Characterizing the Rate-Limiting Step of Trp-Cage Folding by All-Atom Molecular Dynamics Simulations

2004 ◽  
Vol 108 (36) ◽  
pp. 13855-13865 ◽  
Author(s):  
Shibasish Chowdhury ◽  
Mathew C. Lee ◽  
Yong Duan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

Molecular Dynamics Simulations of Solid Phase Epitaxy of Si:Growth Mechanism and Defect Formation

1999 ◽  
Vol 584 ◽  
Author(s):  
T. Motooka ◽  
S. Munetoh ◽  
K. Nisihira ◽  
K. Moriguchi ◽  
A. Shintani
Keyword(s):  
Molecular Dynamics ◽  
Temperature Region ◽  
Defect Formation ◽  
Solid Phase ◽  
Md Simulations ◽  
Solid Phase Epitaxy ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

AbstractWe have investigated crystal growth and defect formation processes during solid phase epitaxy (SPE) of Si in the [001] direction based on molecular dynamics (MD) simulations using the Tersoff potential. From the Arrhenius plot of the growth rates obtained by MD simulations, we have found that the activation energy of SPE at lower temperatures is in good agreement with the experimental value, approximately 2.7 eV, while it becomes lower at higher temperatures. This can be attributed to the difference in the amorphous/crystalline (a/c) interface structure. In the low temperature region, the a/c interface is essentially (001) and the rate-limiting step is two-dimensional nucleation on the (001) a/c interface. On the other hand, the a/c interface becomes rough due to (111) facets formation in the high temperature region and the rate-limiting step is presumably a diffusion process of Si to be trapped at the kink sites associated with these facets. Defect formation is found to be initiated by 5-membered rings created at the a/c interface. These mismatched configurations at the interface give rise to (111) stacking faults during further SPE growth.

scholarly journals Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and Molecular simulations

2021 ◽  
Author(s):  
Mrinal Shekhar ◽  
Chitrak Gupta ◽  
Kano Suzuki ◽  
Abhishek Singharoy ◽  
Takeshi Murata
Keyword(s):  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Hydrolysis Product ◽  
X Ray ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remain an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multi-step rotation process. Here, using Vacuolar or V1-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography a new intermediate or 'dwell' is identified, which enables the release of an inorganic phosphate (or Pi) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transfor-mations, and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the sidechain level interactions transcend into larger scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. Inspection of all known rates encompassing the 4-step rotation mechanism implicates overcoming of the ADP interactions with V1-ATPase to be the rate-limiting step of motor action.

Ornithine Decarboxylase Activity in Cultured Endothelial Cells Stimulated by Serum, Thrombin and Serotonin

1978 ◽  
Vol 39 (02) ◽  
pp. 496-503 ◽  
Author(s):  
P A D’Amore ◽  
H B Hechtman ◽  
D Shepro
Keyword(s):  
Endothelial Cells ◽  
Ornithine Decarboxylase ◽  
Decarboxylase Activity ◽  
Aortic Endothelial Cells ◽  
Ornithine Decarboxylase Activity ◽  
Rate Limiting Step ◽  
Bovine Aortic Endothelial Cells ◽  
Limiting Step ◽  
Rate Limiting ◽  
Serum Serotonin

SummaryOrnithine decarboxylase (ODC) activity, the rate-limiting step in the synthesis of polyamines, can be demonstrated in cultured, bovine, aortic endothelial cells (EC). Serum, serotonin and thrombin produce a rise in ODC activity. The serotonin-induced ODC activity is significantly blocked by imipramine (10-5 M) or Lilly 11 0140 (10-6M). Preincubation of EC with these blockers together almost completely depresses the 5-HT-stimulated ODC activity. These observations suggest a manner by which platelets may maintain EC structural and metabolic soundness.

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