scholarly journals Interplay among the “flipping” glutamine, a conserved phenylalanine, water and hydrogen bonds within a blue-light sensing LOV domain

2020 ◽  
Vol 19 (7) ◽  
pp. 892-904 ◽  
Author(s):  
Eugenia Polverini ◽  
Florian Karl Schackert ◽  
Aba Losi
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Blue Light ◽  
Crucial Role ◽  
Lov Domain ◽  
Light Sensing

A combined photoacoustics and molecular dynamics approach highlights the crucial role of a conserved phenyalanine in photosensing LOV domains.

Mapping the role of aromatic amino acids within a blue-light sensing LOV domain

2021 ◽  
Author(s):  
Yonghong Ding ◽  
Ziyue Zhao ◽  
Jorg Matysik ◽  
Wolfgang Gärtner ◽  
Aba Losi
Keyword(s):  
Amino Acids ◽  
Blue Light ◽  
Aromatic Amino Acids ◽  
Lov Domain ◽  
Light Sensing ◽  
Covalent Adduct

Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of...

scholarly journals From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World

Plants ◽  
2014 ◽  
Vol 3 (1) ◽  
pp. 70-94 ◽  
Author(s):  
Aba Losi ◽  
Carmen Mandalari ◽  
Wolfgang Gärtner
Keyword(s):  
Blue Light ◽  
Growth Patterns ◽  
Light Sensing

scholarly journals Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal–carbon bonding

Nanoscale ◽  
2016 ◽  
Vol 8 (6) ◽  
pp. 3796-3808 ◽  
Author(s):  
Qingming Deng ◽  
Thomas Heine ◽  
Stephan Irle ◽  
Alexey A. Popov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Crucial Role ◽  
Decisive Role ◽  
Endohedral Metallofullerenes ◽  
Dynamics Simulations ◽  
Carbon Bonding

Molecular dynamics simulations of the endohedral metallofullerene formation reveal a crucial role of the cooling gas (He) and the strength of metal–carbon bonding in the formation mechanism.

The crucial role of water in shaping low-barrier hydrogen bonds

2016 ◽  
Vol 18 (7) ◽  
pp. 5521-5528 ◽  
Author(s):  
Michael T. Ruggiero ◽  
Timothy M. Korter
Keyword(s):  
Hydrogen Bonds ◽  
Crucial Role ◽  
Chemical Processes ◽  
Catalytic Applications ◽  
Low Barrier Hydrogen Bonds

Low-barrier hydrogen bonds (LBHBs) are key components in a range of chemical processes, often appearing in metal-mediated catalytic applications.

scholarly journals Molecular Mechanisms on the Selectivity Enhancement of Ascorbic Acid, Dopamine, and Uric Acid by Serine Oligomers Decoration on Graphene Oxide: A Molecular Dynamics Study

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2876
Author(s):  
Threrawee Sanglaow ◽  
Pattanan Oungkanitanon ◽  
Piyapong Asanithi ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Ascorbic Acid ◽  
Uric Acid ◽  
Graphene Oxide ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Simultaneous Detection

The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, and UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, causing a 10-fold increase of hydrogen bonds by the tetraserine adsorption layer. UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies. AA radicals received electrons from serine through hydrogen bonds that promoted oxidation reaction and caused the negative shifts and separation of the oxidation potential in experiments, as DA and UA were less affected by serine. Agreement of the in vitro and in silico results could lead to other in silico designs of selective layers to detect other types of analyte molecules.

scholarly journals Features of Inverted Tetrasulfophenylporphyrin Protonation. Crucial Role of Hydrogen Bonds

2018 ◽  
Vol 11 (4) ◽  
pp. 363-370
Author(s):  
Vladimir B. Sheinin ◽  
Olga M. Kulikova ◽  
Oscar I. Koifman
Keyword(s):  
Hydrogen Bonds ◽  
Crucial Role

Surfactant-Mediated Si/Ge Epitaxial Crystal Growth

1996 ◽  
Vol 448 ◽  
Author(s):  
Eunja Kim ◽  
Chan Wuk OH ◽  
Young Hee Lee
Keyword(s):  
Molecular Dynamics ◽  
Crystal Growth ◽  
Ab Initio ◽  
Crucial Role ◽  
Flat Surface ◽  
Exchange Process ◽  
Epitaxial Crystal Growth

AbstractWe investigate the kinetic role of a surfactant in the epitaxial Si/Ge crystal growth using ab initio molecular dynamics approach. We examine the previously suggested dimer-exchange mechanisms and find that kinetics plays a crucial role in determining the exchange process. We further find that the diffusion of adatoms on an island in the presence of a surfactant is quite different from the dimer-exchange process on a flat surface.

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