Oxygen activation and radical transformations in heme proteins and metalloporphyrins
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply
of metalloproteins for oxidative metabolism and protection against reactive oxygen species …
of metalloproteins for oxidative metabolism and protection against reactive oxygen species …
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” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
Structure and function of haemoglobins
DA Gell - Blood Cells, Molecules, and Diseases, 2018 - Elsevier
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential
for O 2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a …
for O 2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a …
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
P Schmidtke, A Bidon-Chanal, FJ Luque… - Bioinformatics, 2011 - academic.oup.com
Motivation: A variety of pocket detection algorithms are now freely or commercially available
to the scientific community for the analysis of static protein structures. However, since …
to the scientific community for the analysis of static protein structures. However, since …
Modulation of Shigella virulence in response to available oxygen in vivo
Bacteria coordinate expression of virulence determinants in response to localized
microenvironments in their hosts. Here we show that Shigella flexneri, which causes …
microenvironments in their hosts. Here we show that Shigella flexneri, which causes …
QM/MM methods for biological systems
HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
Best practices on QM/MM simulations of biological systems
CM Clemente, L Capece, MA Martí - Journal of Chemical …, 2023 - ACS Publications
During the second half of the 20th century, following structural biology hallmark works on
DNA and proteins, biochemists shifted their questions from “what does this molecule look …
DNA and proteins, biochemists shifted their questions from “what does this molecule look …
Simulation of heme using DFT+ U: A step toward accurate spin-state energetics
DA Scherlis, M Cococcioni, P Sit… - The Journal of Physical …, 2007 - ACS Publications
We investigate the DFT+ U approach as a viable solution to describe the low-lying states of
ligated and unligated iron heme complexes. Besides their central role in organometallic …
ligated and unligated iron heme complexes. Besides their central role in organometallic …
[HTML][HTML] Hemoglobin: a nitric-oxide dioxygenase
PR Gardner - Scientifica, 2012 - hindawi.com
Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and
when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the …
when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the …
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 …
(MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and …