An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types.
J Biomol NMR. 1996 Oct;8(3):360-8
Authors: Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED
A combination of calculation and experiment is used to demonstrate that the global fold of larger proteins can be rapidly determined using limited NMR data. The approach involves a combination of heteronuclear triple resonance NMR experiments with protonation of selected residue types in an otherwise completely deuterated protein. This method of labelling produces proteins with alpha-specific deuteration in the protonated residues, and the results suggest that this will improve the sensitivity of experiments involving correlation of side-chain ((1)H and (13)C) and backbone ((1)H and (15)N) amide resonances. It will allow the rapid assignment of backbone resonances with high sensitivity and the determination of a reasonable structural model of a protein based on limited NOE restraints, an application that is of increasing importance as data from the large number of genome sequencing projects accumulates. The method that we propose should also be of utility in extending the use of NMR spectroscopy to determine the structures of larger proteins.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...
[NMR paper] An algebraic geometry approach to protein structure determination from NMR data.
An algebraic geometry approach to protein structure determination from NMR data.
Related Articles An algebraic geometry approach to protein structure determination from NMR data.
Proc IEEE Comput Syst Bioinform Conf. 2005;:235-46
Authors: Wang L, Mettu RR, Donald BR
Our paper describes the first provably-efficient algorithm for determining protein structures de novo, solely from experimental data. We show how the global nature of a certain kind of NMR data provides quantifiable complexity-theoretic benefits, allowing us to classify our...
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[NMR paper] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
Related Articles Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
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[NMR paper] An approach for high-throughput structure determination of proteins by NMR spectrosco
An approach for high-throughput structure determination of proteins by NMR spectroscopy.
Related Articles An approach for high-throughput structure determination of proteins by NMR spectroscopy.
J Biomol NMR. 2000 Nov;18(3):229-38
Authors: Medek A, Olejniczak ET, Meadows RP, Fesik SW
An approach is described for rapidly determining protein structures by NMR that utilizes proteins containing 13C-methyl labeled Val, Leu, and Ile (delta1) and protonated Phe and Tyr in a deuterated background. Using this strategy, the key NOEs that define the...
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11-19-2010 08:29 PM
[NMR paper] NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calc
NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.
Related Articles NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.
Protein Sci. 1999 Dec;8(12):2580-8
Authors: Aitio H, Annila A, Heikkinen S, Thulin E, Drakenberg T, Kilpeläinen I
Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid...
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11-18-2010 08:31 PM
[NMR paper] NMR structure determination of proteins and protein complexes larger than 20 kDa.
NMR structure determination of proteins and protein complexes larger than 20 kDa.
Related Articles NMR structure determination of proteins and protein complexes larger than 20 kDa.
Curr Opin Chem Biol. 1998 Oct;2(5):564-70
Authors: Clore GM, Gronenborn AM
Recent advances in multidimensional nuclear magnetic resonance methodology to obtain 1H, 15N and 13C resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long-range order, coupled with new methods of structure refinement and novel methods...
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11-17-2010 11:15 PM
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, resid
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
J Comput Chem. 2010 Aug 30;
Authors: Latek D, Kolinski A
Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low-cost global protein fold determination. Here, we present...
An approach to global fold determination using limited NMR data from larger proteins
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