Related ArticlesDetermination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data.
J Biomol Struct Dyn. 1994 Jun;11(6):1377-402
Authors: Fushman D, Ohlenschläger O, Rüterjans H
The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling contributions of NH-bond librations and backbone dihedral angle fluctuations. The former turned out to be similar for all amides, as characterized by correlation times of librational motions in a subpicosecond scale, angular amplitudes of about 10-12 degrees for out-of-peptide-plane displacements of the NH-bond and 3-5 degrees for the in-plane displacements, whereas the contributions of much slower backbone dihedral angle fluctuations strongly depend on the secondary structure. Correlation functions relevant for NMR were obtained and analyzed utilizing the 'model-free' approach (Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570; Clore et al., (1990) J. Am. Chem. Soc. 112, 4989-4991). The dependence of the amplitude of local motion on the residue location in the backbone is in good agreement with the results of NMR relaxation measurements and X-ray data. The protein dynamics is characterized by a highly restricted local motion of those parts of the backbone with defined secondary structure as well as by a high flexibility in loop regions. The comparison of results derived from different periods of the trajectory (of 50 ps and 1 ns duration, 1000 points sampled) reveals a dependence of the observed dynamic picture on the characteristic time scale of the experimental method used. Comparison of the MD data for the free and liganded enzyme clearly indicates a restriction of the mobility within certain regions of the backbone upon inhibitor binding.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR [Biophysics and Computational Biology]
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR
Kato, H., van Ingen, H., Zhou, B.-R., Feng, H., Bustin, M., Kay, L. E., Bai, Y....
Date: 2011-07-26
Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility group nucleosomal (HMGN) protein family that regulates various chromatin functions, including transcription. Here, we report the architecture of the HMGN2-nucleosome...
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Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Proc Natl Acad Sci U S A. 2011 Jul 5;
Authors: Kato H, van Ingen H, Zhou BR, Feng H, Bustin M, Kay LE, Bai Y
Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility...
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07-07-2011 05:12 PM
[NMR paper] Backbone dynamics of the cytotoxic ribonuclease alpha-sarcin by 15N NMR relaxation me
Backbone dynamics of the cytotoxic ribonuclease alpha-sarcin by 15N NMR relaxation methods.
Related Articles Backbone dynamics of the cytotoxic ribonuclease alpha-sarcin by 15N NMR relaxation methods.
J Biomol NMR. 2002 Dec;24(4):301-16
Authors: Pérez-Cañadillas JM, Guenneugues M, Campos-Olivas R, Santoro J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M
The cytotoxic ribonuclease alpha-sarcin is a 150-residue protein that inactivates ribosomes by selectively cleaving a single phosphodiester bond in a strictly conserved rRNA loop. In order...
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11-24-2010 08:58 PM
[NMR paper] NMR solution structure, backbone mobility, and homology modeling of c-type cytochrome
NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
Related Articles NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
Chembiochem. 2002 Apr 2;3(4):299-310
Authors: Banci L, Bertini I, Ciurli S, Dikiy A, Dittmer J, Rosato A, Sciara G, Thompsett AR
The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the...
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[NMR paper] Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15
Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics.
Related Articles Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics.
Biochemistry. 2002 Feb 26;41(8):2655-66
Authors: Pang Y, Buck M, Zuiderweg ER
The nano-pico second backbone dynamics of the ribonuclease binase, homologous to barnase, is investigated with (15)N, (13)C NMR relaxation at 11.74...
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[NMR paper] Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
Biochemistry. 1997 Feb 25;36(8):2278-90
Authors: Hodsdon ME, Cistola DP
The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia...
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08-22-2010 03:03 PM
[NMR paper] Determination of molecular mobility of lyophilized bovine serum albumin and gamma-glo
Determination of molecular mobility of lyophilized bovine serum albumin and gamma-globulin by solid-state 1H NMR and relation to aggregation-susceptibility.
Related Articles Determination of molecular mobility of lyophilized bovine serum albumin and gamma-globulin by solid-state 1H NMR and relation to aggregation-susceptibility.
Pharm Res. 1996 Jun;13(6):926-30
Authors: Yoshioka S, Aso Y, Kojima S
PURPOSE: Feasibility of solid-state 1H NMR for determining the mobility of protein molecules in lyophilized cakes was considered. The mobility in...
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[NMR paper] Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using
Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data.
Related Articles Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data.
J Biomol Struct Dyn. 1994 Jun;11(6):1377-402
Authors: Fushman D, Ohlenschläger O, Rüterjans H
The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification...
Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using
Linear Mode
