Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

2015 ◽  
Vol 143 (13) ◽  
pp. 134113
Author(s):  
Xiaokun Wu ◽  
Min Han ◽  
Dengming Ming
Keyword(s):  
Potassium Channel ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Channel Gating ◽  
Dynamics Simulation ◽  
Mode Analysis ◽  
Analysis Method ◽  
Protein Membrane ◽  
Potassium Channel Gating

The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation

2008 ◽  
Vol 71 (4) ◽  
pp. 1984-1994 ◽  
Author(s):  
Bing Xiong ◽  
David L. Burk ◽  
Jianhua Shen ◽  
Xiaomin Luo ◽  
Hong Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Catalytic Cycle ◽  
Dynamics Simulation ◽  
Mode Analysis ◽  
Type Ia

scholarly journals How alginate lyase produces quasi-monodisperse oligosaccharides: a normal mode analysis-based docking and molecular dynamics simulation study

2021 ◽  
Author(s):  
Hengyue Xu ◽  
Qi Gao ◽  
Dengming Ming
Keyword(s):  
Normal Mode ◽  
Conformational Changes ◽  
Catalytic Domain ◽  
Degradation Products ◽  
Normal Mode Analysis ◽  
Alginate Lyase ◽  
Dynamics Simulation ◽  
Mode Analysis ◽  
Health Food ◽  
Industrial Processing

Polysaccharide degradation products are widely used in medicine, health food, textile and other industries. The preparation of monosaccharides by enzymatic degradation is a key technology in bio industrial production. Unfortunately, most of the known digested products are complex oligosaccharide mixtures, which limit their industrial processing and application. In this study, we explored a docking technique based on normal mode analysis to examine the possible cleavage mechanism of an alginate lyase (AlyB) from Birio Splendidus, which contains the catalytic domain of polysaccharide lyase family 7 (PL7) and a CBM32 sugar binding module, and was observed to produce trisaccharide products with quasi-monosaccharide distribution. We compared the molecular interactions of the enzyme with the natural alginates, the polyMG whose products has the quasi-monodisperse distribution of tri-saccharide and two synthetic polysaccharides, the polyM and polyG whose products has a wider distribution of oligosaccharides. Our calculations quantitatively show that there are a series of deterministic conformational changes in the catalytic pocket, which control the specificity of the substrate; at the same time, it determines the uniformity of the final product together with the spatial position of the key catalytic sites. The dynamic simulations revealed that CBM domain plays a key role in assisting the release of tri-saccharides. Our data highlights the important role of enzyme flexibility in determining product uniformity, which may provide new insight into design of enzymes for the production of high-value mono-distributed oligosaccharides.

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