In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

R Verma, K Mitchell-Koch - Catalysts, 2017 - mdpi.com
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in
enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and …

N1019D Mutant of Limosilactobacillus reuteri 121 4,6-α-Glucanotransferase GtfB Significantly Improved Catalytic Activity

N Wang, J Dong, X Li, B Svensson… - Journal of Agricultural …, 2024 - ACS Publications
Limosilactobacillus reuteri 121 4, 6-α-glucanotransferase GtfB (Lr 121 GtfB), belonging to
glycoside hydrolase family 70 (GH70), synthesizes linear isomalto/malto polysaccharides …

Active site desolvation and thermostability trade-offs in the evolution of catalytically diverse triazine hydrolases

E Sugrue, PD Carr, C Scott, CJ Jackson - Biochemistry, 2016 - ACS Publications
The desolvation of ionizable residues in the active sites of enzymes and the subsequent
effects on catalysis and thermostability have been studied in model systems, yet little about …

Metal Binding and Activity of Ribonucleotide Reductase Protein R2 Mutants: Conditions for Formation of the Mixed Manganese− Iron Cofactor

A Popovic-Bijelic, N Voevodskaya, V Domkin… - Biochemistry, 2009 - ACS Publications
Class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (C. tm.) lacks the
tyrosyl radical and uses a Mn (IV)− Fe (III) cluster for cysteinyl radical initiation in the large …

Electrostatic interactions play a significant role in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn2+

C Sepúlveda, A Poch, R Espinoza, E Cardemil - Biochimie, 2010 - Elsevier
Phosphoenolpyruvate (PEP) carboxykinases catalyse the reversible formation of
oxaloacetate (OAA) and ATP (or GTP) from PEP, ADP (or GDP) and CO2. They are activated …

[HTML][HTML] Dissecting the functional roles of the conserved NXXE and HXE motifs of the ADP-dependent glucokinase from Thermococcus litoralis

MJ Abarca-Lagunas, JA Rivas-Pardo… - FEBS letters, 2015 - Elsevier
The activity of the ADP-dependent glucokinase from Thermococcus litoralis (TlGK) relies on
the highly conserved motifs NXXE (ie Asn-Xaa-Xaa-Glu) and HXE (ie His-Xaa-Glu). Site …

Nature of Protein–CO2 Interactions as Elucidated via Molecular Dynamics

ML Drummond, AK Wilson… - The Journal of Physical …, 2012 - ACS Publications
Rising global temperatures require innovative measures to reduce atmospheric
concentrations of CO2. The most successful carbon capture technology on Earth is the …

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

B Valdebenito‐Maturana, JA Reyes‐Suarez… - 2017 - Wiley Online Library
The electrostatic potential plays a key role in many biological processes like determining the
affinity of a ligand to a given protein target, and they are responsible for the catalytic activity …

Cloning and characterization of Chlorobium tepidum ferritin

AE Yevenes, V Marquez, RK Watt - Biochimie, 2011 - Elsevier
The Chlorobium tepidum ferritin (CtFtn) gene was synthesized and cloned into a pET3a
expression vector (Novagen). CtFtn was expressed in Escherichia coli and purified to …

Relevance of phenylalanine 216 in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn(II)

A Yévenes, FD González-Nilo, E Cardemil - The Protein Journal, 2007 - Springer
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase catalyzes the
reversible formation of oxaloacetate and adenosine triphosphate from PEP, adenosine …