Yashraj Kulkarni
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View article: Structural basis of THC analog activity at the Cannabinoid 1 receptor
Structural basis of THC analog activity at the Cannabinoid 1 receptor Open
View article: Structural basis of Δ9-THC analog activity at the Cannabinoid 1 receptor
Structural basis of Δ9-THC analog activity at the Cannabinoid 1 receptor Open
View article: GproteinDb in 2024: new G protein-GPCR couplings, AlphaFold2-multimer models and interface interactions
GproteinDb in 2024: new G protein-GPCR couplings, AlphaFold2-multimer models and interface interactions Open
G proteins are the major signal proteins of ∼800 receptors for medicines, hormones, neurotransmitters, tastants and odorants. GproteinDb offers integrated genomic, structural, and pharmacological data and tools for analysis, visualization …
View article: A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides
A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides Open
The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymer…
View article: A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides Open
The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymer…
View article: Dual mechanisms by which DNA polymerase epsilon discriminates ribonucleotides
Dual mechanisms by which DNA polymerase epsilon discriminates ribonucleotides Open
Topologies, parameters, and molecular dynamics simulation files to run simulations of the wild-type and M644G variants of DNA Polymerase epsilon bound to deoxyadenosine triphosphate (dATP) and adenosine triphosphate (ATP).
View article: Dual mechanisms by which DNA polymerase epsilon discriminates ribonucleotides
Dual mechanisms by which DNA polymerase epsilon discriminates ribonucleotides Open
Topologies, parameters, and molecular dynamics simulation files to run simulations of the wild-type and M644G variants of DNA Polymerase epsilon bound to deoxyadenosine triphosphate (dATP) and adenosine triphosphate (ATP).
View article: Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems
Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems Open
Proteins are a structurally diverse and functionally versatile class of biomolecules. They perform a variety of life-sustaining biological processes with utmost efficiency. A profound understanding of protein function requires knowledge of…
View article: Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase
Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase Open
We report results of detailed empirical valence bond simulations that model the effect of several amino acid substitutions on the thermodynamic (ΔG°) and kinetic activation (ΔG⧧) barriers to deprotonation of dihydr…
View article: The neutron structure of <i>Leishmania mexicana</i> triose phosphate isomerase with transition state mimics reveals general base catalyst
The neutron structure of <i>Leishmania mexicana</i> triose phosphate isomerase with transition state mimics reveals general base catalyst Open
View article: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε
Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε Open
View article: Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case
Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case Open
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnov…
View article: Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase
Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase Open
We have previously performed empirical valence bond calculations of the kinetic activation barriers, Δ G‡calc, for the deprotonation of complexes between TIM and the whole substrate glyceraldehyde-3-phosphate (GAP, Ku…
View article: Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase Open
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an ex…
View article: Faculty Opinions recommendation of Catalytic scaffolds for phosphoryl group transfer.
Faculty Opinions recommendation of Catalytic scaffolds for phosphoryl group transfer. Open
View article: Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimers disease
Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimers disease Open