Related ArticlesReorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins.
J Am Chem Soc. 2001 Aug 1;123(30):7305-13
Authors: Prompers JJ, Brüschweiler R
An approach is presented for the interpretation of heteronuclear NMR spin relaxation data in mobile protein parts in terms of reorientational eigenmode dynamics. The method is based on the covariance matrix of the spatial functions of the nuclear spin interactions that cause relaxation expressed as spherical harmonics of rank 2. The approach was applied to characterize the dynamics of a loop region of ubiquitin. The covariance matrix was determined from a conformational ensemble generated by a 5 ns molecular dynamics simulation. It was found that the time correlation functions of the dominant eigenmodes decay in good approximation with a single correlation time. From the reorientational eigenmodes, their eigenvalues, and correlation times, NMR relaxation data were calculated in accordance with Bloch-Wangsness-Redfield relaxation theory and directly compared with experimental (15)N relaxation parameters. Using a fitting procedure, agreement between calculated and experimental data was improved significantly by adjusting eigenvalues and correlation times of the dominant modes. The presented procedure provides detailed information on correlated reorientational dynamics of flexible parts in globular proteins. The covariance matrix was linked to the covariance matrix of backbone dihedral angle fluctuations, allowing one to study the motional behavior of these degrees of freedom on nano- and subnanosecond time scales.
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.
J Phys Chem B. 2011 May 2;
Authors: Hwang S, Shao Q, Williams H, Hilty C, Gao YQ
A combined simulation and experimental study was performed to investigate how methanol affects the structure of a model peptide BBA5. BBA5 forms a stable ?-hairpin-?-helix structure in aqueous solutions....
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Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Proteins. 2011 Feb 16;
Authors: Xu X, Ishima R, Ames JB
Recoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, serves as a calcium sensor in retinal rod cells. Ca(2+) -induced conformational changes in recoverin promote extrusion of its...
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Structure. 2010 Dec 8;18(12):1678-1687
Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ
Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...
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[NMR paper] Characterization of micros-ms dynamics of proteins using a combined analysis of 15N N
Characterization of micros-ms dynamics of proteins using a combined analysis of 15N NMR relaxation and chemical shift: conformational exchange in plastocyanin induced by histidine protonations.
Related Articles Characterization of micros-ms dynamics of proteins using a combined analysis of 15N NMR relaxation and chemical shift: conformational exchange in plastocyanin induced by histidine protonations.
J Am Chem Soc. 2004 Jan 28;126(3):753-65
Authors: Hass MA, Thuesen MH, Christensen HE, Led JJ
An approach is presented that allows a detailed,...
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11-24-2010 09:25 PM
[NMR paper] Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics
Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics.
Related Articles Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics.
Biochemistry. 2001 Mar 6;40(9):2743-53
Authors: Viles JH, Donne D, Kroon G, Prusiner SB, Cohen FE, Dyson HJ, Wright PE
A template-assisted conformational change of the cellular prion protein (PrP(C)) from a predominantly helical structure to an amyloid-type structure with a higher proportion of beta-sheet is thought to be the causative factor in prion...
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11-19-2010 08:32 PM
[NMR paper] Structural determinants of protein dynamics: analysis of 15N NMR relaxation measureme
Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.
Related Articles Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.
Biochemistry. 1995 Mar 28;34(12):4041-55
Authors: Buck M, Boyd J, Redfield C, MacKenzie DA, Jeenes DJ, Archer DB, Dobson CM
15N-labeled hen lysozyme has been studied by 2D and 3D NMR in order to characterize its dynamic...
Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for
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