the long loop regions and side-chain packing becomes disordered. Some of the S2 order parameters for backbone N-H vectors derived from NMR relaxation measurements for the hGH at low pH initially seem contradictory. Three isolated residues (15, 20 and 171) in helices A and D exhibit low order-parameter values (< 0.5) indicating flexibility while residue 143 in the centre of a long flexible loop region has a high order parameter (0.82). Using S2 order-parameter restraining MD simulations this paradox is solved. Low S2 values in helices are due to the presence of a mixture of 3_10-helical and alpha-helical hydrogen bonds. High S2 values in relatively disordered parts of a protein may be due to fluctuating networks of hydrogen bonds between backbone and side chains, which restrict the motion of N-H bond vectors.
PMID: 28503764 [PubMed - as supplied by publisher]
[NMR paper] Monitoring Effects of Excipients, Formulation Parameters and Mutations on the High Order Structure of Filgrastim by NMR.
Monitoring Effects of Excipients, Formulation Parameters and Mutations on the High Order Structure of Filgrastim by NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Monitoring Effects of Excipients, Formulation Parameters and Mutations on the High Order Structure of Filgrastim by NMR.
Pharm Res. 2015 Oct;32(10):3365-75
Authors: Aubin Y, Hodgson DJ, Thach WB, Gingras G, Sauvé S
Abstract
PURPOSE: Filgrastim is the generic...
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06-24-2016 12:53 PM
[NMR paper] On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
Protein Sci. 2016 Mar 14;
Authors: O'Brien ES, Wand AJ, Sharp KA
Abstract
Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify molecular dynamics force fields, most...
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03-19-2016 09:23 PM
[NMR paper] On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.
On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.
Related Articles On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.
Proteins. 2015 Mar 4;
Authors: Sharp KA, O'Brien E, Kasinath V, Wand AJ
Abstract
Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the...
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03-06-2015 02:01 PM
[NMR paper] Banding of NMR-derived methyl order parameters: Implications for protein dynamics.
Banding of NMR-derived methyl order parameters: Implications for protein dynamics.
Related Articles Banding of NMR-derived methyl order parameters: Implications for protein dynamics.
Proteins. 2014 Mar 26;
Authors: Sharp KA, Kasinath V, Wand AJ
Abstract
Our understanding of protein folding, stability and function has begun to more explicitly incorporate dynamical aspects. Nuclear magnetic resonance has emerged as a powerful experimental method for obtaining comprehensive site-resolved insight into protein motion. It has been observed that...
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03-29-2014 01:00 PM
[NMR paper] Determination of protein structures consistent with NMR order parameters.
Determination of protein structures consistent with NMR order parameters.
Related Articles Determination of protein structures consistent with NMR order parameters.
J Am Chem Soc. 2004 Jul 7;126(26):8090-1
Authors: Best RB, Vendruscolo M
Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...
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11-24-2010 09:51 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics.
Temperature dependence of NMR order parameters and protein dynamics.
Related Articles Temperature dependence of NMR order parameters and protein dynamics.
J Am Chem Soc. 2003 Sep 17;125(37):11158-9
Authors: Massi F, Palmer AG
The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...
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11-24-2010 09:16 PM
[NMR paper] Protein dynamics using frequency-dependent order parameters from analysis of NMR rela
Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data.
Related Articles Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data.
J Magn Reson. 2003 Mar;161(1):118-25
Authors: Idiyatullin D, Daragan VA, Mayo KH
A novel approach is described to analyze NMR relaxation data on proteins. This method introduces the frequency-dependent order parameter, S(2)(omega), in order to estimate contributions to the generalized order parameter S(2) from different motional...
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Script to obtain order parameters from a structure
A Python script for prediction of order paramter from a structure is available from this website.
The script is based on the following paper
F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.
Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Linear Mode
