Structural coupling throughout the active site hydrogen bond networks of ketosteroid isomerase and photoactive yellow protein

MM Pinney, A Natarajan, F Yabukarski… - Journal of the …, 2018 - ACS Publications
… by molecular mechanics and quantum mechanics/molecular … bonded protons using the
empirical correlation between … , which is less sensitive to delocalization errors since it includes …

Extreme catalytic power of ketosteroid isomerase related to the reversal of proton dislocations in hydrogen-bond network

P Kędzierski, M Zaczkowska… - The Journal of Physical …, 2020 - ACS Publications
… light protons located in a relatively rigid hydrogen-bond network surrounding an active site
have a chance to be coupled with the enzyme … assumptions related to quantum mechanical/…

Charge density in enzyme active site as a descriptor of electrostatic preorganization

J Fuller III, TR Wilson, ME Eberhart… - Journal of chemical …, 2019 - ACS Publications
catalytic base and the residues forming the hydrogen bond network around the substrate and
catalytic … of the enzyme active site charge density serve as quantum mechanically rigorous …

Proton network flexibility enables robustness and large electric fields in the ketosteroid isomerase active site

L Wang, SD Fried, TE Markland - The Journal of Physical …, 2017 - ACS Publications
… in the enzyme’s active site observed in recent experiments. … quantum fluctuations of the
electrons and nuclei in the active-… delocalization of the protons in the hydrogen-bond network

Low-barrier hydrogen bonds in enzyme cooperativity

S Dai, LM Funk, FR von Pappenheim, V Sautner… - Nature, 2019 - nature.com
… part of charge-relay networks at the active site, and to lower … following the change in the
hydrogen-bond network. For λ = 0 … The plots are consistent with the delocalization observed in …

Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase

S Dajnowicz, JM Parks, X Hu, K Gesler… - Journal of Biological …, 2017 - ASBMB
… of PLP through distinct active site environments. In aspartate … We demonstrate that this
hydrogen bond network directly … pyridinium cation induces electronic delocalization in the PLP…

On the case of the misplaced hydrogens

P Kumar, PK Agarwal, MJ Cuneo - ChemBioChem, 2021 - Wiley Online Library
… of active site causing the solvation of the hydrogen bond to … that of a delocalized charge
system of an LBHB. Thus in an … fluctuations in hydrogen bond due to the nuclear quantum effects …

Hydrogen bonds: simple after all?

D Herschlag, MM Pinney - Biochemistry, 2018 - ACS Publications
… (3) High-level quantum mechanical (QM) calculations gave … can aid hydrogen bond formation,
for example, if active sitedelocalization is necessary to correctly determine at least some …

Hydrogen bond design principles

LJ Karas, CH Wu, R Das, JIC Wu - Wiley Interdisciplinary …, 2020 - Wiley Online Library
… Lukin and Leszynski argued based on extensive quantum … + 2] cyclic π-electron delocalization
(aromaticity gain) in the hydrogen … how charges in enzyme active sites affect catalysis and …

Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme

S Dajnowicz, RC Johnston, JM Parks… - Nature …, 2017 - nature.com
… that the local active site environment of the enzyme promotes … a σ or π-bond are delocalized
into an empty or partially filled … aldimine, the hydrogen bond network spanning from N1-PLP …