Local electric fields: from enzyme catalysis to synthetic catalyst design

KD Dubey, T Stuyver, S Shaik - The Journal of Physical Chemistry …, 2022 - ACS Publications
This Mini-Review Article outlines recent advances in the study of local electric field (LEF)
governed enzyme catalysis and the application of the LEF principle in synthetic catalyst …

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

J Borišek, J Aupič, A Magistrato - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Ribonucleoprotein (RNP)‐machineries are comprised of intricate networks of long
noncoding RNAs and proteins that allow them to actively participate in transcription, RNA …

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

E McCarthy, Ş Ekesan, TJ Giese, TJ Wilson… - Nucleic acids …, 2023 - academic.oup.com
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from
exogenous O 6-methylguanine (O 6mG) to a target adenine N1, and recently, high …

Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation

ER Cramer, SA Starcovic, RM Avey, AI Kaya… - Communications …, 2023 - nature.com
Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing
chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be …

Biomolecular electrostatic phenomena: An evergreen field

W Yang, W Rocchia - The Journal of Physical Chemistry B, 2023 - ACS Publications
Microscopic electrostatic phenomena are widely studied in biology due to the great
importance they have in describing molecular behavior in aqueous environments …

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

K Nam, Y Shao, DT Major, M Wolf-Watz - ACS omega, 2024 - ACS Publications
Understanding enzyme mechanisms is essential for unraveling the complex molecular
machinery of life. In this review, we survey the field of computational enzymology …

Sequence-specific structural features and solvation properties of transcription factor binding DNA motifs: insights from molecular dynamics simulation

P Patra, YQ Gao - The Journal of Physical Chemistry B, 2022 - ACS Publications
Sequence-specific recognition of transcription factor (TF) binding motifs in the target site of
DNA over the vast amount of non-target DNA is of primary importance for the transcriptional …

Surface-Accelerated String Method for Locating Minimum Free Energy Paths

TJ Giese, S Ekesan, E McCarthy, Y Tao… - Journal of Chemical …, 2024 - ACS Publications
We present a surface-accelerated string method (SASM) to efficiently optimize low-
dimensional reaction pathways from the sampling performed with expensive quantum …

Aplicaciones de la tecnología de aptámeros en los últimos 15 años

AM Rodríguez Ramírez - 2022 - repositorio.uniandes.edu.co
Los aptámeros son cadenas de oligonucleótidos de ARN o ADN elaborados sintéticamente,
que tienen la propiedad de unirse a moléculas objetivo con alta afinidad y especificidad …