Related ArticlesPrincipal 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 structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
J Comput Chem. 2011 Sep 9;
Authors: Czajlik A, Hudáky I, Perczel A
Abstract
NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...
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09-10-2011 06:51 PM
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
BMC Struct Biol. 2011 May 12;11(1):24
Authors: Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA
ABSTRACT: BACKGROUND: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural...
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05-17-2011 06:21 PM
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
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...
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04-12-2011 11:08 AM
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...
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01-09-2011 12:46 PM
[NMR paper] NMR structural analysis of alpha-bungarotoxin and its complex with the principal alph
NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor.
Related Articles NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor.
J Biol Chem. 2002 Apr 5;277(14):12406-17
Authors: Moise L, Piserchio A, Basus VJ, Hawrot E
We report a new, higher resolution NMR structure of...
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11-24-2010 08:49 PM
[NMR paper] The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR
The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.
Related Articles The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.
Biophys Chem. 1999 Aug 30;80(3):153-63
Authors: Takashima S, Yamaoka K
Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein...
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11-18-2010 08:31 PM
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...
matthias
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08-14-2008 12:54 AM
Programs for alignment of protein NMR ensembles
If you need to align models in your NMR ensemble, you can use the following programs to do so. MolMol
- Official website
- Linux binaries from Patrick Finerty website
- BioXRay distribution
SuperPose server
Suppose