QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

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 …

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

G Jindal, A Warshel - The Journal of Physical Chemistry B, 2016 - ACS Publications
Although QM/MM calculations are the primary current tool for modeling enzymatic reactions,
the reliability of such calculations can be limited by the size of the QM region. Thus, we …

Sarcosine as a potential prostate cancer biomarker—A review

N Cernei, Z Heger, J Gumulec, O Zitka… - International journal of …, 2013 - mdpi.com
Prostate cancer (CaP) is the most common type of tumour disease in men. Early diagnosis of
cancer of the prostate is very important, because the sooner the cancer is detected, the …

Conservation and functional importance of carbon–oxygen hydrogen bonding in AdoMet-dependent methyltransferases

S Horowitz, LMA Dirk, JD Yesselman… - Journal of the …, 2013 - ACS Publications
S-Adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling.
AdoMet-dependent methyltransferases belong to multiple distinct classes and share a …

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

J Lameira, RP Bora, ZT Chu… - … : Structure, Function, and …, 2015 - Wiley Online Library
The enzyme catechol O‐methyltransferase (COMT) catalyzes the transfer of a methyl group
from S‐adenosylmethionine to dopamine and related catechols. The search for the origin of …

Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling

K Swiderek, I Tuñón, IH Williams… - Journal of the American …, 2018 - ACS Publications
The origin of enzyme catalysis remains a question of debate despite much intense study. We
report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine …

QM/MM‐Methoden für biomolekulare Systeme

HM Senn, W Thiel - Angewandte Chemie, 2009 - Wiley Online Library
Quantenmechanische/molekülmechanische (QM/MM‐) Verfahren sind die Methode der
Wahl für die theoretische Behandlung reaktiver oder anderer elektronischer Prozesse in …

High‐throughput computational investigation of protein electrostatics and cavity for SAM‐dependent methyltransferases

C Jurich, ZJ Yang - Protein Science, 2023 - Wiley Online Library
Abstract S‐adenosyl methionine (SAM)–dependent methyl transferases (MTases) are a
ubiquitous class of enzymes catalyzing dozens of essential life processes. Despite targeting …

Structure and Reaction Mechanism of Phosphoethanolamine Methyltransferase from the Malaria Parasite Plasmodium falciparum: AN ANTIPARASITIC DRUG …

SG Lee, Y Kim, TD Alpert, A Nagata, JM Jez - Journal of Biological …, 2012 - ASBMB
In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine
methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to …