Related ArticlesProtein structure elucidation from minimal NMR data: the CLOUDS approach.
Methods Enzymol. 2005;394:261-95
Authors: Grishaev A, Llinás M
In this chapter we review automated methods of protein NMR data analysis and expand on the assignment-independent CLOUDS approach. As presented, given a set of reliable NOEs it is feasible to derive a spatial H-atom distribution that provides a low-resolution image of the protein structure. In order to generate such a list of unambiguous NOEs, a probabilistic assessment of the NOE identities (in terms of frequency-labeled H-atom sources) was developed on the basis of Bayesian inference. The methodology, encompassing programs SPI and BACUS, provides a list of "clean" NOEs that does not hinge on prior knowledge of sequence-specific resonance assignments or a preliminary structural model. As such, the combined SPI/BACUS approach, intrinsically adaptable to include 13C- and/or 15N-edited experiments, affords a useful tool for the analysis of NMR data irrespective of whether the adopted structure calculation protocol is assignment-dependent.
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
J Biol Chem. 2011 Jul 28;
Authors: Samal AB, Ghanam RH, Fernandez TF, Monroe EB, Saad JS
Subcellular distribution of Calmodulin (CaM) in human immunodeficiency virus type-1 (HIV-1) infected cells is distinct from that observed in uninfected cells. CaM has been shown to interact and co-localize with the HIV-1 Gag protein...
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07-30-2011 11:23 AM
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Methods Enzymol. 2011;493:241-75
Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF
Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
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03-05-2011 01:02 PM
[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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11-24-2010 11:14 PM
[NMR paper] Automated protein fold determination using a minimal NMR constraint strategy.
Automated protein fold determination using a minimal NMR constraint strategy.
Related Articles Automated protein fold determination using a minimal NMR constraint strategy.
Protein Sci. 2003 Jun;12(6):1232-46
Authors: Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution...
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11-24-2010 09:01 PM
[NMR paper] Protein structure elucidation from NMR proton densities.
Protein structure elucidation from NMR proton densities.
Related Articles Protein structure elucidation from NMR proton densities.
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6713-8
Authors: Grishaev A, Llinas M
The NMR-generated foc proton density affords a template to which the molecule has to be fitted to derive the structure. Here we present a computational protocol that achieves this goal. H(N) atoms are readily recognizable from (1)H/(2)H exchange or (1)H/(15)N heteronuclear single quantum correlation (HSQC) experiments. The primary...
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11-24-2010 08:49 PM
[NMR paper] MS/NMR: a structure-based approach for discovering protein ligands and for drug desig
MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy.
Related Articles MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy.
Anal Chem. 2001 Feb 1;73(3):571-81
Authors: Moy FJ, Haraki K, Mobilio D, Walker G, Powers R, Tabei K, Tong H, Siegel MM
A protocol is described...
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11-19-2010 08:32 PM
[NMR paper] High-resolution solution NMR structure of the minimal active domain of the human immu
High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
Related Articles High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
Biochemistry. 1998 Dec 22;37(51):17704-13
Authors: Kodera Y, Sato K, Tsukahara T, Komatsu H, Maeda T, Kohno T
The retroviral nucleocapsid (NC) protein is a multifunctional protein essential for RNA genome packaging and viral infectivity. The NC protein, NCp8, of the...
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11-17-2010 11:15 PM
[NMR paper] An approach to global fold determination using limited NMR data from larger proteins
An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types.
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...
Protein structure elucidation from minimal NMR data: the CLOUDS approach.
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