scholarly journals Conformational Transitions of Caspase-6 in Substrate-Induced Activation Process Explored by Perturbation-Response Scanning Combined with Targeted Molecular Dynamics

2021 ◽  
Author(s):  
Shuheng Huang ◽  
Hu Mei ◽  
Laichun Lu ◽  
Zuyin Kuang ◽  
Yu Heng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Transitions ◽  
Activation Process ◽  
Targeted Molecular Dynamics ◽  
Caspase 6

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

scholarly journals Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mario Frezzini ◽  
Leonardo Guidoni ◽  
Stefano Pascarella
Keyword(s):  
Molecular Dynamics ◽  
Bacillus Subtilis ◽  
Closed Form ◽  
Molecular Mechanism ◽  
Aspartate Aminotransferase ◽  
Transcriptional Regulator ◽  
Transcription Activation ◽  
Conformational Transitions ◽  
Winged Helix ◽  
Gaba Binding

AbstractGabR from Bacillus subtilis is a transcriptional regulator of the MocR subfamily of GntR regulators. The MocR architecture is characterized by the presence of an N-terminal winged-Helix-Turn-Helix domain and a C-terminal domain folded as the pyridoxal 5′-phosphate (PLP) dependent aspartate aminotransferase (AAT). The two domains are linked by a peptide bridge. GabR activates transcription of genes involved in γ-amino butyrate (GABA) degradation upon binding of PLP and GABA. This work is aimed at contributing to the understanding of the molecular mechanism underlying the GabR transcription activation upon GABA binding. To this purpose, the structure of the entire GabR dimer with GABA external aldimine (holo-GABA) has been reconstructed using available crystallographic data. The structure of the apo (without any ligand) and holo (with PLP) GabR forms have been derived from the holo-GABA. An extensive 1 μs comparative molecular dynamics (MD) has been applied to the three forms. Results showed that the presence of GABA external aldimine stiffens the GabR, stabilizes the AAT domain in the closed form and couples the AAT and HTH domains dynamics. Apo and holo GabR appear more flexible especially at the level of the HTH and linker portions and small AAT subdomain.

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