scholarly journals Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway

2019 ◽  
Author(s):  
Amy E. Fraley ◽  
Kersti Caddell Haatveit ◽  
Ying Ye ◽  
Samantha P. Kelly ◽  
Sean A. Newmister ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Natural Products ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Enzymatic Reactions ◽  
Computational Studies ◽  
Penicillium Simplicissimum ◽  
Dynamics Simulations

<div> <div> <div> <p>The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a ΔphqK strain of Penicillium simplicissimum, and subsequent enzymatic reactions with these compounds generated two additional metabolites paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L was the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides, and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents. </p></div></div><div><div> </div> </div> </div>

scholarly journals Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway

2019 ◽  
Author(s):  
Amy E. Fraley ◽  
Kersti Caddell Haatveit ◽  
Ying Ye ◽  
Samantha P. Kelly ◽  
Sean A. Newmister ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Natural Products ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Enzymatic Reactions ◽  
Computational Studies ◽  
Penicillium Simplicissimum ◽  
Dynamics Simulations

<div> <div> <div> <p>The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a ΔphqK strain of Penicillium simplicissimum, and subsequent enzymatic reactions with these compounds generated two additional metabolites paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L was the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides, and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents. </p></div></div><div><div> </div> </div> </div>

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>

scholarly journals Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations

PLoS ONE ◽  
2011 ◽  
Vol 6 (10) ◽  
pp. e26014 ◽  
Author(s):  
Nagakumar Bharatham ◽  
Seung-Wook Chi ◽  
Ho Sup Yoon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Dynamics Simulations

Molecular-Dynamics Simulations of Granular Axial Segregation in a Rotating Cylinder

1998 ◽  
Vol 12 (04) ◽  
pp. 115-122 ◽  
Author(s):  
Sakamoto Shoichi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Process ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Rotating Cylinder ◽  
Axial Segregation ◽  
Cohesive Forces ◽  
Dynamics Simulations ◽  
Different Diameters ◽  
Narrow Bands

In order to investigate segregation of granular binary-mixtures in a horizontally rotating cylinder, three-dimensional molecular dynamics simulations are carried out. Two kinds of particles, which have different diameters and/or different roughness of surfaces, are segregated into three bands. It is found that particles receive averaged force cohesively at the boundaries of segregated bands. The present analysis shows that segregated narrow bands are formed by diffusion process and that the cohesive forces operating at the boundaries stabilize them.

Molecular Dynamics Simulations of Coupling between Flow and Heat Transfer in a Nanochannel

2012 ◽  
Vol 455-456 ◽  
pp. 155-160
Author(s):  
Zhi Hai Kou ◽  
Min Li Bai
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wall Temperature ◽  
Solid Wall ◽  
Slip Length ◽  
Three Dimensional ◽  
Flow And Heat Transfer ◽  
Kapitza Length ◽  
Dynamics Simulations

Simulation of microscale thermo-fluidic transport has attracted considerable attention in recent years owing to rapid advances in nanoscience and nanotechnology. The three-dimensional molecular dynamics simulations are performed for coupling between flow and heat transfer in a nanochannel. Effects of interface wettability, shear rate and wall temperature are discussed. It is found that there exist the relatively immobile solid-like layers adjacent to each solid wall with higher number density. Both slip length and Kapitza length at the solid-liquid interface increase linearly with the increasing wall temperature. The Kapitza length decreases monotonously with the increasing shear rates. The slip length is found to be overestimated by 5.10% to 10.27%, while Kapitza length is overestimated by 8.92% to 19.09% for the solid-solid interaction modeled by the Lennard-Jones potential.

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