Stability and characterization of the structure II binary clathrate hydrate of the refrigerant trans-1,3,3,3-tetrafluoropropene + methane

2019 ◽  
Vol 43 (33) ◽  
pp. 13068-13074 ◽  
Author(s):  
Kotaro Nemoto ◽  
Takumi Ikeda ◽  
Hiroyuki Mori ◽  
Saman Alavi ◽  
Satoshi Takeya ◽  
...  
Keyword(s):  
Phase Equilibrium ◽  
Md Simulations ◽  
Clathrate Hydrate

A new clathrate hydrate formed with trans-1,3,3,3-tetrafluoropropene and methane was characterized by phase equilibrium and PXRD measurements and MD simulations.

Phase Equilibrium Measurements of Hydrogen−Tetrahydrofuran and Hydrogen−Cyclopentane Binary Clathrate Hydrate Systems

2010 ◽  
Vol 55 (6) ◽  
pp. 2214-2218 ◽  
Author(s):  
Hiroyuki Komatsu ◽  
Hiroki Yoshioka ◽  
Masaki Ota ◽  
Yoshiyuki Sato ◽  
Masaru Watanabe ◽  
...  
Keyword(s):  
Phase Equilibrium ◽  
Clathrate Hydrate

An assessment test for phase equilibrium data of water soluble and insoluble clathrate hydrate formers

2013 ◽  
Vol 360 ◽  
pp. 68-76 ◽  
Author(s):  
Poorandokht Ilani-Kashkouli ◽  
Saeedeh Babaee ◽  
Farhad Gharagheizi ◽  
Hamed Hashemi ◽  
Amir H. Mohammadi ◽  
...  
Keyword(s):  
Phase Equilibrium ◽  
Clathrate Hydrate ◽  
Water Soluble ◽  
Phase Equilibrium Data ◽  
Equilibrium Data

Prediction and characterization of the stability enhancing effect of the Cherry-Tag™ in highly concentrated protein solutions by complex rheological measurements and MD simulations

2017 ◽  
Vol 531 (1) ◽  
pp. 360-371 ◽  
Author(s):  
Pascal Baumann ◽  
Marie-Therese Schermeyer ◽  
Hannah Burghardt ◽  
Cathrin Dürr ◽  
Jonas Gärtner ◽  
...  
Keyword(s):  
Md Simulations ◽  
Protein Solutions ◽  
Enhancing Effect ◽  
Rheological Measurements ◽  
The Stability

scholarly journals Biophysical characterization of the SARS-CoV-2 E protein

2021 ◽  
Author(s):  
Aujan Mehregan ◽  
Sergio Perez-Conesa ◽  
Yuxuan Zhuang ◽  
Ahmad Elbahnsi ◽  
Diletta Pasini ◽  
...  
Keyword(s):  
Recombinant Expression ◽  
Structural Data ◽  
Md Simulations ◽  
Full Length ◽  
Coarse Grained ◽  
Biophysical Characterization ◽  
Viral Budding ◽  
Nmr Structures ◽  
E Protein

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic which continues to wreak havoc across the world, over a year and a half after its effects were first reported in the general media. Current fundamental research efforts largely focus on the SARS-CoV-2 Spike protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length E protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.

scholarly journals Engineering P450 TamI as an Iterative Biocatalyst for Selective Late-Stage C-H Functionalization and Epoxidation of Tirandamycin Antibiotics

2021 ◽  
Author(s):  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
S. Wald Grossman ◽  
Jin Yi Tan ◽  
Caylie A. McGlade ◽  
...  
Keyword(s):  
Natural Product ◽  
Late Stage ◽  
Md Simulations ◽  
Cascade Reactions ◽  
Direct Access ◽  
Tetramic Acid ◽  
Reaction Sequence ◽  
Substrate Reactivity ◽  
Continuous Oxidation

<div> <div> <div> <p>Iterative P450 enzymes are powerful biocatalysts for selective late-stage C-H oxidation of complex natural product scaffolds. These enzymes represent new tools for selectivity and cascade reactions, facilitating direct access to core structure diversification. Recently, we reported the structure of the multifunctional bacterial P450 TamI and elucidated the molecular basis of its substrate binding and strict reaction sequence at distinct carbon atoms of the substrate. Here, we report the design and characterization of a toolbox of TamI biocatalysts, generated by mutations at Leu101, Leu244 and/or Leu295, that alter the native selectivity, step sequence and number of reactions catalyzed, including the engineering of a variant capable of catalyzing a four-step oxidative cascade without the assistance of the flavoprotein and oxidative partner TamL. The tuned enzymes override inherent substrate reactivity enabling catalyst- controlled C-H functionalization and alkene epoxidation of the tetramic acid-containing natural product tirandamycin. Five new, bioactive tirandamycin derivatives (6-10) were generated through TamI-mediated enzymatic synthesis. Quantum mechanics calculations and MD simulations provide important insights on the basis of altered selectivity and underlying biocatalytic mechanisms for enhanced continuous oxidation of the iterative P450 TamI. </p> </div> </div> </div>

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

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