Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations

ACS Catalysis ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 11404-11412 ◽  
Author(s):  
Fabiola E. Medina ◽  
Maria J. Ramos ◽  
Pedro A. Fernandes
Keyword(s):  
Quantum Mechanics ◽  
Fatty Acid ◽  
Double Bond ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Fatty Acid Synthase ◽  
Molecular Mechanics Calculations

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling

2009 ◽  
Vol 37 (2) ◽  
pp. 363-367 ◽  
Author(s):  
Alessio Lodola ◽  
Marco Mor ◽  
Jitnapa Sirirak ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Fatty Acid ◽  
Molecular Mechanics ◽  
Fatty Acid Amide Hydrolase ◽  
Acid Amide ◽  
Catalytic Triad ◽  
Molecular Mechanics Calculations ◽  
Covalent Inhibitors ◽  
Amide Hydrolase ◽  
Fatty Acid Amide

FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identified the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.

New insights into the stereospecific reduction by an (S) specific carbonyl reductase from Candida parapsilosis ATCC 7330: experimental and QM/MM studies

2020 ◽  
Vol 10 (17) ◽  
pp. 5925-5934 ◽  
Author(s):  
Sneha Sudhakara ◽  
Chandrasekaran Ramakrishnan ◽  
M. Michael Gromiha ◽  
Anju Chadha
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Candida Parapsilosis ◽  
Carbonyl Reductase ◽  
Stereospecific Reduction ◽  
Candida Parapsilosis Atcc 7330 ◽  
Reduction Of Ketones

The quantum mechanics/molecular mechanics study of an (S) specific carbonyl reductase from C. parapsilosis ATCC 7330 showing a dual kinetic response for the reduction of ketones and α-ketoesters suggests different reaction mechanisms for the same.

Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

2020 ◽  
Vol 22 (42) ◽  
pp. 24213-24225
Author(s):  
Masao Yamamoto ◽  
Shin Nakamura ◽  
Takumi Noguchi
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Vibrations ◽  
Molecular Mechanics Calculations ◽  
Water Oxidizing Complex

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

scholarly journals Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme

2014 ◽  
Vol 11 (96) ◽  
pp. 20140090 ◽  
Author(s):  
Elisabeth Ortega-Carrasco ◽  
Agustí Lledós ◽  
Jean-Didier Maréchal
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Resting State ◽  
Structural Features ◽  
Activation Process ◽  
Biological Macromolecules ◽  
The Novel ◽  
Molecular Mechanics Calculations ◽  
Artificial Metalloenzymes ◽  
Artificial Metalloenzyme

In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

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