Related ArticlesComparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.
Proteins. 2017 Oct 16;:
Authors: Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ
Abstract
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins. This article is protected by copyright. All rights reserved.
PMID: 29044728 [PubMed - as supplied by publisher]
[NMR paper] High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.
J Biomol NMR. 2016 Dec 29;:
Authors: Tian Y, Schwieters CD, Opella SJ, Marassi FM
Abstract
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR...
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12-31-2016 12:18 PM
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH
High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH
Abstract
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and...
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12-29-2016 09:23 PM
Crystal and NMR structures of a Trp-cage [Biophysics and Computational Biology]
Crystal and NMR structures of a Trp-cage
Scian, M., Lin, J. C., Le Trong, I., Makhatadze, G. I., Stenkamp, R. E., Andersen, N. H....
Date: 2012-07-31
To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data,...
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07-31-2012 08:27 PM
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
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02-05-2011 05:28 PM
Solution NMR and X-ray crystal structures of membrane-associated Lipoprotein-17 domain reveal a novel fold.
Solution NMR and X-ray crystal structures of membrane-associated Lipoprotein-17 domain reveal a novel fold.
Solution NMR and X-ray crystal structures of membrane-associated Lipoprotein-17 domain reveal a novel fold.
J Struct Funct Genomics. 2010 Dec 14;
Authors: Mani R, Vorobiev S, Swapna GV, Neely H, Janjua H, Ciccosanti C, Xiao R, Acton TB, Everett JK, Hunt J, Montelione GT
The conserved Lipoprotein-17 domain of membrane-associated protein Q9PRA0_UREPA from Ureaplasma parvum was selected for structure determination by the Northeast Structural...
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12-15-2010 12:03 PM
[NMR paper] Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures
Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures tell us.
Related Articles Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures tell us.
Prog Lipid Res. 2004 May;43(3):177-99
Authors: Hamilton JA
The interactions of fatty acids with proteins have been studied by a variety of conventional approaches for decades. However, only limited aspects of fatty acid-protein interactions have been elucidated, even with the integration of information gleaned from the many techniques....
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11-24-2010 09:51 PM
Comparison of NMR and crystal structures highlights conformational isomerism in prote
Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Related Articles Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1393-405
Authors: Serrano P, Pedrini B, Geralt M, Jaudzems K, Mohanty B, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K
The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this...
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10-16-2010 03:56 PM
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Related Articles Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1381-92
Authors: Mohanty B, Serrano P, Pedrini B, Jaudzems K, Geralt M, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K
The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for...
Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.
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