Search Results - "Agarwal, Pratul K."

A Biophysical Perspective on Enzyme Catalysis by Agarwal, Pratul K

“…Even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to…”
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Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis by Ramanathan, Arvind, Agarwal, Pratul K

“…Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure…”
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AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop by Hoitsma, Nicole M, Whitaker, Amy M, Beckwitt, Emily C, Jang, Sunbok, Agarwal, Pratul K, Van Houten, Bennett, Freudenthal, Bret D

“…Abstract Base excision repair (BER) maintains genomic stability through the repair of DNA damage. Within BER, AP-endonuclease 1 (APE1) is a multifunctional…”
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Protein Conformational Populations and Functionally Relevant Substates by Ramanathan, Arvind, Savol, Andrej, Burger, Virginia, Chennubhotla, Chakra S, Agarwal, Pratul K

“…Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein…”
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Role of Protein Dynamics in Reaction Rate Enhancement by Enzymes by Agarwal, Pratul K

“…An integrated view of protein structure, dynamics, and function is emerging, where proteins are considered as dynamically active assemblies and internal…”
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Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics by Galdadas, Ioannis, Qu, Shen, Oliveira, Ana Sofia F, Olehnovics, Edgar, Mack, Andrew R, Mojica, Maria F, Agarwal, Pratul K, Tooke, Catherine L, Gervasio, Francesco Luigi, Spencer, James, Bonomo, Robert A, Mulholland, Adrian J, Haider, Shozeb

“…Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of…”
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Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1 by Weaver, Tyler M., Click, Timothy H., Khoang, Thu H., Todd Washington, M., Agarwal, Pratul K., Freudenthal, Bret D.

“…Rev1 is a translesion DNA synthesis (TLS) polymerase involved in the bypass of adducted-guanine bases and abasic sites during DNA replication. During damage…”
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Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics by Shukla, Shantanu, Bafna, Khushboo, Gullett, Caeley, Myles, Dean A. A, Agarwal, Pratul K, Cuneo, Matthew J

“…The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-,…”
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Nucleotide substrate binding characterization in human pancreatic-type ribonucleases by Bafna, Khushboo, Narayanan, Chitra, Chennubhotla, S Chakra, Doucet, Nicolas, Agarwal, Pratul K

“…Human genome contains a group of more than a dozen similar genes with diverse biological functions including antiviral, antibacterial and angiogenesis…”
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Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance by Najar, Fares Z, Linde, Evan, Murphy, Chelsea L, Borin, Veniamin A, Wang, Huan, Haider, Shozeb, Agarwal, Pratul K

“…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…”
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Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 by Wang, Huan, Rizvi, Syed R A, Dong, Danni, Lou, Jiaqi, Wang, Qian, Sopipong, Watanyoo, Su, Yufeng, Najar, Fares, Agarwal, Pratul K, Kozielski, Frank, Haider, Shozeb

“…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…”
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Enzymes: An integrated view of structure, dynamics and function by Agarwal, Pratul K

“…Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past,…”
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Discovering conformational sub-states relevant to protein function by Ramanathan, Arvind, Savol, Andrej J, Langmead, Christopher J, Agarwal, Pratul K, Chennubhotla, Chakra S

“…Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the…”
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SARS-CoV-2 Genomes From Oklahoma, United States by Narayanan, Sai, Ritchey, John C, Patil, Girish, Narasaraju, Teluguakula, More, Sunil, Malayer, Jerry, Saliki, Jeremiah, Kaul, Anil, Agarwal, Pratul K, Ramachandran, Akhilesh

“…Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current…”
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Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker by Hoitsma, Nicole M., Click, Timothy H., Agarwal, Pratul K., Freudenthal, Bret D.

“…[Display omitted] Ribonucleotides (rNTPs) are predicted to be incorporated into the genome at a rate of up to 3 million times per cell division, making rNTPs…”
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Network of Coupled Promoting Motions in Enzyme Catalysis by Agarwal, Pratul K., Billeter, Salomon R., P. T. Ravi Rajagopalan, Benkovic, Stephen J., Hammes-Schiffer, Sharon

“…A network of coupled promoting motions in the enzyme dihydrofolate reductase is identified and characterized. The present identification is based on genomic…”
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Myelin Basic Protein Phospholipid Complexation Likely Competes with Deimination in Experimental Autoimmune Encephalomyelitis Mouse Model by Valdivia, Anddre Osmar, Agarwal, Pratul K, Bhattacharya, Sanjoy K

“…Multiple sclerosis has complex pathogenesis encompassing a variety of components (immunologic, genetic, and environmental). The autoimmunogenicity against the…”
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Electrostatic Switching Controls Channel Dynamics of the Sensor Protein VirB10 in A. tumefaciens Type IV Secretion System by Darbari, Vidya Chandran, Ciccone, Jonah, Patel, Jagdish Suresh, Islam, Barira, Agarwal, Pratul K, Haider, Shozeb

“…Type IV secretion systems are large nanomachines assembled across the bacterial cell envelope for effector translocation and conjugation. VirB10 traverses the…”
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Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily by Narayanan, Chitra, Bernard, David N, Bafna, Khushboo, Gagné, Donald, Agarwal, Pratul K, Doucet, Nicolas

“…Enzyme catalysis is a complex process involving several steps along the reaction coordinates, including substrate recognition and binding, chemical…”
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Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis by Agarwal, Pratul K, Billeter, Salomon R, Hammes-Schiffer, Sharon

“…Mixed quantum/classical molecular dynamics simulations of the hydride transfer reaction catalyzed by dihydrofolate reductase are presented. The nuclear quantum…”
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