The atomic-level understanding of structural and mechanistic details of specific enzymatic targets can aid in the refinement and/or development of drug therapies…
We have developed a comprehensive approach to find and characterize the impact of cancer mutants on any protein, and have applied it to DNA modification enzymes. This approach is an extension of conventional genome wide–association studies (GWAS)…
DNA methylation is an important epigenetic feature that most commonly results in 5-methylcytosine (5mC). The TET2 enzyme mediates the stepwise oxidation of 5mC to 5-carboxylcytosine (5caC) using Fe(II) and α-ketoglutarate as co-substrates…
DNA replication is fast and highly efficient due to the polymerases that carry out this process. DNA Polymerase III (Pol III) is the main replicative polymerase of _E. coli_ composed of over 10 proteins…
The atomic-level understanding of structural and mechanistic details of specific enzymatic targets can aid in the refinement and/or development of drug therapies. Two important targets in SARS-CoV-2 are the Main Protease (MPro) and the RNA directed RNA polymerase (RdRp)…
We will discuss the development of AMOEBA parameters for ionic liquids and water with the use of distributed multipoles derived from the Gaussian Electrostatic Model (GEM), as well as our own molecular density-based GEM model for water including an improved dispersion term, and their implementation…
Xanthine oxidase (XO) is a molybdopterin-containing enzyme that performs the interconversion of xanthine to uric acid within the last step of the purine catabolism in the human body. High blood concentrations of uric acid can lead to gout and hyperuricemia…
DNA Polymerase κ (polκ) is a Y-family polymerase that performs translesion synthesis. While it is recruited during DNA replication to continue past sites of unrepaired damage, the enzyme is understood to have low-fidelity when complexed with undamaged DNA…
We have developed a comprehensive approach to find and characterize the impact of cancer mutants on target proteins, and have applied it to DNA modification enzymes. This approach is an extension of conventional genome wide-association studies (GWAS)…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is the investigation of reaction mechanisms in condensed–phase and biological systems…
DNA Polymerase III of _E. coli_ is a multi-subunit enzyme that efficiently catalyzes the replication of DNA. Four of the subunits termed Pol III* include the polymerase (α) and exonuclease (ε) domain, the clamp (β) and an accessory protein (θ)…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is the investigation of reaction mechanisms in condensed--phase and biological systems…
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family, interconverting xanthine to uric acid as the last step of purine catabolism in the human body. High blood concentrations of uric acid can lead to gout and hyperuricemia…
The archaeo-eukaryotic primase superfamily is a diverse group of enzymes that can carry out replication, repair, and primer synthesis in order to maintain a healthy genome…
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family, interconverting xanthine to uric acid as the last step of purine catabolism in the human body. High blood concentrations of uric acid can lead to gout and hyperuricemia…
The archaeo-eukaryotic primase superfamily is a diverse group of enzymes that can carry out replication, repair, and primer synthesis in order to maintain a healthy genome…
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family, interconverting xanthine to uric acid as the last step of purine catabolism in the human body. High blood concentrations of uric acid can lead to gout and hyperuricemia…
The archaeo-eukaryotic primase superfamily is a diverse group of enzymes that can carry out replication, repair, and primer synthesis in order to maintain a healthy genome…
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family, interconverting xanthine to uric acid as the last step of purine catabolism in the human body. High blood concentrations of uric acid can lead to gout and hyperuricemia…
Lysyl hydroxylase-2 (LH2) is a Fe(II)/alpha-ketoglutarate-dependent oxygenase superfamily member. This enzyme catalyzes the hydroxylation of lysine to hydroxylysine in collagen, which results in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs)…
DNA polymerase γ (Pol γ), the mitochondrial DNA polymerase, plays a critical role in the replication and maintenance of mitochondrial DNA. Mutations in Pol γ have been linked to various diseases…
Mutations caused by single nucleotide polymorphisms (SNPs) have been associated with the development of cancer cells. On the protection of telomeres 1 (POT1), they have been shown to increase the length of telomeres and facilitate the development of melanoma…
Polyketide synthases (PKSs) are a class of large and complex enzymes that are involved in the biosynthesis of various bioactive natural products, which have multiple applications in medicine and agriculture…
Atomistic computational simulations have become a useful tool for biomolecular research. These tools are now becoming sufficiently accurate to quantify possible changes in the electronic environment around an enzyme active site…
DNA polymerases play a crucial role in managing genetic information by facilitating the synthesis of DNA strands with exceptional precision, thus upholding the integrity and stability of the human genetic blueprint…
Horseradish peroxidase (HRP) is an important enzyme for industrial purposes due to its ability to oxidize pollutants from wastewater. A previous report indicated that peroxidases can have up to a 20% increase in enzymatic activity in 0…
Protection of telomeres 1 (POT1) is a protein that plays an essential role in the shelterin complex by binding to the telomere and signaling the end of the chromosome. In our previous work, we demonstrated the effects of 3 melanoma-associated mutations on its ability to bind to ssDNA…
Exposure to reactive oxygen species (ROS) results oxidative DNA damage which induces genome instability and mutations. 8-oxo-7,8-dihydro-guanine (OG) is one of the most common DNA lesions resulting from ROS…