The molecular mechanism of the catalase reaction

M Alfonso-Prieto, X Biarnés, P Vidossich… - Journal of the …, 2009 - ACS Publications
Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading
hydrogen peroxide to water and oxygen (2H2O2→ 2 H2O+ O2) with high efficiency. The …

Nitroxyl (azanone) trapping by metalloporphyrins

F Doctorovich, D Bikiel, J Pellegrino, SA Suárez… - Coordination Chemistry …, 2011 - Elsevier
The present review starts describing nitroxyl (azanone, 1HNO) biological relevance, in
relation with NO physiology, from a chemical reactivity perspective. After a description of …

Studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis‐Histidine and histidine …

G Zoppellaro, KL Bren, AA Ensign… - Biopolymers …, 2009 - Wiley Online Library
Six‐coordinated heme groups are involved in a large variety of electron transfer reactions
because of their ability to exist in both the ferrous (Fe2+) and ferric (Fe3+) state without any …

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the …

E Papaleo, P Mereghetti, P Fantucci, R Grandori… - Journal of molecular …, 2009 - Elsevier
Several molecular dynamics (MD) simulations were used to sample conformations in the
neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories …

Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle

K Shahrokh, A Orendt, GS Yost… - Journal of …, 2012 - Wiley Online Library
Molecular mechanics (MM) methods are computationally affordable tools for screening
chemical libraries of novel compounds for sites of P450 metabolism. One challenge for MM …

Local energy decomposition of open-shell molecular systems in the domain-based local pair natural orbital coupled cluster framework

A Altun, M Saitow, F Neese… - Journal of chemical theory …, 2019 - ACS Publications
Local energy decomposition (LED) analysis decomposes the interaction energy between
two fragments calculated at the domain-based local pair natural orbital CCSD (T)(DLPNO …

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

NV Di Russo, DA Estrin, MA Martí… - PLoS computational …, 2012 - journals.plos.org
The acid-base behavior of amino acids is an important subject of study due to their
prominent role in enzyme catalysis, substrate binding and protein structure. Due to …

Factors controlling the reactivity of hydrogen sulfide with hemeproteins

R Pietri, A Lewis, RG León, G Casabona, L Kiger… - Biochemistry, 2009 - ACS Publications
Hemoglobin I (HbI) from the clam Lucina pectinata is an intriguing hemeprotein that binds
and transports H2S to sulfide-oxidizing chemoautotrophic bacteria to maintain a symbiotic …

Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study

M Freindorf, E Kraka - Journal of Molecular Modeling, 2020 - Springer
The interplay between FeC and CO bonding in carboxymyoglobin (MbCO) and the role of
potential hydrogen bonding between the CO moiety and the side chains of the surrounding …

Multireference and multiconfiguration ab initio methods in heme-related systems: What have we learned so far?

H Chen, W Lai, S Shaik - The Journal of Physical Chemistry B, 2011 - ACS Publications
This work reviews the recent applications of ab initio multireference/multiconfiguration
(MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and …