Hydrogen bonds: simple after all?

D Herschlag, MM Pinney - Biochemistry, 2018 - ACS Publications
Hydrogen bonds play integral roles in biological structure, function, and conformational
dynamics and are fundamental to life as it has evolved on Earth. However, our …

Low barrier hydrogen bonds in protein structure and function

MT Kemp, EM Lewandowski, Y Chen - Biochimica et Biophysica Acta (BBA) …, 2021 - Elsevier
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is
characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of …

Parallel molecular mechanisms for enzyme temperature adaptation

MM Pinney, DA Mokhtari, E Akiva, F Yabukarski… - Science, 2021 - science.org
INTRODUCTION Over billions of years, organisms and their enzymes have been evolving
and adapting in response to selection pressures from their environments. In particular …

Fluctuations of electric fields in the active site of the enzyme ketosteroid isomerase

VV Welborn, T Head-Gordon - Journal of the American Chemical …, 2019 - ACS Publications
We report the effect of conformational dynamics on the fluctuations of electric fields in the
active site of the enzyme ketosteroid isomerase (KSI). While KSI is considered to be a rigid …

2-Pyridone natural products as inhibitors of SARS-CoV-2 main protease

KL Forrestall, DE Burley, MK Cash, IR Pottie… - Chemico-biological …, 2021 - Elsevier
Abstract The disease, COVID-19, is caused by the severe acute respiratory coronavirus 2
(SARS-CoV-2) for which there is currently no treatment. The SARS-CoV-2 main protease (M …

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

F Yabukarski, T Doukov, MM Pinney, JT Biel… - Science …, 2022 - science.org
Decades of structure-function studies have established our current extensive understanding
of enzymes. However, traditional structural models are snapshots of broader conformational …

Halogen bonding organocatalysis enhanced through intramolecular hydrogen bonds

AMS Riel, DA Decato, J Sun… - Chemical …, 2022 - pubs.rsc.org
Recent results indicate a halogen bond donor is strengthened through direct interaction with
a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond …

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

F Yabukarski, JT Biel, MM Pinney… - Proceedings of the …, 2020 - National Acad Sciences
How enzymes achieve their enormous rate enhancements remains a central question in
biology, and our understanding to date has impacted drug development, influenced enzyme …

High throughput and quantitative enzymology in the genomic era

DA Mokhtari, MJ Appel, PM Fordyce… - Current opinion in …, 2021 - Elsevier
Accurate predictions from models based on physical principles are the ultimate metric of our
biophysical understanding. Although there has been stunning progress toward structure …

Unraveling the structural and chemical features of biological short hydrogen bonds

S Zhou, L Wang - Chemical Science, 2019 - pubs.rsc.org
The three-dimensional architecture of biomolecules often creates specialized structural
elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å …