Pratul K. Agarwal
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View article: Asymmetric Dynamics Between the Protomers of the σ2 Receptor Homodimer
Asymmetric Dynamics Between the Protomers of the σ2 Receptor Homodimer Open
The sigma-2 receptor (σ2R/TMEM97) is a clinically relevant membrane protein involved in cholesterol regulation and overexpressed in cancer and neurodegenerative diseases. Despite its therapeutic potential, the dynamic mechanisms…
View article: What can we learn from millions of viral genome sequences?
What can we learn from millions of viral genome sequences? Open
What can we learn from millions of viral genome sequences? David Ussery and Pratul Agarwal, Professors in the Department of Physiological Sciences at Oklahoma State University, discuss their work using high-performance computing for the an…
View article: Dynamical Signatures of <i>Thermotoga maritima</i> Maltose-Binding Proteins Affected by Ligand Binding
Dynamical Signatures of <i>Thermotoga maritima</i> Maltose-Binding Proteins Affected by Ligand Binding Open
Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent diff…
View article: APE1 active site residue Asn174 stabilizes the AP site and is essential for catalysis
APE1 active site residue Asn174 stabilizes the AP site and is essential for catalysis Open
View article: A novel non-catalytic function of PA2803-encoded PcrP contributes to polymyxin B resistance in P. aeruginosa and redefines the functional role of the PA2803 subfamily.
A novel non-catalytic function of PA2803-encoded PcrP contributes to polymyxin B resistance in P. aeruginosa and redefines the functional role of the PA2803 subfamily. Open
The opportunistic human pathogen Pseudomonas aeruginosa (Pa), a leading cause of severe infections, becomes increasingly resistant to antibiotics, including the last resort antibiotic, polymyxin-B (PMB). Previous studies have shown that ca…
View article: Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from <i>Burkholderia</i> spp.
Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from <i>Burkholderia</i> spp. Open
Antimicrobial resistance (AMR) is a global threat, with Burkholderia species contributing significantly to difficult-to-treat infections. The Pen family of β-lactamases are produced by all Burkholderia spp., and their mutatio…
View article: Modelling protein-protein interactions for the design of vaccine chimeric antigens with protective epitopes
Modelling protein-protein interactions for the design of vaccine chimeric antigens with protective epitopes Open
Ticks and tick-borne diseases are a growing burden worldwide and vaccines are effective control interventions. Vaccine formulations with tick antigens such as BM86/BM95 (BM) and Subolesin (SUB) have shown reduction in tick fitness and infe…
View article: APE1 active site residue Asn174 stabilizes the AP-site and is essential for catalysis
APE1 active site residue Asn174 stabilizes the AP-site and is essential for catalysis Open
Apurinic/Apyrimidinic (AP)-sites are common and highly mutagenic DNA lesions that can arise spontaneously or as intermediates during Base Excision Repair (BER). The enzyme apurinic/apyrimidinic endonuclease 1 (APE1) initiates repair of AP-…
View article: Dynamic Differences in Clinically relevant Pen β-Lactamases from Burkholderia spp.
Dynamic Differences in Clinically relevant Pen β-Lactamases from Burkholderia spp. Open
Antimicrobial resistance (AMR) is a global threat, with Burkholderia species contributing significantly to difficult-to-treat infections. Ambler Class A Pen β-lactamases are produced by all Burkholderia spp., and their mutation or overprod…
View article: Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases
Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases Open
View article: Author Response: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Author Response: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
Full text Figures and data Side by side Abstract eLife assessment Introduction Results Discussion Materials and methods Data availability References Peer review Author response Article and author information Metrics Abstract The coronaviru…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Joint Public Review: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Joint Public Review: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5' end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2'-O-m…
View article: Author Response: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Author Response: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Pandemic preparedness through genomic surveillance: Overview of mutations in SARS-CoV-2 over the course of COVID-19 outbreak
Pandemic preparedness through genomic surveillance: Overview of mutations in SARS-CoV-2 over the course of COVID-19 outbreak Open
Genomic surveillance is a vital strategy for preparedness against the spread of infectious diseases and to aid in development of new treatments. In an unprecedented effort, millions of samples from COVID-19 patients have been sequenced wor…
View article: Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle Open
Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Identification and modification of dynamical regions in proteins for alteration of enzyme catalytic effect
Identification and modification of dynamical regions in proteins for alteration of enzyme catalytic effect Open
A method for analysis, control, and manipulation for improvement of the chemical reaction rate of a protein-mediated reaction is provided. Enzymes, which typically comprise protein molecules, are very efficient catalysts that enhance chemi…
View article: Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants
Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants Open
Telomere biology disorders (TBDs) are a spectrum of diseases that arise from mutations in genes responsible for maintaining telomere integrity. Human telomerase reverse transcriptase (hTERT) adds nucleotides to chromosome ends and is frequ…
View article: Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance Open
COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate combined with high rates of transmission and fatality can cause a deadly worldwide pandemic in a matter of weeks (Plato et al., 2021). A…
View article: Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases
Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases Open
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 Open
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5’ end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2’-O-m…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16 Open
The data set contains: (1) topology (prmtop), (2) coordinate files to the run the simulation (3) A plumed.dat file (4) COLVAR and (5) HILLS files; (6) Trajectory (xtc) file and (7) corresponding pdb file. The simulations were run as replic…
View article: Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16
Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16 Open
The data set contains: (1) topology (prmtop), (2) coordinate files to the run the simulation (3) A plumed.dat file (4) COLVAR and (5) HILLS files; (6) Trajectory (xtc) file and (7) corresponding pdb file. The simulations were run as replic…
View article: Author response: Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
Author response: Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance Open
Article Figures and data Abstract Editor's evaluation Introduction Materials and methods Results Discussion Data availability References Decision letter Author response Article and author information Metrics Abstract COVID19 has aptly reve…
View article: Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance Open
COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks. 1 Apart from vaccine…
View article: Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1
Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1 Open
View article: Conformational Exchange Divergence Along the Evolutionary Pathway of Eosinophil-Associated Ribonucleases
Conformational Exchange Divergence Along the Evolutionary Pathway of Eosinophil-Associated Ribonucleases Open