Related ArticlesDirect Determination of Site-specific Noncovalent Interaction Strengths of Proteins from NMR-derived Fast Side Chain Motional Parameters.
J Phys Chem B. 2017 Apr 28;:
Authors: Tatikonda RR, Krishnan M
Abstract
A novel approach to accurately determine residue-specific noncovalent interaction strengths (?) of proteins from NMR-measured fast side chain motional parameters (O(2)axis) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ?, O(2)axis, conformational entropy (Sconf), conformational barriers and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ? and that for each residue type there exists a critical range of ?, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with O(2)axis ~ 0) to highly restricted (with O(2)axis ~ 1) by increasing ? by ~3 kcal/mol. Beyond this critical range of ?, both side chain flexibility and conformational entropy are insensitive to ?. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.
PMID: 28452484 [PubMed - as supplied by publisher]
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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[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
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
Direct NMR Observationand pKa Determination of the Asp102 Side Chain in a SerineProtease
Direct NMR Observationand pKa Determination of the Asp102 Side Chain in a SerineProtease
Paul Everill, James L. Sudmeier and William W. Bachovchin
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja210091q/aop/images/medium/ja-2011-10091q_0008.gif
Journal of the American Chemical Society
DOI: 10.1021/ja210091q
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/k51DxgP9CaI
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Site-specific (19)F NMR chemical shift and side chain relaxation analysis of a membra
Site-specific (19)F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid.
Related Articles Site-specific (19)F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid.
Protein Sci. 2010 Nov 15;
Authors: Shi P, Wang H, Xi Z, Shi C, Xiong Y, Tian C
Site-specific (19)F chemical shift and side chain relaxation analysis can be applied on large size proteins. Here, one dimensional (19)F spectra and T(1), T(2) relaxation data were acquired...
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11-17-2010 05:49 PM
Site-Specific Protein Backbone and Side-Chain NMR Chemical Shift and Relaxation Analy
Site-Specific Protein Backbone and Side-Chain NMR Chemical Shift and Relaxation Analysis of Human Vinexin SH3 Domain using a Genetically Encoded (15)N/(19)F-Labeled Unnatural Amino Acid.
Related Articles Site-Specific Protein Backbone and Side-Chain NMR Chemical Shift and Relaxation Analysis of Human Vinexin SH3 Domain using a Genetically Encoded (15)N/(19)F-Labeled Unnatural Amino Acid.
Biochem Biophys Res Commun. 2010 Oct 11;
Authors: Shi P, Xi Z, Wang H, Shi C, Xiong Y, Tian C
SH3 is a ubiquitous domain mediating protein-protein interactions....
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10-16-2010 03:56 PM
[NMR paper] Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 ph
Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide.
Biochemistry. 1997 Apr 8;36(14):4118-24
Authors: Olejniczak ET, Zhou MM, Fesik SW
Proteins recognize...
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08-22-2010 03:31 PM
[NMR paper] Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 ph
Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide.
Biochemistry. 1997 Apr 8;36(14):4118-24
Authors: Olejniczak ET, Zhou MM, Fesik SW
Proteins recognize...
Direct Determination of Site-specific Noncovalent Interaction Strengths of Proteins from NMR-derived Fast Side Chain Motional Parameters.
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