Generalized Spring Tensor Models for Protein Fluctuation Dynamics and Conformation Changes

2013 ◽  
pp. 107-135 ◽  
Author(s):  
Hyuntae Na ◽  
Tu-Liang Lin ◽  
Guang Song
Keyword(s):  
Conformation Changes ◽  
Tensor Models ◽  
Fluctuation Dynamics

Kategorisierung der Schädelform des Cavalier King Charles Spaniels

2019 ◽  
Vol 47 (02) ◽  
pp. 133-133
Keyword(s):  
Pilot Study ◽  
Cavalier King Charles Spaniel ◽  
Conformation Changes ◽  
Veterinary Record ◽  
Changes Over Time ◽  
Over Time

Knowler SP, Gillstedt L, Mitchell TJ et al. Pilot study of head conformation changes over time in the Cavalier King Charles spaniel breed. Veterinary Record 2019. doi:10.1136/vr.105135.

scholarly journals Electronic and fluctuation dynamics following a quench to the superconducting phase

2021 ◽  
Vol 103 (3) ◽  
Author(s):  
Christopher Stahl ◽  
Martin Eckstein
Keyword(s):  
Superconducting Phase ◽  
Fluctuation Dynamics

scholarly journals Time-resolved detection of SDS-induced conformational changes in α-synuclein by a micro-stopped-flow system

RSC Advances ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 1086-1097
Author(s):  
Shunki Takaramoto ◽  
Yusuke Nakasone ◽  
Kei Sadakane ◽  
Shinsaku Maruta ◽  
Masahide Terazima
Keyword(s):  
Conformational Changes ◽  
Flow System ◽  
Stopped Flow ◽  
Time Resolved ◽  
Sds Micelles ◽  
Conformation Changes ◽  
System P

Dynamics of conformation changes of α-synuclein induced by the presence of SDS micelles are revealed using time-resolved diffusion, CD, and FRET measurements combined with a micro-stopped flow system.

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.

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