Comparative Study of REDOR and CPPI Derived Order Parameters by (1)H-Detected MAS NMR and MD Simulations.
J Phys Chem B. 2017 Aug 25;:
Authors: Asami S, Reif B
Abstract
The measurement of dipolar couplings among directly bonded nuclei yields direct information on the amplitude of dynamic processes in the solid-state. For a reliable motional analysis using e.g. the model-free approach, a correct quantification of the absolute values of these order parameters is absolutely essential. In the absence of a reference value for the rigid limit, too low dipolar coupling values might be misinterpreted as motion. Therefore, a detailed understanding of the experimental effects that influence the quantification of order parameters is necessary. We compare here experimentally REDOR and CPPI derived order parameters assessed in 1H detected experiments, and discuss the influence of remote protons and rf inhomogeneity on the extracted dipolar coupling constant for MAS rotation frequencies in the range of 20-100 kHz. Experimental results are furthermore compared with the order parameter obtained from a molecular dynamics simulation. We find that fast magic-angle spinning up to 100 kHz can yield artifact free REDOR based 1H,15N order parameters for perdeuterated and 100 % amide back-exchanged proteins, and even in uniformly protonated samples. We believe, that awareness on systematic errors introduced by the measurement and in the analysis of order parameters will yield a better understanding of the dynamic properties of a protein derived from solid-state NMR observables.
PMID: 28841025 [PubMed - as supplied by publisher]
[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.
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Abstract
At low pH human growth hormone (hGH) adopts a partially folded state...
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05-16-2017 10:27 PM
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters
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 MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari–Szabo squared generalized order parameter (O2)...
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04-04-2016 12:40 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.
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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
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
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 are based on largely structural parameters such as the root mean square deviation from experimental coordinates or NMR chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O2) values of...
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03-15-2016 11:57 AM
[NMR paper] On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.
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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.
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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
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.