Results 41 to 50 of about 81,085 (254)

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

AUGUR, a flexible and efficient optimization algorithm for identification of optimal adsorption sites

npj Computational Materials
In this paper, we propose a novel flexible optimization pipeline for determining the optimal adsorption sites, named AUGUR (Aware of Uncertainty Graph Unit Regression). Our model combines graph neural networks and Gaussian processes to create a flexible,
Ioannis Kouroudis, Poonam, Neel Misciasci, Felix Mayr, Leon Müller, Zhaosu Gu, Alessio Gagliardi   +6 more
doaj   +1 more source

Efficient Atomistic Simulation of Heterostructure Field-Effect Transistors

IEEE Journal of the Electron Devices Society, 2019
In this paper, atomistic-level quantum mechanical simulations are performed for nanoscale field-effect transistors (FETs) with lateral or vertical heterojunction, within the non-equilibrium Green's function formalism.
Yongsoo Ahn, Mincheol Shin
doaj   +1 more source

Efficient potential of mean force calculation from multiscale simulations: solute insertion in a lipid membrane

, 2017
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues.
Bereau, Tristan, Kremer, Kurt, Menichetti, Roberto   +2 more
core   +1 more source

C2α‐carbanion‐protonating glutamate discloses tradeoffs between substrate accommodation and reaction rate in actinobacterial 2‐hydroxyacyl‐CoA lyase

FEBS Open Bio, EarlyView.
Enzymes of the 2‐hydroxyacyl‐CoA lyase group catalyze the condensation of formyl‐CoA with aldehydes or ketones. Thus, by structural adaptation of active sites, practically any pharmaceutically and industrially important 2‐hydroxyacid could be biotechnologically synthesized. Combining crystal structure analysis, active site mutations and kinetic assays,
Michael Zahn, Barbara Seroka, Ryszard Lazny, Zenon Lotowski, Thore Rohwerder   +4 more
wiley   +1 more source

Molecular dynamic simulation study on interaction mechanism between biopolymer and kaolinite [PDF]

E3S Web of Conferences
The mining industry produces enormous amounts of waste annually. These wastes – mine tailings – predominantly consist of clay size particles with the major clay mineral being kaolinite.
Chandregowda Shreyas Aralumallige, Bhatia Shobha K., Palomino Angelica M.   +2 more
doaj   +1 more source

Coordination polymer design for fast proton conduction: Hybrid atomistic approach based on kinetic Monte Carlo and molecular dynamics methods

Materials & Design, 2022
Fast proton conductors are important materials for catalysis and energy conversion applications. The glassy coordination polymers are an important class of proton conductors due to their good mechanical moldability; however, their conductivity has been ...
Albert M. Iskandarov, Tomofumi Tada
doaj   +1 more source

A light‐triggered Time‐Resolved X‐ray Solution Scattering (TR‐XSS) workflow with application to protein conformational dynamics

FEBS Open Bio, EarlyView.
Time‐resolved X‐ray solution scattering captures how proteins change shape in real time under near‐native conditions. This article presents a practical workflow for light‐triggered TR‐XSS experiments, from data collection to structural refinement. Using a calcium‐transporting membrane protein as an example, the approach can be broadly applied to study ...
Fatemeh Sabzian‐Molaei, Fredrik Orädd, Konstantinos Magkakis, Magnus Andersson   +3 more
wiley   +1 more source

Investigating Interactions of Biomembranes and Alcohols: A Multiscale Approach

, 2004
We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer.
Adachi, Ayton, Balali-Mood, Bandyopadhyay, Bemporad, Berendsen, Berendsen, Berger, Bisson, Cramer, de Vries, Essmann, Falck, Faller, Feller, Feller, Goetz, Guo, Gurtovenko, Husslein, Kranenburg, Lee, Leontiadou, Lindahl, Ly, Ly, Marrink, Marrink, Mashl, Mou, Mouritsen, Müller, Nagle, Pandit, Pandit, Patra, Patra, Patra, Pereira, Rog, Saiz, Shelley, Smit, Smondryev, Smondryev, Soddemann, Sum, Sum, Tieleman, Tobias, Tu   +50 more
core   +1 more source

Chameleon sequences reveal structural effects in proteins representing micelle‐like distribution of hydrophobicity

FEBS Open Bio, EarlyView.
Amino acids sequence of two different proteins with the same sequence (chameleon sequence—black boxes) represent in 3D structure of the proteins different secondary structures: HHHH—helical and BBB—Beta‐structural. The chains folded in water environment adopt different III‐order structures in which the chameleon fragments appear to adopt similar status
Irena Roterman, Katarzyna Stapor, Leszek Konieczny, Krzysztof Gądek, Piotr Nowakowski   +4 more
wiley   +1 more source