Direct Observation of Salt Effects on Molecular Interactions through Explicit-Solvent Molecular Dynamics Simulations:  Differential Effects on Electrostatic and Hydrophobic Interactions and Comparisons to Poisson−Boltzmann Theory

2006 ◽  
Vol 128 (24) ◽  
pp. 7796-7806 ◽  
Author(s):  
Andrew S. Thomas ◽  
Adrian H. Elcock
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Direct Observation ◽  
Molecular Interactions ◽  
Hydrophobic Interactions ◽  
Salt Effects ◽  
Explicit Solvent ◽  
Electrostatic And Hydrophobic Interactions ◽  
Poisson Boltzmann ◽  
Dynamics Simulations

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

Direct observation of long chain enrichment in flow-induced nuclei from molecular dynamics simulations of bimodal blends

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2872-2882
Author(s):  
Muhammad Anwar ◽  
Richard S. Graham
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Direct Observation ◽  
Dynamics Simulations ◽  
Long Chain ◽  
Long Chains

Modelling of flow-induced nucleation in polymers suggest that long chains are enriched in nuclei, relative to their melt concentration.

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

2020 ◽  
Vol 22 (15) ◽  
pp. 8021-8034
Author(s):  
Daniel Sadowsky ◽  
J. Samuel Arey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Ionic Solutes

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water.

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