Exploring the Dynamics of Prolyl-tRNA Synthetases: Towards Developing a Screening Method for Species-Specific Inhibitors

探索脯氨酰-tRNA 合成酶的动力学：开发物种特异性抑制剂的筛选方法

• 批准号: 10797882
• 负责人: Sudeep Bhattacharyay
• 金额: $ 9.99万
• 依托单位: UNIVERSITY OF WISCONSIN EAU CLAIRE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-02-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10797882
• 关键词: Affect; Amino Acid Sequence; Amino Acyl-tRNA Synthetases; Anti-Infective Agents; Architecture; Atomic Force Microscopy; Binding; Biochemistry; Biological Assay; Calorimetry; Catalysis; Cells; Chemicals; Coupling; Crowding; Data; Distant; Docking; Drug Design; Drug Targeting; Educational process of instructing; Electrostatics; Environment; Enzymatic Biochemistry; Enzyme Interaction; Enzyme Kinetics; Enzymes; Equilibrium; Equipment; Escherichia coli; Event; Family; Fluorescence Spectroscopy; Grain; In Vitro; Industrialization; Kinetics; Knowledge; Label; Laboratories; Ligand Binding; Measurement; Mediating; Methods; Modeling; Molecular; Molecular Conformation; NMR Spectroscopy; Nature; Nuclear Magnetic Resonance; Organism; Pathogenicity; Pharmaceutical Preparations; Pharmacologic Substance; Physiological; Play; Polymers; Process; Property; Protein Biosynthesis; Protein Conformation; Protein Dynamics; Protein Engineering; Proteins; Quantum Mechanics; Radiolabeled; Reaction; Regulation; Research; Research Project Grants; Role; Sampling; Shapes; Site; Site-Directed Mutagenesis; Solvents; Structure; Students; System; Tertiary Protein Structure; Thermodynamics; Titrations; Uncertainty; Variant; Work; absorption; antimicrobial drug; biophysical chemistry; design; drug development; drug discovery; enzyme model; enzyme structure; experience; experimental study; flexibility; inhibitor; member; molecular dynamics; molecular mechanics; molecular recognition; novel; pathogen; proline-tRNA; quantum; screening; side effect; simulation; small molecule

Broadly speaking, our research group studies the interplay between enzyme dynamics and catalysis. This supplemental proposal is developed to acquire Isothermal Titration Calorimeter, which will aid in investigating the effects of molecular crowding on enzyme structure-dynamics- functions. The interior of a cell is extremely crowded, which can potentially impact protein properties such as structure, folding, stability, ligand binding, and enzyme catalysis. The crowding effects could mediate through hard/steric/entropic and/or soft/chemical/enthalpic interactions. Our objective is to investigate the exact mechanism of crowding/confinement and their impacts on substrate binding and catalysis. We are studying the multidomain prolyl-tRNA synthetases (ProRSs), which play a vital role in protein synthesis in all living organisms. Earlier, we demonstrated that domain dynamics is central to ProRSs functions, which are impacted by the crowder-induced shift in the conformational ensemble. Currently, the impact of the “uniform crowding environment” (nonprotein-based crowders) and “structured crowding environment” (protein-based crowders) on conformational dynamics and function of Escherichia coli (Ec) ProRS is being probed. The mechanistic implications of crowding and confinement effects are significant as these enzymes are promising anti-microbial drug targets. The conformational change and crowder-enzyme interactions are being probed by fluorescence spectroscopy, molecular dynamics simulations, and small molecule docking studies, while varying the size, shape, chemical nature, and concentration of the crowders. We are examining the role of molecular crowders on the substrate binding using Saturation Transfer Difference - Nuclear Magnetic Resonance, which requires a large quantity of proteins and kinetics parameters are obtained from enzyme kinetics assays using radiolabeled substrates. The isothermal titration calorimetry (ITC) method is a label-free direct measurement of the heat evolved or absorbed during a binding event between interacting molecules and enzyme-catalyzed reactions and requires less sample. ITC experiments provide the thermodynamic profiles, which would enable us to establish the molecular mechanism of crowding and confinement resulting in enzyme's altered function. A detailed understanding of crowding effects on the properties of multidomain proteins like Ec ProRS could open up new possibilities for protein designing and drug discovery. Moreover, the ITC equipment would enable us to provide hands-on experiences to students in biochemistry and biophysical chemistry courses (~25 students/semester) by designing course-embedded research projects on calorimetry and teaching them the ligand binding thermodynamics in drug discovery.

一般来说，我们的研究小组研究酶动力学和

项目成果

Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review.

• DOI: 10.1007/s10930-020-09935-8
• 发表时间: 2020-12
• 期刊: The protein journal
• 作者: Suhail S;Zajac J;Fossum C;Lowater H;McCracken C;Severson N;Laatsch B;Narkiewicz-Jodko A;Johnson B;Liebau J;Bhattacharyya S;Hati S
• 通讯作者: Hati S

Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations.

• DOI: 10.1021/acscatal.8b04193
• 发表时间: 2018-11
• 期刊: ACS catalysis
• 影响因子: 12.9
• 作者: Clorice R. Reinhardt;Quin H. Hu;Caitlin G. Bresnahan;S. Hati;S. Bhattacharyya

Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.

• DOI: 10.1021/acscatal.0c02381
• 发表时间: 2020-09-04
• 期刊: ACS catalysis
• 影响因子: 12.9
• 作者: Hu QH;Williams MT;Shulgina I;Fossum CJ;Weeks KM;Adams LM;Reinhardt CR;Musier-Forsyth K;Hati S;Bhattacharyya S
• 通讯作者: Bhattacharyya S

Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations.

• DOI: 10.1007/s10930-022-10065-6
• 发表时间: 2022-10
• 期刊: PROTEIN JOURNAL
• 影响因子: 3
• 作者: Wozney, Alec J.;Smith, Macey A.;Abdrabbo, Mobeen;Birch, Cole M.;Cicigoi, Kelsey A.;Dolan, Connor C.;Gerzema, Audrey E. L.;Hansen, Abby;Henseler, Ethan J.;LaBerge, Ben;Leavens, Caterra M.;Le, Christine N.;Lindquist, Allison C.;Ludwig, Rikaela K.;O'Reilly, Maggie G.;Reynolds, Jacob H.;Sherman, Brandon A.;Sillman, Hunter W.;Smith, Michael A.;Snortheim, Marissa J.;Svaren, Levi M.;Vanderpas, Emily C.;Voon, Aidan;Wackett, Miles J.;Weiss, Moriah M.;Hati, Sanchita;Bhattacharyya, Sudeep
• 通讯作者: Bhattacharyya, Sudeep

Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase.

• DOI: 10.1007/s10930-020-09910-3
• 发表时间: 2020-10
• 期刊: The protein journal
• 作者: Zajac J;Anderson H;Adams L;Wangmo D;Suhail S;Almen A;Berns L;Coerber B;Dawson L;Hunger A;Jehn J;Johnson J;Plack N;Strasser S;Williams M;Bhattacharyya S;Hati S
• 通讯作者: Hati S