Abstract We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly 15N,13C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s218â??289 fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9517-1
Authors
Kan-Nian Hu, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520, USA
Wei Qiang, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520, USA
Robert Tycko, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520, USA
Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers
Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers
Abstract Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring 1H-15N dipolar couplings (DC) and 15N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal...
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[NMRpipe Yahoo group] Re: Monte Carlo Error using modelXY
Re: Monte Carlo Error using modelXY
By default, the modelXY program reports an error range which accounts for 90% of the monte carlo trials (argument -cf 0.9). It may well be that the other
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[NMRpipe Yahoo group] Monte Carlo Error using modelXY
Monte Carlo Error using modelXY
Hello dear NMRPipe users, I'm using the modelXY program provided by NMRpipe to fit T1 relaxation curves. It seems to work fine but when I compare to the
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[NMR paper] Protein heteronuclear NMR assignments using mean-field simulated annealing.
Protein heteronuclear NMR assignments using mean-field simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein heteronuclear NMR assignments using mean-field simulated annealing.
J Magn Reson. 1997 Mar;125(1):34-42
Authors: Buchler NE, Zuiderweg ER, Wang H, Goldstein RA
A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic...
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08-22-2010 03:31 PM
[NMR paper] Protein heteronuclear NMR assignments using mean-field simulated annealing.
Protein heteronuclear NMR assignments using mean-field simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein heteronuclear NMR assignments using mean-field simulated annealing.
J Magn Reson. 1997 Mar;125(1):34-42
Authors: Buchler NE, Zuiderweg ER, Wang H, Goldstein RA
A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic...
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08-22-2010 03:03 PM
[NMR paper] Simulated annealing with restrained molecular dynamics using a flexible restraint pot
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
...
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[NMR paper] Simulated annealing with restrained molecular dynamics using CONGEN: energy refinemen
Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha...
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Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Alexander Lemak, Carlos A. Steren, Cheryl H. Arrowsmith and Miguel Llinás
Journal of Biomolecular NMR; 2008; 41(1); pp 29 - 41
Abstract:
ABACUS is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic...