NMR paper Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

		BioNMR > Educational resources > Journal club
[NMR paper] Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-14-2014, 08:40 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,185

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

Related Articles Fine 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.

PMID: 24605867 [PubMed - indexed for MEDLINE]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[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...	nmrlearner	Journal club	0	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	nmrlearner	Journal club	0	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...	nmrlearner	Journal club	0	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 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/6EE7uthrnLg	nmrlearner	Journal club	0	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> YeTian, 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...	nmrlearner	Journal club	0	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...	nmrlearner	Journal club	0	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...	nmrlearner	Journal club	0	11-19-2010 08:29 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off