Related ArticlesFine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.
J Phys Chem B. 2014 Mar 27;118(12):3298-309
Authors: Pawlak T, Potrzebowski MJ
Abstract
This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.
[NMR paper] NMR-Based Modeling and Refinement of Protein 3D Structures.
NMR-Based Modeling and Refinement of Protein 3D Structures.
Related Articles NMR-Based Modeling and Refinement of Protein 3D Structures.
Methods Mol Biol. 2015;1215:351-80
Authors: Vranken WF, Vuister GW, Bonvin AM
Abstract
NMR is a well-established method to characterize the structure and dynamics of biomolecules in solution. High-quality structures can now be produced thanks to both experimental advances and computational developments that incorporate new NMR parameters and improved protocols and force fields in the structure...
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10-22-2014 12:34 PM
Applications of NMR Crystallography to Problems in Biomineralization: Refinement of the Crystal Structure and 31P Solid-State NMR Spectral Assignment of Octacalcium Phosphate
Applications of NMR Crystallography to Problems in Biomineralization: Refinement of the Crystal Structure and 31P Solid-State NMR Spectral Assignment of Octacalcium Phosphate
Erika Davies, Melinda J. Duer, Sharon E. Ashbrook and John M. Griffin
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja3017544/aop/images/medium/ja-2012-017544_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja3017544
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/S1bxaQtphuA
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07-24-2012 08:19 AM
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure
Abstract Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utilityâ??using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterionsâ??by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5...
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06-25-2012 04:41 AM
Revealing Protein Structures in Solid-Phase Peptide Synthesis by 13C Solid-State NMR: Evidence of Excessive Misfolding for Alzheimer’s ?
Revealing Protein Structures in Solid-Phase Peptide Synthesis by 13C Solid-State NMR: Evidence of Excessive Misfolding for Alzheimer’s ?
Songlin Wang and Yoshitaka Ishii
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja212190z/aop/images/medium/ja-2011-12190z_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja212190z
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http://feeds.feedburner.com/~r/acs/jacsat/~4/6EE7uthrnLg
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01-31-2012 08:34 PM
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 8 October 2011</br>
Ye*Tian, Charles D.*Schwieters, Stanley J.*Opella, Francesca M.*Marassi</br>
AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between...
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10-10-2011 06:27 AM
[NMR paper] Relative stability of protein structures determined by X-ray crystallography or NMR s
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
Related Articles Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
Proteins. 2003 Oct 1;53(1):111-20
Authors: Fan H, Mark AE
The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation...
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11-24-2010 09:16 PM
[NMR paper] Atomic refinement using orientational restraints from solid-state NMR.
Atomic refinement using orientational restraints from solid-state NMR.
Related Articles Atomic refinement using orientational restraints from solid-state NMR.
J Magn Reson. 2000 Nov;147(1):9-16
Authors: Bertram R, Quine JR, Chapman MS, Cross TA
We describe a procedure for using orientational restraints from solid-state NMR in the atomic refinement of molecular structures. Minimization of an energy function can be performed through either (or both) least-squares minimization or molecular dynamics employing simulated annealing. The energy, or...