Thermal unfolding molecular dynamics simulation ofEscherichia coli dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway

2002 ◽  
Vol 46 (3) ◽  
pp. 308-320 ◽  
Author(s):  
Yuk Yin Sham ◽  
Buyong Ma ◽  
Chung-Jung Tsai ◽  
Ruth Nussinov
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Dihydrofolate Reductase ◽  
Protein Domains ◽  
Ofescherichia Coli ◽  
Dynamics Simulation ◽  
Thermal Unfolding ◽  
Thermal Stability Of

scholarly journals Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Zhiguo Chen ◽  
Yi Fu ◽  
Wenbo Xu ◽  
Ming Li
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Clinical Medicine ◽  
Intramolecular Interaction ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Thermal Stability Of

Bacillus amyloliquefaciensribonuclease Barnase (RNase Ba) is a 12 kD (kilodalton) small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73) have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

ReaxFF molecular dynamics simulation of thermal stability of a Cu3(BTC)2 metal–organic framework

2012 ◽  
Vol 14 (32) ◽  
pp. 11327 ◽  
Author(s):  
Liangliang Huang ◽  
Kaushik L. Joshi ◽  
Adri C. T. van Duin ◽  
Teresa J. Bandosz ◽  
Keith E. Gubbins
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Metal Organic ◽  
Thermal Stability Of ◽  
Organic Framework

scholarly journals Thermal Stability of Modified Insulation Paper Cellulose Based on Molecular Dynamics Simulation

Energies ◽  
2017 ◽  
Vol 10 (3) ◽  
pp. 397 ◽  
Author(s):  
Chao Tang ◽  
Song Zhang ◽  
Qian Wang ◽  
Xiaobo Wang ◽  
Jian Hao
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Thermal Stability Of

Molecular dynamics simulation of thermal stability of nanocrystalline vanadium

2006 ◽  
Vol 49 (4) ◽  
pp. 400-407 ◽  
Author(s):  
Mingzhi Wei ◽  
Shifang Xiao ◽  
Xiaojian Yuan ◽  
Wangyu Hu
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Thermal Stability Of
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