Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein

RSC Advances ◽  
2015 ◽  
Vol 5 (6) ◽  
pp. 4191-4199 ◽  
Author(s):  
Qiang Shao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Enhanced Sampling ◽  
Helix Bundle ◽  
Α Helix ◽  
Bundle Protein ◽  
Charge Interactions

An enhanced-sampling molecular dynamics simulation is presented to quantitatively demonstrate the important roles of hydrophobic and charge interactions in the folding and misfolding of α-helix bundle protein, respectively.

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

2014 ◽  
Vol 68 (11) ◽  
Author(s):  
Mehdi Sahihi ◽  
Yousef Ghayeb
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Mean Value ◽  
Transport Protein ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Accessible Surface ◽  
Β Lactoglobulin

AbstractBiguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.

The influence of a type III antifreeze protein and its mutants on methane hydrate adsorption–inhibition: a molecular dynamics simulation study

2019 ◽  
Vol 21 (39) ◽  
pp. 21836-21846 ◽  
Author(s):  
Mitra Maddah ◽  
Mina Maddah ◽  
Kiana Peyvandi
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Simulation Study ◽  
Methane Hydrate ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Antifreeze Activity ◽  
Adsorption Inhibition

Antifreeze proteins inhibit hydrate growth by hydrophobic interactions in cooperation with hydrogen bonds. Mutation of three polar amino acids (Asn14, Thr18, and Gln44) elucidates the molecular mechanism of AFP III antifreeze activity.

scholarly journals Probing into Methylene Blue Interaction with Polyglutamic Acid: Spectroscopic and Molecular Dynamics Simulation Studies

2019 ◽  
Vol 31 (9) ◽  
pp. 1949-1958
Author(s):  
Poonam Mishra Chatterjee ◽  
Deepika Pandey Tiwari ◽  
Silpi Datta ◽  
Suman Chakrabarty ◽  
Ritu Raval ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Methylene Blue ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Interaction Mechanism ◽  
Higher Order ◽  
Dynamics Simulation ◽  
Polyglutamic Acid ◽  
Quenching Effect ◽  
Electrostatic And Hydrophobic Interactions

Polyglutamic acid (PGA) is an anionic biopolymer which is stained with methylene blue (MB) in agar or polyacrylamide gels for analysis. Polyglutamic acid identification involves a tedious extraction and analytical process. The molecular association of polyglutamic acid and methylene blue can be used for rapid spectroscopic detection of polyglutamic acid production during fermentation. This triggered the study on investigation of polymer-dye interaction mechanism. Concentration range of polyglutamic acid, 0.001 to 0.06 μM with a fixed methylene blue concentration of 25 μM exhibited significant differences in the spectra. Preferential higher order aggregate formation of methylene blue molecules was substantiated with molecular dynamics simulation results. Fluorescence spectroscopy demonstrated a quenching effect of polyglutamic acid on methylene blue fluorescence until a certain concentration range, beyond which the Stern-Volmer (SV) plot shows a negative deviation. Polyglutamic acid was observed to promote higher order of intramolecular stacking interactions of methylene blue, possibly due to interplay of electrostatic and hydrophobic interactions between polyglutamic acid, methylene blue alone and PGA-MB systems

scholarly journals Molecular dynamics simulation of four-α-helix bundles that bind the anesthetic halothane

FEBS Letters ◽  
2000 ◽  
Vol 478 (1-2) ◽  
pp. 61-66 ◽  
Author(s):  
Lowri A. Davies ◽  
Qingfeng Zhong ◽  
Michael L. Klein ◽  
Daphna Scharf
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Α Helix
Sign in / Sign up

Export Citation Format

Share Document