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 …
Hemeproteins as targets for sulfide species
FM Boubeta, SA Bieza, M Bringas… - Antioxidants & Redox …, 2020 - liebertpub.com
Significance: Sulfides are endogenous and ubiquitous signaling species that share the
hemeproteins as biochemical targets with O2, nitric oxide, and carbon monoxide. The …
hemeproteins as biochemical targets with O2, nitric oxide, and carbon monoxide. The …
[HTML][HTML] The Role of Host-Generated H2S in Microbial Pathogenesis: New Perspectives on Tuberculosis
MA Rahman, JN Glasgow, S Nadeem… - Frontiers in Cellular …, 2020 - frontiersin.org
For centuries, hydrogen sulfide (H2S) was considered primarily as a poisonous gas and
environmental hazard. However, with the discovery of prokaryotic and eukaryotic enzymes …
environmental hazard. However, with the discovery of prokaryotic and eukaryotic enzymes …
Evolutionary and functional relationships in the truncated hemoglobin family
Predicting function from sequence is an important goal in current biological research, and
although, broad functional assignment is possible when a protein is assigned to a family …
although, broad functional assignment is possible when a protein is assigned to a family …
Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of
allosterism over 60 years ago, with the introduction of the MWC model based on Perutz …
allosterism over 60 years ago, with the introduction of the MWC model based on Perutz …
Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation
A Messias, A Pasquadibisceglie, DA de Armiño… - Journal of Inorganic …, 2023 - Elsevier
Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins
displaying a highly solvent-exposed heme-Fe (III) atom, coordinated by a proximal His …
displaying a highly solvent-exposed heme-Fe (III) atom, coordinated by a proximal His …
[HTML][HTML] Mycobacterium tuberculosis DosS binds H2S through its Fe3+ heme iron to regulate the DosR dormancy regulon
Mycobacterium tuberculosis (Mtb) senses and responds to host-derived gasotransmitters
NO and CO via heme-containing sensor kinases DosS and DosT and the response …
NO and CO via heme-containing sensor kinases DosS and DosT and the response …
QM/MM study of the C—C coupling reaction mechanism of CYP121, an essential Cytochrome p450 of Mycobacterium tuberculosis
VG Dumas, LA Defelipe, AA Petruk… - Proteins: Structure …, 2014 - Wiley Online Library
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding
interest, not only due to its essentiality for bacterial viability but also because it catalyzes an …
interest, not only due to its essentiality for bacterial viability but also because it catalyzes an …
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata
Hydrogen sulfide (H2S) was recently discovered as a gasotransmitter, capable of
coordinating to the heme iron of hemeproteins. H2S is unique for its ability to render varying …
coordinating to the heme iron of hemeproteins. H2S is unique for its ability to render varying …
Molecular mechanism of myoglobin autoxidation: insights from computer simulations
Myoglobin (Mb) and hemoglobin have the biological ability to carry/store oxygen (O2), a
property which requires its heme iron atom to be in the ferrous-Fe (II)-state. However, the …
property which requires its heme iron atom to be in the ferrous-Fe (II)-state. However, the …