Artificial molecular ratchets: Tools enabling endergonic processes

T Sangchai, S Al Shehimy, E Penocchio… - Angewandte Chemie …, 2023 - Wiley Online Library
Non‐equilibrium chemical systems underpin multiple domains of contemporary interest,
including supramolecular chemistry, molecular machines, systems chemistry, prebiotic …

[HTML][HTML] From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

SS Chaturvedi, D Bím, CZ Christov… - Chemical Science, 2023 - pubs.rsc.org
Enzymes are versatile and efficient biological catalysts that drive numerous cellular
processes, motivating the development of enzyme design approaches to tailor catalysts for …

Proton Relay for the Rate Enhancement of Electrochemical Hydrogen Reactions at Heterogeneous Interfaces

Y Qiu, D Ray, L Yan, X Li, M Song… - Journal of the …, 2023 - ACS Publications
Proton transfer is critically important to many electrocatalytic reactions, and directed proton
delivery could open new avenues for the design of electrocatalysts. However, although this …

Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling

S Liang, C Zhang, M Zhu - Journal of Chemical Information and …, 2023 - ACS Publications
Residue-level potentials of mean force were widely used for protein backbone refinements
to avoid simultaneous sampling of side-chain conformations. The interaction energy …

Designing Efficient Enzymes: Eight Predicted Mutations Convert a Hydroxynitrile Lyase into an Efficient Esterase

G Casadevall, CT Pierce, B Guan… - bioRxiv, 2023 - biorxiv.org
Hydroxynitrile lyase from rubber tree (HbHNL) shares 45% identical amino acid residues
with the homologous esterase from tobacco, SABP2, but the two enzymes catalyze different …

NMR and smFRET insights into fast protein motions and their relation to function

P Schanda, G Haran - 2023 - chemrxiv.org
Proteins often undergo large-scale conformational transitions, in which secondary and
tertiary structure elements (loops, helices and domains) change their structures or their …

Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatases

K Zinovjev, P Guénon, CA Ramos-Guzmán… - 2023 - chemrxiv.org
Protein loop dynamics have recently been recognized as central to enzymatic activity,
specificity and stability. However, the factors controlling loop opening and closing kinetics …

Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase

P Roy, Z Walter, L Berish, H Ramage, M McCullagh - bioRxiv, 2023 - biorxiv.org
The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus
replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h …