Probing the Hirudin−Thrombin Interaction by Incorporation of Noncoded Amino Acids and Molecular Dynamics Simulation†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (46) ◽  
pp. 13556-13569 ◽  
Author(s):  
Vincenzo De Filippis ◽  
Giorgio Colombo ◽  
Ilaria Russo ◽  
Barbara Spadari ◽  
Angelo Fontana
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

Potent cyclometallated Pd(ii) antitumor complexes bearing α-amino acids: synthesis, structural characterization, DNA/BSA binding, cytotoxicity and molecular dynamics simulation

2020 ◽  
Vol 49 (42) ◽  
pp. 14891-14907
Author(s):  
Sedigheh Abedanzadeh ◽  
Kazem Karami ◽  
Mostafa Rahimi ◽  
Masoud Edalati ◽  
Mozhgan Abedanzadeh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulation ◽  
Structural Characterization ◽  
Dynamics Simulation ◽  
Bsa Binding ◽  
Modeling Studies ◽  
Molecular Modeling Studies ◽  
Antitumor Complexes

Synthesis, characterization, spectroscopic, biological, and molecular modeling studies on the DNA/BSA binding interactions of new cyclometallated Pd(ii) complexes bearing α-amino acids were investigated.

Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation

2011 ◽  
Vol 7 (6) ◽  
pp. 1951-1961 ◽  
Author(s):  
Martina Mangold ◽  
Leslie Rolland ◽  
Francesca Costanzo ◽  
Michiel Sprik ◽  
Marialore Sulpizi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Density Functional ◽  
Dynamics Simulation ◽  
Pka Values ◽  
Solvation Structure

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.

A study of the effect of amino acids on pasting and short-term retrogradation properties of rice starch based on molecular dynamics simulation

2017 ◽  
Vol 69 (9-10) ◽  
pp. 1600238 ◽  
Author(s):  
Jie Wan ◽  
Guohui Zhou ◽  
Shunjing Luo ◽  
Risi Wang ◽  
Chengmei Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Rice Starch ◽  
Short Term

Molecular Dynamics Simulation of Cationic and Anionic Clays Containing Amino Acids

Langmuir ◽  
2002 ◽  
Vol 18 (7) ◽  
pp. 2933-2939 ◽  
Author(s):  
Steven P. Newman ◽  
Tiziana Di Cristina ◽  
Peter V. Coveney ◽  
William Jones
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Anionic Clays

Excess electron reactivity in amino acid aqueous solution revealed by ab initio molecular dynamics simulation: anion-centered localization and anion-relayed electron transfer dissociation

2015 ◽  
Vol 17 (40) ◽  
pp. 26854-26863 ◽  
Author(s):  
Xiuxiu Wu ◽  
Liang Gao ◽  
Jinxiang Liu ◽  
Hongfang Yang ◽  
Shoushan Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Amino Acids ◽  
Electron Transfer ◽  
Molecular Dynamics Simulation ◽  
Electron Transfer Dissociation ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Secondary Electrons ◽  
Acid Aqueous Solution

Radiation-generated secondary electrons can interact with glycine or the backbone parts of amino acids in different modes in aqueous solution.

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