Using AMBER18 for relative free energy calculations
With renewed interest in free energy methods in contemporary structure-based drug design,
there is a pressing need to validate against multiple targets and force fields to assess the …
there is a pressing need to validate against multiple targets and force fields to assess the …
Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology
I Geronimo, P Vidossich, E Donati… - Wiley Interdisciplinary …, 2021 - Wiley Online Library
DNA and RNA polymerases (Pols) are central to life, health, and biotechnology because
they allow the flow of genetic information in biological systems. Importantly, Pol function and …
they allow the flow of genetic information in biological systems. Importantly, Pol function and …
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations
are key tools in both improving our understanding of a wide variety of biological processes …
are key tools in both improving our understanding of a wide variety of biological processes …
A self-activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases
The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all
living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here …
living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here …
Exploring the role of the third active site metal ion in DNA polymerase η with QM/MM free energy simulations
DR Stevens, S Hammes-Schiffer - Journal of the American …, 2018 - ACS Publications
The enzyme human DNA polymerase η (Pol η) is critical for bypassing lesions during DNA
replication. In addition to the two Mg2+ ions aligning the active site, experiments suggest …
replication. In addition to the two Mg2+ ions aligning the active site, experiments suggest …
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η
Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell
survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism …
survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism …
The catalytic mechanism of DNA and RNA polymerases
DNA and RNA polymerases (Pols) catalyze nucleic acid biosynthesis in all domains of life,
with implications for human diseases and health. Pols carry out nucleic acid extension …
with implications for human diseases and health. Pols carry out nucleic acid extension …
A strategically located Arg/Lys residue promotes correct base paring during nucleic acid biosynthesis in polymerases
Polymerases (Pols) synthesize the double-stranded nucleic acids in the Watson–Crick (W–
C) conformation, which is critical for DNA and RNA functioning. Yet, the molecular basis to …
C) conformation, which is critical for DNA and RNA functioning. Yet, the molecular basis to …
Basic, translational and clinical relevance of the DNA repair and redox signaling protein APE1 in human diseases
Apurinic/apyrimidinic endonuclease–reduction/oxidation factor 1 (APE1/ref. 1, also called
APE1) is a multifunctional enzyme with essential tasks in DNA repair and …
APE1) is a multifunctional enzyme with essential tasks in DNA repair and …
Structural Rationalization for the Nonmutagenic and Mutagenic Bypass of the Tobacco-Derived O4-4-(3-Pyridyl)-4-oxobut-1-yl-thymine Lesion by Human Polymerase …
P Bhutani, MT Murray, CW Sommer… - Chemical Research …, 2021 - ACS Publications
Tobacco-derived pyridyloxobutyl (POB) DNA adducts are unique due to the large size and
flexibility of the alkyl chain connecting the pyridyl ring to the nucleobase. Recent …
flexibility of the alkyl chain connecting the pyridyl ring to the nucleobase. Recent …