Related Articles3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.
J Biomol Struct Dyn. 1992 Apr;9(5):935-49
Authors: Braatz JA, Paulsen MD, Ornstein RL
Mainly due to computational limitations, past protein molecular dynamics simulations have rarely been extended to 300 psec; we are not aware of any published results beyond 350 psec. The present work compares a 3000 psec simulation of the protein ubiquitin with the available x-ray crystallographic and solution NMR structures. Aside from experimental structure availability, ubiquitin was studied because of its relatively small size (76 amino acids) and lack of disulfide bridges. An implicit solvent model was used except for explicit treatment of waters of crystallization. We found that the simulated average structure retains most of the character of the starting x-ray crystal structure. In two highly surface accessible regions, the simulation was not in agreement with the x-ray structure. In addition, there are six backbone-backbone hydrogen bonds that are in conflict between the solution NMR and x-ray crystallographic structures; two are bonds that the NMR does not locate, and four are ones that the two methods disagree upon the donor. Concerning these six backbone-backbone hydrogen bonds, the present simulation agrees with the solution NMR structure in five out-of-the six cases, in that if a hydrogen bond is present in the x-ray structure and not in the NMR structure, the bond breaks within 700 psec. Of the two hydrogen bonds that are found in the NMR structure and not in the x-ray structure, one forms at 1400 psec and the other forms rarely. The present results suggest that relatively long molecular dynamics simulations, that use protein x-ray crystal coordinates for the starting structure and a computationally efficient solvent representation, may be used to gain an understanding of conformational and dynamic differences between the solid-crystal and dilute-solution states.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Biophys J. 2010 Nov 17;99(10):3282-9
Authors: Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A
Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to...
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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
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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[NMR paper] Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations
Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data.
Related Articles Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data.
J Comput Chem. 2002 Dec;23(16):1577-86
Authors: Barthe P, Roumestand C, Déméné H, Chiche L
The human p8(MTCP1) protein is constituted by an original disulfide bridged alpha-hairpin motif, and a third hydrophilic helix that appeared mobile and independent in NMR analysis. To get atomic...
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[NMR paper] Nmr probes of molecular dynamics: overview and comparison with other techniques.
Nmr probes of molecular dynamics: overview and comparison with other techniques.
Related Articles Nmr probes of molecular dynamics: overview and comparison with other techniques.
Annu Rev Biophys Biomol Struct. 2001;30:129-55
Authors: Palmer AG
NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together...
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11-19-2010 08:32 PM
[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.
Related Articles Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
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...
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11-17-2010 11:06 PM
[NMR paper] Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation wit
Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.
J Mol Biol. 1995 Dec 8;254(4):771-92
Authors: Philippopoulos M, Lim C
A 500 ps molecular dynamics simulation of Escherichia coli RNase...
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[NMR paper] A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation:
A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Related Articles A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Proteins. 1993 Dec;17(4):375-90
Authors: Eriksson MA, Berglund H, Härd T, Nilsson L
The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using...