Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Amino Acids. 2011 Apr 9;
Authors: Hu M, Li Y, Yang G, Li G, Li M, Wen Z
Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and facilitate investigating the internal positional fluctuations of enzymes within nuclear magnetic resonance (NMR) structure ensembles. Moreover, potential active sites were identified by combining with positional fluctuation score, sequence conservation, and solvent accessible surface area. Among the total 107 catalytic residues in 44 examined enzymes, 69 residues were identified correctly. Our results suggest that wavelet transform analysis of structure ensemble is applicable to extract essential fluctuation information of proteins; furthermore, analysis of positional fluctuations is helpful for the identification of catalytic residues.
PMID: 21479702 [PubMed - as supplied by publisher]
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101896j/aop/images/medium/bi-2010-01896j_0004.gif
Biochemistry
DOI: 10.1021/bi101896j
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NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
Biochemistry. 2011 Jan 4;
Authors: Parkesh R, Disney MD, Fountain M
The NMR structure of an RNA with a copy of the 5'CUG/3'GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single...
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01-06-2011 11:21 AM
[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat
Principal components analysis of protein structure ensembles calculated using NMR data.
Related Articles Principal components analysis of protein structure ensembles calculated using NMR data.
J Biomol NMR. 2001 May;20(1):61-70
Authors: Howe PW
One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated...
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[NMR paper] Essential spaces defined by NMR structure ensembles and molecular dynamics simulation
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
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Proteins. 1998 Jun 1;31(4):370-82
Authors: Abseher R, Horstink L, Hilbers CW, Nilges M
Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation...
Structure-based protein NMR assignments using native structural ensembles
Structure-based protein NMR assignments using native structural ensembles
Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald
Journal of Biomolecular NMR; 2008; 40(4); pp 263-276
Abstract:
An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
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