Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP ‐dependent vitamin kinase family members

2021 ◽  
Author(s):  
Felipe Gonzalez‐Ordenes ◽  
Felipe Bravo‐Moraga ◽  
Evelin Gonzalez ◽  
Leslie Hernandez‐Cabello ◽  
Jans Alzate‐Morales ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Epistatic Interaction ◽  
Substrate Binding ◽  
Family Members ◽  
Kinase Family ◽  
Dynamics Simulations

scholarly journals Structural Basis for Selectivity in Flavin-Dependent Monooxygenase-Catalyzed Oxidative Dearomatization

2018 ◽  
Author(s):  
Attabey Rodríguez Benítez ◽  
Sara Tweedy ◽  
Summer A. Baker Dockrey ◽  
April L. Lukowski ◽  
Troy Wymore ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Molecular Dynamics ◽  
Protein Engineering ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
Structural Basis ◽  
Oxidative Dearomatization ◽  
Dynamics Simulations

Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by the first crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data.

scholarly journals Structural Basis for Selectivity in Flavin-Dependent Monooxygenase-Catalyzed Oxidative Dearomatization

2018 ◽  
Author(s):  
Attabey Rodríguez Benítez ◽  
Sara Tweedy ◽  
Summer A. Baker Dockrey ◽  
April L. Lukowski ◽  
Troy Wymore ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Molecular Dynamics ◽  
Protein Engineering ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
Structural Basis ◽  
Oxidative Dearomatization ◽  
Dynamics Simulations

Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by the first crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data.

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

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

scholarly journals [UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations

2015 ◽  
Vol 44 (16) ◽  
pp. 7332-7337 ◽  
Author(s):  
Patrick Woidy ◽  
Michael Bühl ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Bond Strength ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Liquid Ammonia ◽  
Ammonia Solution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dynamics Simulations

X-Ray diffraction and Car–Parrinello molecular dynamics simulations furnish insights into the speciation of uranyl(vi) in liquid ammonia, calling special attention to the effect of solvation on the U–N bond length and bond strength.

Sign in / Sign up

Export Citation Format

Share Document