The biologically relevant coordination chemistry of iron and nitric oxide: electronic structure and reactivity
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of
physiological and pathological events in biology. Metal coordination chemistry, especially …
physiological and pathological events in biology. Metal coordination chemistry, especially …
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 …
Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity
OmcZ nanowires produced by Geobacter species have high electron conductivity (> 30 S
cm− 1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire …
cm− 1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire …
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 …
Hemoglobins dioxygenate nitric oxide with high fidelity
PR Gardner, AM Gardner, WT Brashear… - Journal of Inorganic …, 2006 - Elsevier
Distantly related members of the hemoglobin (Hb) superfamily including red blood cell Hb,
muscle myoglobin (Mb) and the microbial flavohemoglobin (flavoHb) dioxygenate nitric …
muscle myoglobin (Mb) and the microbial flavohemoglobin (flavoHb) dioxygenate nitric …
Principal components analysis: a review of its application on molecular dynamics data
SAM Stein, AE Loccisano, SM Firestine… - Annual Reports in …, 2006 - Elsevier
Publisher Summary This chapter discusses the need for multivariate analysis in biophysical
studies, presents the way principal components analysis (PCA) can be implemented in the …
studies, presents the way principal components analysis (PCA) can be implemented in the …
Mechanisms of peroxynitrite interactions with heme proteins
J Su, JT Groves - Inorganic chemistry, 2010 - ACS Publications
Oxygenated heme proteins are known to react rapidly with nitric oxide (NO) to produce
peroxynitrite (PN) at the heme site. This process could lead either to attenuation of the …
peroxynitrite (PN) at the heme site. This process could lead either to attenuation of the …
[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 …
GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying
chemical reactivity in complex environments. This paper presents an implementation of …
chemical reactivity in complex environments. This paper presents an implementation of …
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 …