scholarly journals Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3

1997 ◽  
Vol 73 (3) ◽  
pp. 1147-1159 ◽  
Author(s):  
G.E. Arnold ◽  
R.L. Ornstein
Keyword(s):  
Molecular Dynamics ◽  
Protein Domain ◽  
Molecular Flexibility ◽  
Domain Motions

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Unusual origins of isotope effects in enzyme-catalysed reactions

2006 ◽  
Vol 361 (1472) ◽  
pp. 1341-1349 ◽  
Author(s):  
Dexter B Northrop
Keyword(s):  
High Pressure ◽  
Isotope Effects ◽  
Heavy Atom ◽  
Zero Point ◽  
Protein Domain ◽  
Enzymatic Reactions ◽  
Volume Changes ◽  
Mass Unit ◽  
Deuterium Isotope Effects ◽  
Domain Motions

High hydrostatic pressure is a neglected tool for probing the origins of isotope effects. In chemical reactions, normal primary deuterium isotope effects (DIEs) arising solely from differences in zero point energies are unaffected by pressure; but some anomalous isotope effects in which hydrogen tunnelling is suspected are partially suppressed. In some enzymatic reactions, high pressure completely suppresses the DIE. We have now measured the effects of high pressure on the parallel 13 C heavy atom isotope effect of yeast alcohol dehydrogenase and found that it is also suppressed by high pressure and, similarly, suppressed in its entirety. Moreover, the volume changes associated with the suppression of both deuterium and heavy atom isotope effects are virtually identical. The equivalent decrease in activation volumes for hydride transfer, when one mass unit is added to the carbon end of a scissile C–H bond as when one mass unit is added to the hydrogen end, suggests a common origin. Given that carbon is highly unlikely to undergo tunnelling, it follows that hydrogen is not doing so either. The origin of these isotope effects must lie elsewhere. We offer protein domain motions as a possibility.

Docking of ATP to Ca-ATPase:  Considering Protein Domain Motions

2007 ◽  
Vol 47 (3) ◽  
pp. 1171-1181 ◽  
Author(s):  
Timothy V. Pyrkov ◽  
Yuri A. Kosinsky ◽  
Alexander S. Arseniev ◽  
John P. Priestle ◽  
Edgar Jacoby ◽  
...  
Keyword(s):  
Protein Domain ◽  
Domain Motions

Observation of Protein Domain Motions by Neutron Spectroscopy

ChemPhysChem ◽  
2010 ◽  
Vol 11 (6) ◽  
pp. 1188-1194 ◽  
Author(s):  
Michael Monkenbusch ◽  
Dieter Richter ◽  
Ralf Biehl
Keyword(s):  
Protein Domain ◽  
Neutron Spectroscopy ◽  
Domain Motions

Molecular dynamics simulations of domain motions of substrate-freeS-adenosyl- L-homocysteine hydrolase in solution

2008 ◽  
Vol 71 (1) ◽  
pp. 131-143 ◽  
Author(s):  
Chen Hu ◽  
Jianwen Fang ◽  
Ronald T. Borchardt ◽  
Richard L. Schowen ◽  
Krzysztof Kuczera
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Domain Motions

Homology modeling of mouse NLRP3 NACHT protein domain and molecular dynamics simulation of its ATP binding properties

2020 ◽  
Vol 31 (03) ◽  
pp. 2050036
Author(s):  
Hien T. T. Lai ◽  
Do Minh Ha ◽  
Duc Manh Nguyen ◽  
Toan T. Nguyen
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Structural Model ◽  
Protein Domain ◽  
New Drugs ◽  
Dynamics Simulation ◽  
Receptor Protein ◽  
Caspase 1 ◽  
Dynamics Simulations ◽  
Msu Crystals

Gout is an extremely painful form of inflammatory arthritis, caused by the formation of monosodium urate (MSU) crystals in the joints. MSU crystals are one of the triggers for the activation of nucleotide-binding domain (NOD)-like receptor protein 3 (NLRP3) inflammasome (NACHT, LRR and PYD domains-containing protein), which in turn induces caspase-1 activation and a nonspecific immune responses that cause inflammation. Further structural studies and ligand designs are needed to block the interaction of NLRP3 with MSU or allow the interaction without activating caspase-1. This would facilitate the screening of new drugs for the treatment of gout. Using computational methods for homology modeling and molecular dynamics simulations, the structural model of mouse NLRP3 protein with its domains, three potential structural models were consistently constructed and tested to find the most stable structural model. Adenosine triphosphate (ATP) — an activator of NACHT (the central domain of mouse NLRP3 protein) — was docked and simulated. Ligand effects to activate as well as limit this protein were analyzed. This study provides insights to deeper understanding about gout development pathway via the NLRP3 protein.

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