[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy].
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 diseases including Alzheimer's disease. Therefore development of a method for structure calculation of small peptides in a water environment using the most realistic force fields seems to be of current importance. Such algorithm has been developed using the Amber-03 force field and software package Gromacs after updating its program code. The algorithm of calculation has been verified on a model peptide for which the solution structure is known, and on the metal binding fragment of rat beta-amyloid for which structure has been determined by alternative methods. The developed algorithm substantially increases quality of structures, in particular Ramachandran plot statistics, and decreases RMSD of coordinates of atoms inside calculated family. The described protocol of calculation can be used for determination of conformation of short peptides, and also for structure optimization of larger proteins containing poorly structured fragments.
[NMR paper] Multidimensional NMR methods for protein structure determination.
Multidimensional NMR methods for protein structure determination.
Related Articles Multidimensional NMR methods for protein structure determination.
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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Fully automated high-quality NMR structure determination of small (2)H-enriched prote
Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
Related Articles Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
J Struct Funct Genomics. 2010 Aug 24;
Authors: Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT
Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands...
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08-25-2010 02:04 PM
[NMR paper] Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy.
Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy.
J Mol Biol. 1995 Jun 2;249(2):441-62
Authors: Skelton NJ, Kördel J, Chazin WJ
The three-dimensional structure of apo calbindin D9k has been determined using constraints generated from nuclear magnetic resonance spectroscopy. The family of solution structures...
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08-22-2010 03:41 AM
[NMR paper] Solution structure determination by NMR spectroscopy of a synthetic peptide correspon
Solution structure determination by NMR spectroscopy of a synthetic peptide corresponding to a putative amphipathic alpha-helix of spiralin: resonance assignment, distance geometry and simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution structure determination by NMR spectroscopy of a synthetic peptide corresponding to a putative amphipathic alpha-helix of spiralin: resonance assignment, distance geometry and simulated annealing.
Biochim Biophys Acta. 1995 May...
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[NMR paper] NMR sequential assignments and solution structure of chlorotoxin, a small scorpion to
NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels.
Related Articles NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels.
Biochemistry. 1995 Jan 10;34(1):13-21
Authors: Lippens G, Najib J, Wodak SJ, Tartar A
The solution structure of chlorotoxin, a small toxin purified from the venom of the Leiurus quinquestriatus scorpion, has been determined using 2D 1H NMR spectroscopy. Analysis of the NMR data shows that...
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[NMR paper] Protein structure determination in solution by NMR spectroscopy.
Protein structure determination in solution by NMR spectroscopy.
Related Articles Protein structure determination in solution by NMR spectroscopy.
J Biol Chem. 1990 Dec 25;265(36):22059-62
Authors: Wüthrich K
The introduction of nuclear magnetic resonance (NMR) spectroscopy as a second method for protein structure determination at atomic resolution, in addition to x-ray diffraction in single crystals, has already led to a significant increase in the number of known protein structures. The NMR method provides data that are in many ways...
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08-21-2010 11:04 PM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
Related Articles Combining 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...
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Combining NMR and EPR Methods for Homodimer Protein Structure Determination
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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 ...