Related ArticlesRefinement of the NMR structures for acyl carrier protein with scalar coupling data.
Proteins. 1990;8(4):377-85
Authors: Kim Y, Prestegard JH
Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
NMR structure of an acyl-carrier protein from Borrelia burgdorferi.
NMR structure of an acyl-carrier protein from Borrelia burgdorferi.
NMR structure of an acyl-carrier protein from Borrelia burgdorferi.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Sep 1;67(Pt 9):1137-40
Authors: Barnwal RP, Van Voorhis WC, Varani G
Abstract
Nearly complete resonance assignment and the high-resolution NMR structure of the acyl-carrier protein from Borrelia burgdorferi, a target of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure-determination pipeline, are reported. This protein...
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[NMR paper] Sources of and solutions to problems in the refinement of protein NMR structures agai
Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.
Related Articles Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.
J Magn Reson. 2000 Oct;146(2):249-54
Authors: Kuszewski J, Clore GM
It is often the case that a substantial number of torsion angles (both backbone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and...
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11-19-2010 08:29 PM
[NMR paper] Sensitivity enhanced NMR spectroscopy by quenching scalar coupling mediated relaxatio
Sensitivity enhanced NMR spectroscopy by quenching scalar coupling mediated relaxation: application to the direct observation of hydrogen bonds in 13C/15N-labeled proteins.
Related Articles Sensitivity enhanced NMR spectroscopy by quenching scalar coupling mediated relaxation: application to the direct observation of hydrogen bonds in 13C/15N-labeled proteins.
J Biomol NMR. 2000 May;17(1):55-61
Authors: Liu A, Hu W, Qamar S, Majumdar A
In this paper, we demonstrate that the sensitivity of triple-resonance NMR experiments can be enhanced...
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NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermo
NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermophilus HB8 show conformational changes.
Related Articles NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermophilus HB8 show conformational changes.
J Struct Funct Genomics. 2010 Oct 5;
Authors: Goroncy AK, Murayama K, Shirouzu M, Kuramitsu S, Kigawa T, Yokoyama S
Sterol carrier protein 2 (SCP-2), also known as nonspecific lipid transfer protein, is a ubiquitous intracellular ~13*kDa protein found in mammals, insects, plants,...
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[NMR paper] Calculating protein structures from NMR data.
Calculating protein structures from NMR data.
Related Articles Calculating protein structures from NMR data.
Methods Mol Biol. 1997;60:157-94
Authors: Güntert P
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[NMR paper] The impact of direct refinement against three-bond HN-C alpha H coupling constants on
The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.
Related Articles The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.
J Magn Reson B. 1994 May;104(1):99-103
Authors: Garrett DS, Kuszewski J, Hancock TJ, Lodi PJ, Vuister GW, Gronenborn AM, Clore GM
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[NMR paper] The impact of direct refinement against three-bond HN-C alpha H coupling constants on
The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.
Related Articles The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.
J Magn Reson B. 1994 May;104(1):99-103
Authors: Garrett DS, Kuszewski J, Hancock TJ, Lodi PJ, Vuister GW, Gronenborn AM, Clore GM
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[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se
A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
J Mol Biol. 1999 Jan 29;285(4):1691-710
Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE
We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...