Related ArticlesCombining NMR and EPR Methods for Homodimer Protein Structure Determination.
J Am Chem Soc. 2010 Aug 10;
Authors: Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.
PMID: 20698532 [PubMed - as supplied by publisher]
[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy].
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Mol Biol (Mosk). 2010 Nov-Dec;44(6):1075-85
Authors:
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative...
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[NMR paper] Structural genomics and the metabolome: combining computational and NMR methods to id
Structural genomics and the metabolome: combining computational and NMR methods to identify target ligands.
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Curr Opin Drug Discov Devel. 2004 Jan;7(1):62-8
Authors: Parsons L, Orban J
One of the goals of structural genomics is to use three-dimensional structures to gain insights into the function of poorly understood or hypothetical proteins. Approximate functions are often apparent from the protein fold, but more...
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11-24-2010 09:25 PM
[NMR paper] NMR methods for the determination of protein-ligand dissociation constants.
NMR methods for the determination of protein-ligand dissociation constants.
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Curr Top Med Chem. 2003;3(1):39-53
Authors: Fielding L
This article is a review with 83 references of the application of NMR to the measurement of the dissociation constants of protein-ligand complexes. After briefly discussing some general concepts of molecular stability, the text turns to consider which NMR parameters are reporters of complex formation. The available data...
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[NMR paper] Multidimensional NMR methods for protein structure determination.
Multidimensional NMR methods for protein structure determination.
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IUBMB Life. 2001 Dec;52(6):291-302
Authors: Kanelis V, Forman-Kay JD, Kay LE
Structural studies of proteins are critical for understanding biological processes at the molecular level. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for obtaining structural and dynamic information on proteins and protein-ligand complexes. In the present review, methodologies for NMR structure...
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[NMR paper] Expression and secondary structure determination by NMR methods of the major house du
Expression and secondary structure determination by NMR methods of the major house dust mite allergen Der p 2.
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J Biol Chem. 1997 Oct 24;272(43):26893-8
Authors: Mueller GA, Smith AM, Williams DC, Hakkaart GA, Aalberse RC, Chapman MD, Rule GS, Benjamin DC
There exists a strong...
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J Biomol NMR. 1992 Jul;2(4):373-88
Authors: Liu Y, Zhao D, Altman R, Jardetzky O
We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...
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Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and
Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins
Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 12 June 2010</br>
Dominique, Marion</br>
Resonance assignment of intrinsically disordered proteins is made difficult by the extensive spectral overlaps. High-resolution 3D and 4D spectra are thus essential for this purpose. We have adapted the series of 3D BEST experiments proposed by Lescop et al to the case of unfolded proteins. Longer acquisitions...
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08-16-2010 03:50 AM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination
http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja105080h/aop/images/medium/ja-2010-05080h_0003.gif
Combining NMR and EPR Methods for Homodimer Protein Structure Determination
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein ...