Probing flexibility and “induced-fit” phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations

2004 ◽  
Vol 56 (1) ◽  
pp. 52-66 ◽  
Author(s):  
Christoph A. Sotriffer ◽  
Oliver Krämer ◽  
Gerhard Klebe
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Aldose Reductase ◽  
Crystal Structure Analysis ◽  
Induced Fit ◽  
Dynamics Simulations

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations

2017 ◽  
Vol 1865 (11) ◽  
pp. 1406-1415 ◽  
Author(s):  
Bhaskar Sharma ◽  
Sahayog N. Jamdar ◽  
Biplab Ghosh ◽  
Pooja Yadav ◽  
Ashwani Kumar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamics Simulations

Crystal structure analysis of molecular dynamics using synchrotron X-rays

CrystEngComm ◽  
2015 ◽  
Vol 17 (46) ◽  
pp. 8786-8795 ◽  
Author(s):  
Manabu Hoshino ◽  
Shin-ichi Adachi ◽  
Shin-ya Koshihara
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
X Rays ◽  
X Ray ◽  
X Ray Crystallography

X-ray crystallography using synchrotron X-rays enables observation of molecular dynamics in a crystal.

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