1
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Tran TTQ, Narayanan C, Loes AN, Click TH, Pham NTH, Létourneau M, Harms MJ, Calmettes C, Agarwal PK, Doucet N. Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases. J Biol Chem 2024:107280. [PMID: 38588810 DOI: 10.1016/j.jbc.2024.107280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024] Open
Abstract
Evolutionarily conserved structural folds can give rise to diverse biological functions, yet predicting atomic-scale interactions that contribute to the emergence of novel activities within such folds remains challenging. Pancreatic-type ribonucleases illustrate this complexity, sharing a core structure that has evolved to accommodate varied functions. In this study, we used ancestral sequence reconstruction to probe evolutionary and molecular determinants that distinguish biological activities within eosinophil members of the RNase 2/3 subfamily. Our investigation unveils functional, structural, and dynamical behaviors that differentiate the evolved ancestor AncRNase from its contemporary eosinophil RNase orthologs. Leveraging the potential of ancestral reconstruction for protein engineering, we used AncRNase predictions to design a minimal 4-residue variant that transforms human RNase 2 into a chimeric enzyme endowed with the antimicrobial and cytotoxic activities of RNase 3 members. This work provides unique insights into mutational and evolutionary pathways governing structure, function, and conformational states within the eosinophil RNase subfamily, offering potential for targeted modulation of RNase-associated functions.
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Affiliation(s)
- Thi Thanh Quynh Tran
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Chitra Narayanan
- Department of Chemistry, York College, City University of New York (CUNY), Jamaica, Queens, NY, USA
| | - Andrea N Loes
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Timothy H Click
- Chemistry and Biochemistry, University of Mary, Bismarck, ND, USA
| | - N T Hang Pham
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Michael J Harms
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Charles Calmettes
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC, Canada; PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, UQAM, Montréal, QC, Canada
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK, USA
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC, Canada; PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, UQAM, Montréal, QC, Canada.
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2
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Wang H, Rizvi SRA, Dong D, Lou J, Wang Q, Sopipong W, Su Y, Najar F, Agarwal PK, Kozielski F, Haider S. Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16. eLife 2023; 12:RP87884. [PMID: 38127066 PMCID: PMC10735223 DOI: 10.7554/elife.87884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
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-methyltransferase and NSP14 through its N7 methyltransferase activity, which are essential for the replication of the viral genome as well as evading the host's innate immunity. NSP10 acts as a crucial cofactor and stimulator of NSP14 and NSP16. To further understand the role of NSP10, we carried out a comprehensive analysis of >13 million globally collected whole-genome sequences (WGS) of SARS-CoV-2 obtained from the Global Initiative Sharing All Influenza Data (GISAID) and compared it with the reference genome Wuhan/WIV04/2019 to identify all currently known variants in NSP10. T12I, T102I, and A104V in NSP10 have been identified as the three most frequent variants and characterized using X-ray crystallography, biophysical assays, and enhanced sampling simulations. In contrast to other proteins such as spike and NSP6, NSP10 is significantly less prone to mutation due to its crucial role in replication. The functional effects of the variants were examined for their impact on the binding affinity and stability of both NSP14-NSP10 and NSP16-NSP10 complexes. These results highlight the limited changes induced by variant evolution in NSP10 and reflect on the critical roles NSP10 plays during the SARS-CoV-2 life cycle. These results also indicate that there is limited capacity for the virus to overcome inhibitors targeting NSP10 via the generation of variants in inhibitor binding pockets.
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Affiliation(s)
- Huan Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Syed RA Rizvi
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Danni Dong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Jiaqi Lou
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Qian Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Watanyoo Sopipong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Yufeng Su
- College of Engineering, Design and Physical Sciences, Brunel University LondonUxbridgeUnited Kingdom
| | - Fares Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
- UCL Centre for Advanced Research Computing, University College LondonLondonUnited Kingdom
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3
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Bernard DN, Narayanan C, Hempel T, Bafna K, Bhojane PP, Létourneau M, Howell EE, Agarwal PK, Doucet N. Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases. Structure 2023; 31:329-342.e4. [PMID: 36649708 PMCID: PMC9992247 DOI: 10.1016/j.str.2022.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/24/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]
Abstract
The evolutionary role of conformational exchange in the emergence and preservation of function within structural homologs remains elusive. While protein engineering has revealed the importance of flexibility in function, productive modulation of atomic-scale dynamics has only been achieved on a finite number of distinct folds. Allosteric control of unique members within dynamically diverse structural families requires a better appreciation of exchange phenomena. Here, we examined the functional and structural role of conformational exchange within eosinophil-associated ribonucleases. Biological and catalytic activity of various EARs was performed in parallel to mapping their conformational behavior on multiple timescales using NMR and computational analyses. Despite functional conservation and conformational seclusion to a specific domain, we show that EARs can display similar or distinct motional profiles, implying divergence rather than conservation of flexibility. Comparing progressively more distant enzymes should unravel how this subfamily has evolved new functions and/or altered their behavior at the molecular level.
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Affiliation(s)
- David N Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; Department of Chemistry, New Jersey City University, Jersey City, NJ 07305, USA
| | - Tim Hempel
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany; Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Khushboo Bafna
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Purva Prashant Bhojane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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4
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Najar FZ, Linde E, Murphy CL, Borin VA, Wang H, Haider S, Agarwal PK. Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance. eLife 2023; 12:82980. [PMID: 36655992 PMCID: PMC9894583 DOI: 10.7554/elife.82980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
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). Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections ('surges') before they occur. We describe here real-time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.
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Affiliation(s)
- Fares Z Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Evan Linde
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Chelsea L Murphy
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Veniamin A Borin
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Huan Wang
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
- University College London Centre for Advanced Research ComputingLondonUnited Kingdom
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
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5
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Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chem Sci 2022; 13:13303-13320. [PMID: 36507176 PMCID: PMC9683017 DOI: 10.1039/d2sc05031e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Simon P. Webb
- VeraChem LLC12850 Middlebrook Rd. Ste 205GermantownMD 20874-5244USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterOK 74078USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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6
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Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD. Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nat Commun 2022; 13:2876. [PMID: 35610266 PMCID: PMC9130138 DOI: 10.1038/s41467-022-30577-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022] Open
Abstract
Rev1 is a translesion DNA synthesis (TLS) polymerase involved in the bypass of adducted-guanine bases and abasic sites during DNA replication. During damage bypass, Rev1 utilizes a protein-template mechanism of DNA synthesis, where the templating DNA base is evicted from the Rev1 active site and replaced by an arginine side chain that preferentially binds incoming dCTP. Here, we utilize X-ray crystallography and molecular dynamics simulations to obtain structural insight into the dCTP specificity of Rev1. We show the Rev1 R324 protein-template forms sub-optimal hydrogen bonds with incoming dTTP, dGTP, and dATP that prevents Rev1 from adopting a catalytically competent conformation. Additionally, we show the Rev1 R324 protein-template forms optimal hydrogen bonds with incoming rCTP. However, the incoming rCTP adopts an altered sugar pucker, which prevents the formation of a catalytically competent Rev1 active site. This work provides novel insight into the mechanisms for nucleotide discrimination by the TLS polymerase Rev1.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
| | - Timothy H Click
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma, 74048, USA
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
| | - M Todd Washington
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma, 74048, USA.
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA. .,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
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7
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Galdadas I, Qu S, Oliveira ASF, Olehnovics E, Mack AR, Mojica MF, Agarwal PK, Tooke CL, Gervasio FL, Spencer J, Bonomo RA, Mulholland AJ, Haider S. Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics. eLife 2021; 10:e66567. [PMID: 33755013 PMCID: PMC8060031 DOI: 10.7554/elife.66567] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover, and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.
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Affiliation(s)
- Ioannis Galdadas
- University College London, Department of ChemistryLondonUnited Kingdom
| | - Shen Qu
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Ana Sofia F Oliveira
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Edgar Olehnovics
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Andrew R Mack
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
| | - Maria F Mojica
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Catherine L Tooke
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Francesco Luigi Gervasio
- University College London, Department of ChemistryLondonUnited Kingdom
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
- University of Geneva, Pharmaceutical SciencesGenevaSwitzerland
| | - James Spencer
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Robert A Bonomo
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
- Case Western Reserve University, Department of BiochemistryClevelandUnited States
- Case Western Reserve University, Department of PharmacologyClevelandUnited States
- Case Western Reserve University, Department of Proteomics and BioinformaticsClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
| | - Adrian J Mulholland
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
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8
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Narayanan S, Ritchey JC, Patil G, Narasaraju T, More S, Malayer J, Saliki J, Kaul A, Agarwal PK, Ramachandran A. SARS-CoV-2 Genomes From Oklahoma, United States. Front Genet 2021; 11:612571. [PMID: 33613621 PMCID: PMC7886813 DOI: 10.3389/fgene.2020.612571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/31/2020] [Indexed: 11/13/2022] Open
Abstract
Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study, we sequenced SARS-CoV-2 from five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.
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Affiliation(s)
- Sai Narayanan
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - John C. Ritchey
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Girish Patil
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Teluguakula Narasaraju
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Sunil More
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jerry Malayer
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jeremiah Saliki
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Anil Kaul
- Center for Health Sciences, Oklahoma State University, Tulsa, OK, United States
| | - Pratul K. Agarwal
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- High-Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
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9
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Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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10
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Babajide R, Labbate C, Saoud R, Agarwal PK. Early Experience with Intravesical Gemcitabine-Docetaxel for BCG-Naïve Patients with High Grade Non-Muscle Invasive Bladder Cancer. Urol Oncol 2020. [DOI: 10.1016/j.urolonc.2020.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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12
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Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD. AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop. Nucleic Acids Res 2020; 48:7345-7355. [PMID: 32542366 PMCID: PMC7367167 DOI: 10.1093/nar/gkaa496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023] Open
Abstract
Base excision repair (BER) maintains genomic stability through the repair of DNA damage. Within BER, AP-endonuclease 1 (APE1) is a multifunctional enzyme that processes DNA intermediates through its backbone cleavage activity. To accomplish these repair activities, APE1 must recognize and accommodate several diverse DNA substrates. This is hypothesized to occur through a DNA sculpting mechanism where structural adjustments of the DNA substrate are imposed by the protein; however, how APE1 uniquely sculpts each substrate within a single rigid active site remains unclear. Here, we utilize structural and biochemical approaches to probe the DNA sculpting mechanism of APE1, specifically by characterizing a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop). Pre-steady-state kinetics reveal a tyrosine residue within the intercalating loop (Y269) that is critical for AP-endonuclease activity. Using X-ray crystallography and molecular dynamics simulations, we determined the Y269 residue acts to anchor the intercalating loop on abasic DNA. Atomic force microscopy reveals the Y269 residue is required for proper DNA bending by APE1, providing evidence for the importance of this mechanism. We conclude that this previously unappreciated tyrosine residue is key to anchoring the intercalating loop and stabilizing the DNA in the APE1 active site.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA.,Laboratory of DNA Replication, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sunbok Jang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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13
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Valdivia A, Agarwal PK, Bhattacharya SK. Myelin Basic Protein Phospholipid Complexation Likely Competes with Deimination in Experimental Autoimmune Encephalomyelitis Mouse Model. ACS Omega 2020; 5:15454-15467. [PMID: 32637820 PMCID: PMC7331039 DOI: 10.1021/acsomega.0c01590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Multiple sclerosis has complex pathogenesis encompassing a variety of components (immunologic, genetic, and environmental). The autoimmunogenicity against the host's myelin basic protein is a major contributor. An increase in myelin basic protein deimination (a post-translational modification) and a change in phospholipid composition have been associated with multiple sclerosis. The interaction of myelin basic protein with phospholipids in the myelin membrane is an important contributor to the stability and maintenance of proper myelin sheath function. The study of this aspect of multiple sclerosis is an area that has yet to be fully explored and that the present study seeks to understand. Several biochemical methods, a capillary electrophoresis coupled system and mass spectrometry, were used in this study. These methods identified four specific phospholipids complexing with myelin basic protein. We show that lysophosphatidylcholine 18:1 provides a robust competitive effect against hyper-deimination. Our data suggest that lysophosphatidylcholine 18:1 has a different biochemical behavior when compared to other phospholipids and lysophosphatidylcholines 14:0, 16:0, and 18:0.
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Affiliation(s)
- Anddre
Osmar Valdivia
- Department
of Ophthalmology, Bascom Palmer Eye Institute, University of Miami, Miami, Florida 33136, United States
- Neuroscience
Graduate Program, University of Miami, Miami, Florida 33136, United States
| | - Pratul K. Agarwal
- Department
of Biochemistry & Cell and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Physiological
Sciences andHigh Performance Computing Center, Oklahoma
State University, Stillwater, 106 Math Sciences, Stillwater, Oklahoma 74078-1010, United States
| | - Sanjoy K. Bhattacharya
- Department
of Ophthalmology, Bascom Palmer Eye Institute, University of Miami, Miami, Florida 33136, United States
- Neuroscience
Graduate Program, University of Miami, Miami, Florida 33136, United States
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14
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Darbari VC, Ciccone J, Patel JS, Islam B, Agarwal PK, Haider S. Electrostatic Switching Controls Channel Dynamics of the Sensor Protein VirB10 in A. tumefaciens Type IV Secretion System. ACS Omega 2020; 5:3271-3281. [PMID: 32118142 PMCID: PMC7045316 DOI: 10.1021/acsomega.9b03313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/20/2020] [Indexed: 05/19/2023]
Abstract
Type IV secretion systems are large nanomachines assembled across the bacterial cell envelope for effector translocation and conjugation. VirB10 traverses the inner and outer membranes, sensing cellular signals for coordinating the conformational switch for pilus biogenesis and/or secretion. Mutations uncoupling secretion from pilus biogenesis were identified in Agrobacterium tumefaciens VirB10 including a gating defect mutation G272R that made VirB10 unresponsive to intracellular ATP, causing unregulated secretion of VirE2 in a contact-independent manner. Comparative long-timescale molecular dynamics of the wild type and G272R mutant of the A. tumefaciens VirB10CTD tetradecamer reveals how the G272R mutation locks the oligomer in a rigid conformation by swapping the ionic interactions between the loops from the β-barrel close to the inner leaflet of the outer membrane. This electrostatic switching changes the allosteric communication pathway from the extracellular loop to the base of the barrel, suggesting that the local conformational dynamics in the loops can gate information across VirB10.
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Affiliation(s)
- Vidya Chandran Darbari
- School
of Biological and Chemical Sciences, Queen
Mary University of London, Mile End Road, London E1 4NS, United Kingdom
- E-mail: . Tel: +44 (0)
20 7882 6360 (V.C.D.)
| | - Jonah Ciccone
- Department
of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, WC1N 1AX London, United Kingdom
| | - Jagdish Suresh Patel
- Department
of Biological Sciences, University of Idaho, C/O IRIC 333, 875 Perimeter MS 1122, Moscow, Idaho 83844-1122, United States
| | - Barira Islam
- Centre
for Biomarker Research, School of Applied Sciences, University of Huddersfield, HD1 3DH Huddersfield, United Kingdom
| | - Pratul K Agarwal
- Department
of Biochemistry & Cellular and Molecular Biology Department, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Shozeb Haider
- Department
of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, WC1N 1AX London, United Kingdom
- E-mail: . Tel: +44 (0) 20 7753 5883 (S.H.)
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15
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Agarwal PK, Naughton T, Park BH, Bernholdt DE, Hursey JJ, Geist A. Application Health Monitoring for Extreme-scale Resiliency using Cooperative Fault Management. Concurr Comput 2020; 32:e5449. [PMID: 33897303 PMCID: PMC8064409 DOI: 10.1002/cpe.5449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/14/2019] [Indexed: 06/12/2023]
Abstract
Resiliency is and will be a critical factor in determining scientific productivity on current and exascale supercomputers, and beyond. Applications oblivious to and incapable of handling transient soft and hard errors could waste supercomputing resources or, worse, yield misleading scientific insights. We introduce a novel application-driven silent error detection and recovery strategy based on application health monitoring. Our methodology uses application output that follows known patterns as indicators of an application's health, and knowledge that violation of these patterns could be indication of faults. Information from system monitors that report hardware and software health status is used to corroborate faults. Collectively, this information is used by a fault coordinator agent to take preventive and corrective measures by applying computational steering to an application between checkpoints. This cooperative fault management system uses the Fault Tolerance Backplane as a communication channel. The benefits of this framework are demonstrated with two real application case studies, molecular dynamics and quantum chemistry simulations, on scalable clusters with simulated memory and I/O corruptions. The developed approach is general and can be easily applied to other applications.
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Affiliation(s)
- Pratul K Agarwal
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Thomas Naughton
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Byung H Park
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David E Bernholdt
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joshua J Hursey
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Present address: IBM Systems, IBM, Rochester, Minnesota, USA
| | - Al Geist
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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16
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Narayanan C, Bernard DN, Létourneau M, Gagnon J, Gagné D, Bafna K, Calmettes C, Couture JF, Agarwal PK, Doucet N. Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding. Biochemistry 2020; 59:755-765. [PMID: 31909602 DOI: 10.1021/acs.biochem.9b00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities. Recently solved crystal structures of this enzyme in its nucleotide-free form show the conservation of the prototypical kidney-shaped fold preserved among vertebrate RNases, in addition to revealing the presence of a unique secondary active site. In this study, we determine the structural and conformational properties experienced by RNase 6 upon binding to substrate and product analogues. We present the first crystal structures of RNase 6 bound to a nucleotide ligand (adenosine 5'-monophosphate), in addition to RNase 6 bound to phosphate ions. While the enzyme preserves B2 subsite ligand preferences, our results show a lack of typical B2 subsite interactions normally observed in homologous ligand-bound RNases. A comparison of the dynamical properties of RNase 6 in its apo-, substrate-, and product-bound states highlight the unique dynamical properties experienced on time scales ranging from nano- to milliseconds. Overall, our results confirm the specific evolutionary adaptation of RNase 6 relative to its unique catalytic and biological activities.
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Affiliation(s)
- Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - David N Bernard
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Jacinthe Gagnon
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Donald Gagné
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Khushboo Bafna
- Genome Science and Technology , University of Tennesse , Knoxville , Tennessee 37996 , United States
| | - Charles Calmettes
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology , University of Ottawa , 451 Smyth Road , Ottawa , Ontario K1H 8M5 , Canada
| | - Pratul K Agarwal
- Department of Biochemistry, Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
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17
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low‐Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology University of Tennessee Knoxville TN 37996 USA
- Present address: Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Pratul K. Agarwal
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Tanja Mittag
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Engin H. Serpersu
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
- National Science Foundation Alexandria VA 22314 USA
| | - Matthew J. Cuneo
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
- Oak Ridge National Laboratory Oak Ridge TN 37830 USA
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18
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019; 58:16260-16266. [PMID: 31515870 DOI: 10.1002/anie.201908535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Indexed: 01/14/2023]
Abstract
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.
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Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Present address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Engin H Serpersu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.,National Science Foundation, Alexandria, VA, 22314, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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19
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Abstract
Understanding protein motions and their role in enzymatic reactions is an important and timely topic in enzymology. Protein motions that are involved in the chemical step of catalysis are particularly intriguing but difficult to identify. A global network of coupled residues in Escherichia coli dihydrofolate reductase (E. coli DHFR), which assists in catalyzing the chemical step, has previously been demonstrated through quantum mechanical/molecular mechanical and molecular dynamics simulations as well as bioinformatic analyses. A few specific residues (M42, G121, F125, and I14) were shown to function synergistically with measurements of single-turnover rates and the temperature dependence of intrinsic kinetic isotope effects (KIEsint) of site-directed mutants. This study hypothesizes that the global network of residues involved in the chemical step is evolutionarily conserved and probes homologous residues of the potential global network in human DHFR through measurements of the temperature dependence of KIEsint and computer simulations based on the empirical valence bond method. We study mutants M53W and S145V. Both of these remote residues are homologous to network residues in E. coli DHFR. Non-additive isotope effects on activation energy are observed between M53 and S145, indicating their synergistic effect on the chemical step in human DHFR, which suggests that both of these residues are part of a network affecting the chemical step in enzyme catalysis. This finding supports the hypothesis that human and E. coli DHFR share similar networks, consistent with evolutionary preservation of such networks.
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Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | | | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
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20
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Hester KP, Bhattarai K, Jiang H, Agarwal PK, Pope C. Engineering Dynamic Surface Peptide Networks on Butyrylcholinesterase G117H for Enhanced Organophosphosphorus Anticholinesterase Catalysis. Chem Res Toxicol 2019; 32:1801-1810. [PMID: 31411024 DOI: 10.1021/acs.chemrestox.9b00146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The single residue mutation of butyrylcholinesterase (BChEG117H) hydrolyzes a number of organophosphosphorus (OP) anticholinesterases. Whereas other BChE active site/proximal mutations have been investigated, none are sufficiently active to be prophylactically useful. In a fundamentally different computer simulations driven strategy, we identified a surface peptide loop (residues 278-285) exhibiting dynamic motions during catalysis and modified it via residue insertions. We evaluated these loop mutants using computer simulations, substrate kinetics, resistance to inhibition, and enzyme reactivation assays using both the choline ester and OP substrates. A slight but significant increase in reactivation was noted with paraoxon with one of the mutants, and changes in KM and catalytic efficiency were noted in others. Simulations suggested weaker interactions between OP versus choline substrates and the active site of all engineered versions of the enzyme. The results indicate that an improvement of OP anticholinesterase hydrolysis through surface loop engineering may be a more effective strategy in an enzyme with higher intrinsic OP compound hydrolase activity.
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Affiliation(s)
- Kirstin P Hester
- Department of Physiological Sciences , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Krishna Bhattarai
- Department of Entomology and Plant Pathology , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Haobo Jiang
- Department of Entomology and Plant Pathology , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Arium BioLabs , 2519 Caspian Drive , Knoxville , Tennessee 37932 , United States
| | - Carey Pope
- Department of Physiological Sciences , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
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21
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Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLoS One 2019; 14:e0220037. [PMID: 31393891 PMCID: PMC6687278 DOI: 10.1371/journal.pone.0220037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/07/2019] [Indexed: 12/15/2022] Open
Abstract
Human genome contains a group of more than a dozen similar genes with diverse biological functions including antiviral, antibacterial and angiogenesis activities. The characterized gene products of this group show significant sequence similarity and a common structural fold associated with binding and cleavage of ribonucleic acid (RNA) substrates. Therefore, these proteins have been categorized as members of human pancreatic-type ribonucleases (hRNases). hRNases differ in cell/tissue localization and display distinct substrate binding preferences and a wide range of ribonucleolytic catalytic efficiencies. Limited information is available about structural and dynamical properties that influence this diversity among these homologous RNases. Here, we use computer simulations to characterize substrate interactions, electrostatics and dynamical properties of hRNases 1-7 associated with binding to two nucleotide substrates (ACAC and AUAU). Results indicate that even with complete conservation of active-site catalytic triad associated with ribonucleolytic activity, these enzymes show significant differences in substrate interactions. Detailed characterization suggests that in addition to binding site electrostatic and van der Waals interactions, dynamics of distal regions may also play a role in binding. Another key insight is that a small difference in temperature of 300 K (used in experimental studies) and 310 K (physiological temperature) shows significant changes in enzyme-substrate interactions.
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Affiliation(s)
- Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - S. Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Québec, Quebec, Canada
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
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22
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Bafna K, Narayanan C, Bhojane PP, Bernard D, Howell EE, Doucet N, Agarwal PK. Functionally Important Conformational Sub‐States in Human Ribonuclease Family. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.781.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Khushboo Bafna
- Genome Science and TechnologyUniversity of Tennessee, KnoxvilleKnoxvilleTN
| | | | - Purva P Bhojane
- Biochemistry and Molecular BiologyUniversity of Tennessee, KnoxvilleKnoxvilleTN
| | | | - Elizabeth E Howell
- Biochemistry and Molecular BiologyUniversity of Tennessee, KnoxvilleKnoxvilleTN
| | | | - Pratul K Agarwal
- Biochemistry and Molecular BiologyUniversity of Tennessee, KnoxvilleKnoxvilleTN
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23
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Duff MR, Desai N, Craig MA, Agarwal PK, Howell EE. Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions. Biochemistry 2019; 58:1198-1213. [PMID: 30724552 DOI: 10.1021/acs.biochem.8b01110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) reduces dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. Due to its role in one carbon metabolism, chromosomal DHFR is the target of the antibacterial drug, trimethoprim. Resistance to trimethoprim has resulted in a type II DHFR that is not structurally related to the chromosomal enzyme target. Because of its metabolic significance, understanding DHFR kinetics and ligand binding behavior in more cell-like conditions, where the total macromolecule concentration can be as great as 300 mg/mL, is important. The progress-curve kinetics and ligand binding properties of the drug target (chromosomal E. coli DHFR) and the drug resistant (R67 DHFR) enzymes were studied in the presence of macromolecular cosolutes. There were varied effects on NADPH oxidation and binding to the two DHFRs, with some cosolutes increasing affinity and others weakening binding. However, DHF binding and reduction in both DHFRs decreased in the presence of all cosolutes. The decreased binding of ligands is mostly attributed to weak associations with the macromolecules, as opposed to crowder effects on the DHFRs. Computer simulations found weak, transient interactions for both ligands with several proteins. The net charge of protein cosolutes correlated with effects on NADP+ binding, with near neutral and positively charged proteins having more detrimental effects on binding. For DHF binding, effects correlated more with the size of binding pockets on the protein crowders. These nonspecific interactions between DHFR ligands and proteins predict that the in vivo efficiency of DHFRs may be much lower than expected from their in vitro rates.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Nidhi Desai
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael A Craig
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
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24
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Abstract
Even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve high catalytic efficiencies remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bring together and properly orient the participants so that the reaction can proceed; therefore, leading to enzymes being viewed as only passive participants in the catalyzed reaction. A growing body of evidence shows that enzymes are not rigid structures but are constantly undergoing a wide range of internal motions and conformational fluctuations. In this Perspective, on the basis of studies from our group, we discuss the emerging biophysical model of enzyme catalysis that provides a detailed understanding of the interconnection among internal protein motions, conformational substates, enzyme mechanisms, and the catalytic efficiency of enzymes. For a number of enzymes, networks of conserved residues that extend from the surface of the enzyme all the way to the active site have been discovered. These networks are hypothesized to serve as pathways of energy transfer that enables thermodynamical coupling of the surrounding solvent with enzyme catalysis and play a role in promoting enzyme function. Additionally, the role of enzyme structure and electrostatic effects has been well acknowledged for quite some time. Collectively, the recent knowledge gained about enzyme mechanisms suggests that the conventional paradigm of enzyme structure encoding function is incomplete and needs to be extended to structure encodes dynamics, and together these enzyme features encode function including catalytic rate acceleration.
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Affiliation(s)
- Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
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Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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26
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Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Correction to: Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Biomol NMR Assign 2018; 12:365-367. [PMID: 30083869 DOI: 10.1007/s12104-018-9833-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
After publication of this article, the authors noticed that a 15N-13C dimension error was unwillingly coded in the 3D NMR spectrum "fid.com" processing script used to perform backbone assignments for this enzyme. The authors noticed that some OBS, CAR and LAB values in the "fid.com" had been switched in the y and z dimensions, probably resulting from a wrong NMRPipe selection when reading the Varian NMR experimental parameters. They have carefully re-processed, re-analyzed, re-assigned, in addition to checking all scripts to evaluate the extent of this processing error on the published assignments. Authors determined that the "fid.com" error resulted in a significant number of incorrect backbone resonance assignments, requiring us to issue corrections in Figs. 2, 3 and 4 of this published manuscript, in addition to Table S1. New versions of these figures and table are provided below. The corresponding BMRB entry has also been revised. The authors note that these modifications do not change the global message, conclusions, and molecular dynamics simulations presented in this article. The authors are grateful to David N. Bernard (INRS) for help with finding and correcting these errors.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Laurie-Anne Charest
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, The Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada.
- GRASP, The Groupe de recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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Duff MR, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Biochemistry 2018; 57:4263-4275. [PMID: 29901984 DOI: 10.1021/acs.biochem.8b00424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent khydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased khydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.
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Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Jose M Borreguero
- Neutron Data Analysis and Visualization Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Matthew J Cuneo
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Arvind Ramanathan
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Junhong He
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Ganesh Kamath
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology , University of Pittsburgh , Pittsburgh , Pennsylvania , United States
| | - Flora Meilleur
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States.,Molecular and Structural Biochemistry Department , North Carolina State University , Raleigh , North Carolina , United States
| | - Elizabeth E Howell
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Kenneth W Herwig
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Dean A A Myles
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Pratul K Agarwal
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States.,Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
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28
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Narayanan C, Bernard DN, Bafna K, Gagné D, Agarwal PK, Doucet N. Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily. Front Mol Biosci 2018; 5:54. [PMID: 29946547 PMCID: PMC6005897 DOI: 10.3389/fmolb.2018.00054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/23/2018] [Indexed: 01/28/2023] Open
Abstract
Enzyme catalysis is a complex process involving several steps along the reaction coordinates, including substrate recognition and binding, chemical transformation, and product release. Evidence continues to emerge linking the functional and evolutionary role of conformational exchange processes in optimal catalytic activity. Ligand binding changes the conformational landscape of enzymes, inducing long-range conformational rearrangements. Using functionally distinct members of the pancreatic ribonuclease superfamily as a model system, we characterized the structural and conformational changes associated with the binding of two mononucleotide ligands. By combining NMR chemical shift titration experiments with the chemical shift projection analysis (CHESPA) and relaxation dispersion experiments, we show that biologically distinct members of the RNase superfamily display discrete chemical shift perturbations upon ligand binding that are not conserved even in structurally related members. Amino acid networks exhibiting coordinated chemical shift displacements upon binding of the two ligands are unique to each of the RNases analyzed. Our results reveal the contribution of conformational rearrangements to the observed chemical shift perturbations. These observations provide important insights into the contribution of the different ligand binding specificities and effects of conformational exchange on the observed perturbations associated with ligand binding for functionally diverse members of the pancreatic RNase superfamily.
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Affiliation(s)
- Chitra Narayanan
- INRS - Institut Armand-Frappier, Université du Québec, Laval, QC, Canada
| | - David N Bernard
- INRS - Institut Armand-Frappier, Université du Québec, Laval, QC, Canada
| | - Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - Donald Gagné
- INRS - Institut Armand-Frappier, Université du Québec, Laval, QC, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Nicolas Doucet
- INRS - Institut Armand-Frappier, Université du Québec, Laval, QC, Canada.,PROTEO, The Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada
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29
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Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Biomol NMR Assign 2017; 11:143-149. [PMID: 28271277 PMCID: PMC5589483 DOI: 10.1007/s12104-017-9736-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1H, 13C and 15N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Laurie-Anne Charest
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, The Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada.
- GRASP, The Groupe de recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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30
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Li L, Ghimire-Rijal S, Lucas SL, Stanley CB, Wright E, Agarwal PK, Myles DA, Cuneo MJ. Periplasmic Binding Protein Dimer Has a Second Allosteric Event Tied to Ligand Binding. Biochemistry 2017; 56:5328-5337. [PMID: 28876049 DOI: 10.1021/acs.biochem.7b00657] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ligand-induced conformational changes of periplasmic binding proteins (PBP) play a key role in the acquisition of metabolites in ATP binding cassette (ABC) transport systems. This conformational change allows for differential recognition of the ligand occupancy of the PBP by the ABC transporter. This minimizes futile ATP hydrolysis in the transporter, a phenomenon in which ATP hydrolysis is not coupled to metabolite transport. In many systems, the PBP conformational change is insufficient at eliminating futile ATP hydrolysis. Here we identify an additional state of the PBP that is also allosterically regulated by the ligand. Ligand binding to the homodimeric apo PBP leads to a tightening of the interface α-helices so that the hydrogen bonding pattern shifts to that of a 310 helix, in-turn altering the contacts and the dynamics of the protein interface so that the monomer exists in the presence of ligand.
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Affiliation(s)
| | | | - Sarah L Lucas
- Department of Biomedical Engineering, North Carolina State University , Raleigh North Carolina 27607, United States
| | | | - Edward Wright
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
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31
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Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N. Applications of NMR and computational methodologies to study protein dynamics. Arch Biochem Biophys 2017; 628:71-80. [PMID: 28483383 DOI: 10.1016/j.abb.2017.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.
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Affiliation(s)
- Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Pratul K Agarwal
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, The Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada; GRASP, The Groupe de Recherche Axé sur la Structure des Protéines, 3649 Promenade Sir William Osler, McGill University, Montréal, QC H3G 0B1, Canada.
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Abstract
The construction of switchable, radiation-controlled, aptameric enzymes - "swenzymes" - is, in principle, feasible. We propose a strategy to make such catalysts from 2 (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a 2-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker, thus bringing together the substrates. In the presence of the substrates, some linked aptamer pairs catalyze the reaction when exposed to external energy in the form of a specific frequency of low-intensity, nonionizing electromagnetic or acoustic radiation. Such swenzymes are detected via a separate product-capturing aptamer that changes conformation on capturing the product; this altered conformation allows it (1) to bind to every potential swenzyme in its vicinity (thereby giving a higher probability of capture to the swenzymes that generate the product) and (2) to bind to a sequence on a magnetic bead (thereby permitting purification of the swenzyme plus product-capturing aptamer by precipitation). Attempts to implement the swenzyme strategy may help elucidate fundamental problems in enzyme catalysis.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, EA 4312, Department of Biology, University of Rouen, Mont Saint Aignan, France
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O'Dell WB, Agarwal PK, Meilleur F. Inside Cover: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase (Angew. Chem. Int. Ed. 3/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201611987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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O'Dell WB, Agarwal PK, Meilleur F. Innentitelbild: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase (Angew. Chem. 3/2017). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201611987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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35
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Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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36
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O'Dell WB, Agarwal PK, Meilleur F. Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew Chem Int Ed Engl 2016; 56:767-770. [PMID: 28004877 DOI: 10.1002/anie.201610502] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Indexed: 01/26/2023]
Abstract
Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. We have determined high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed "pre-bound" molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. These results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme-substrate complex.
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Affiliation(s)
- William B O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
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Bhojane P, Duff MR, Bafna K, Rimmer GP, Agarwal PK, Howell EE. Aspects of Weak Interactions between Folate and Glycine Betaine. Biochemistry 2016; 55:6282-6294. [PMID: 27768285 PMCID: PMC5198541 DOI: 10.1021/acs.biochem.6b00873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/19/2016] [Indexed: 01/22/2023]
Abstract
Folate, or vitamin B9, is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value). This value is concentration-dependent as folate dimerizes. The μ23/RT value also tracks the deprotonation of folate's N3-O4 keto-enol group, yielding a pKa of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ23/RT values into α values for atom types was achieved. This allows prediction of μ23/RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ23/RT values from -0.18 to 0.09 m-1, where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ23/RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities.
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Affiliation(s)
- Purva
P. Bhojane
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Michael R. Duff
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Khushboo Bafna
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Gabriella P. Rimmer
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Pratul K. Agarwal
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Computer
Science and Mathematics Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E. Howell
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
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Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry 2016; 55:4184-96. [PMID: 27387012 DOI: 10.1021/acs.biochem.6b00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Nhung Nguyen-Thi
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - David N Bernard
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , 320 East Superior Street, Chicago, Illinois 60611, United States
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
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Bansal A, Mittal S, Dass J, Gupta N, Agarwal PK, Kotwal J. A Case Presenting with Splenic Infarct Diagnosed as Primary Bone Marrow CD5 Positive DLBCL: A Clinicopathological Correlation. Indian J Hematol Blood Transfus 2016; 32:159-62. [PMID: 27408381 DOI: 10.1007/s12288-016-0646-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/15/2016] [Indexed: 12/22/2022] Open
Abstract
De novo CD5+ Diffuse large B cell lymphoma (DLBCL) is a rare and aggressive subtype of DLBCL. It is a distinct clinicopathologic entity with complex molecular profile and poor prognosis. A 59 year old female presented with pyrexia of unknown origin since 1 month. On examination, there was severe pallor, hepatosplenomegaly and no palpable lymphadenopathy. Complete blood count revealed bicytopenia with normal total leucocyte count. Liver and renal function tests were normal. Ultrasonography abdomen revealed splenic enlargement with two focal lesions attributed to either splenic abscess or infarcts. Patient was being managed as splenic infarct but continued to have bicytopenia. Further investigation showed elevated serum ferritin, triglycerides and LDH. With a clinical suspicion of infection and haemophagocytic lymphohistiocytosis bone marrow aspiration (BMA) and biopsy (BMBx) was done. BMA showed extensive haemophagocytosis and ~7.4 % large lymphoma-like cells. On this basis PET-CT was suggested which showed enlarged spleen with diffuse uptake. BMBx showed nodular and intrasinusoidal collection of abnormal lymphoid cells. On immunohistochemistry, these cells were positive for CD20, CD5, MUM1, BCL-2, BCL-6 and negative for CD3, CD10 and CD23. CD34 highlighted focal intrasinusoidal pattern. The complete clinicopathological profile suggested the diagnosis of de novo CD5+ DLBCL, with primary hepatosplenic pattern of involvement. CD5+ DLBCL presenting as splenic infarct is very rare. This case was unusual as the diagnosis of a primary aggressive lymphoma with haemophagocytosis was established in a patient who presented with fever and splenic infarct without lymphadenopathy. This indicates the importance of good morphological assessment of a bone marrow aspirate and biopsy to make a correct diagnosis.
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Affiliation(s)
- Anupriya Bansal
- Department of Hematology, Sir Ganga Ram Hospital, 1st Floor, SSRB Building, New Delhi, India
| | - Suchi Mittal
- Department of Hematology, Sir Ganga Ram Hospital, 1st Floor, SSRB Building, New Delhi, India
| | - Jasmita Dass
- Department of Hematology, Sir Ganga Ram Hospital, 1st Floor, SSRB Building, New Delhi, India
| | - Nitin Gupta
- Department of Clinical Hematology, Sir Ganga Ram Hospital, New Delhi, India
| | - P K Agarwal
- Department of Medicine, Sir Ganga Ram Hospital, New Delhi, India
| | - Jyoti Kotwal
- Department of Hematology, Sir Ganga Ram Hospital, 1st Floor, SSRB Building, New Delhi, India
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Abstract
Enzyme function involves substrate and cofactor binding, precise positioning of reactants in the active site, chemical turnover, and release of products. In addition to formation of crucial structural interactions between enzyme and substrate(s), coordinated motions within the enzyme-substrate complex allow reaction to proceed at a much faster rate, compared to the reaction in solution and in the absence of enzyme. An increasing number of enzyme systems show the presence of conserved protein motions that are important for function. A wide variety of motions are naturally sampled (over femtosecond to millisecond time-scales) as the enzyme complex moves along the energetic landscape, driven by temperature and dynamical events from the surrounding environment. Areas of low energy along the landscape form conformational sub-states, which show higher conformational populations than surrounding areas. A small number of these protein conformational sub-states contain functionally important structural and dynamical features, which assist the enzyme mechanism along the catalytic cycle. Identification and characterization of these higher-energy (also called excited) sub-states and the associated populations are challenging, as these sub-states are very short-lived and therefore rarely populated. Specialized techniques based on computer simulations, theoretical modeling, and nuclear magnetic resonance have been developed for quantitative characterization of these sub-states and populations. This chapter discusses these techniques and provides examples of their applications to enzyme systems.
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Affiliation(s)
- P K Agarwal
- Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States; University of Tennessee, Knoxville, TN, United States.
| | - N Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, QC, Canada
| | | | - A Ramanathan
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, Laval, QC, Canada
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Abstract
Homotetrameric R67 dihydrofolate reductase possesses 222 symmetry and a single active site pore. This situation results in a promiscuous binding site that accommodates either the substrate, dihydrofolate (DHF), or the cofactor, NADPH. NADPH interacts more directly with the protein as it is larger than the substrate. In contrast, the p-aminobenzoyl-glutamate tail of DHF, as monitored by nuclear magnetic resonance and crystallography, is disordered when bound. To explore whether smaller active site volumes (which should decrease the level of tail disorder by confinement effects) alter steady state rates, asymmetric mutations that decreased the half-pore volume by ∼35% were constructed. Only minor effects on k(cat) were observed. To continue exploring the role of tail disorder in catalysis, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide-mediated cross-linking between R67 DHFR and folate was performed. A two-folate, one-tetramer complex results in the loss of enzyme activity where two symmetry-related K32 residues in the protein are cross-linked to the carboxylates of two bound folates. The tethered folate could be reduced, although with a ≤30-fold decreased rate, suggesting decreased dynamics and/or suboptimal positioning of the cross-linked folate for catalysis. Computer simulations that restrain the dihydrofolate tail near K32 indicate that cross-linking still allows movement of the p-aminobenzoyl ring, which allows the reaction to occur. Finally, a bis-ethylene-diamine-α,γ-amide folate adduct was synthesized; both negatively charged carboxylates in the glutamate tail were replaced with positively charged amines. The K(i) for this adduct was ∼9-fold higher than for folate. These various results indicate a balance between folate tail disorder, which helps the enzyme bind substrate while dynamics facilitates catalysis.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Shaileja Chopra
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Michael Brad Strader
- Laboratory of Biochemistry and Vascular Biology, Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993, United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States.,Computer Science and Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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Gagné D, French RL, Narayanan C, Simonović M, Agarwal PK, Doucet N. Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity. Structure 2015; 23:2256-2266. [PMID: 26655472 DOI: 10.1016/j.str.2015.10.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/05/2015] [Accepted: 10/13/2015] [Indexed: 01/28/2023]
Abstract
The role of internal dynamics in enzyme function is highly debated. Specifically, how small changes in structure far away from the reaction site alter protein dynamics and overall enzyme mechanisms is of wide interest in protein engineering. Using RNase A as a model, we demonstrate that elimination of a single methyl group located >10 Å away from the reaction site significantly alters conformational integrity and binding properties of the enzyme. This A109G mutation does not perturb structure or thermodynamic stability, both in the apo and ligand-bound states. However, significant enhancement in conformational dynamics was observed for the bound variant, as probed over nano- to millisecond timescales, resulting in major ligand repositioning. These results illustrate the large effects caused by small changes in structure on long-range conformational dynamics and ligand specificities within proteins, further supporting the importance of preserving wild-type dynamics in enzyme systems that rely on flexibility for function.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Rachel L French
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 South Ashland, Chicago, IL 60607, USA
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 South Ashland, Chicago, IL 60607, USA
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA; Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, 1045 Avenue de la Médecine, Université Laval, QC G1V 0A6, Canada; GRASP, the Groupe de Recherche Axé sur la Structure des Protéines, 3649 Promenade Sir William Osler, McGill University, Montréal, QC H3G 0B1, Canada.
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Raviraj KS, Miglani P, Garg A, Agarwal PK. Gastric Mucormycosis with Hemolytic Uremic Syndrome. J Assoc Physicians India 2015; 63:75-76. [PMID: 27608699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Mucormycosis, is an emerging fungal infection in immunocompromised and diabetic individuals, usually affects rhino-orbito-cerebral, cutaneous and pulmonary regions. But mucormycosis in immunocompetent environment is rare and occurrence of gastric mucormycosis is unusual. We report a case of 19 year old female, with no pre-existing co-morbidities, presented with fever, dysentery, vomiting, and melena for 4 days. On evaluation she was found to have pancytopenia, acute kidney injury, hemolytic anemia, coagulopathy and hepatic derangement and treated with hemodialysis, plasmapheresis along with antibiotics and packed cell RBC transfusion. Upper gastrointestinal endoscopy revealed presence of extensive esophageal and gastric ulcer. In view of persistent bleeding despite endoscopic sclerotherapy, repetition of upper gastrointestinal endoscopy and CT abdomen with oral contrast was done, which revealed perforated gastric ulcer. Exploratory laparotomy and excision of ulcer was done. The biopsy of gastric ulcer had shown the presence of granulomatous necrotic areas positive for mucormycosis. Then she was managed with amphotericin-B, posoconazole with which she improved.
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Affiliation(s)
| | | | | | - P K Agarwal
- Senior Consultant, Ganga Ram Institute of Post-Graduation Medical Education (GRIPMER), New Delhi
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Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Acc Chem Res 2014; 47:149-56. [PMID: 23988159 DOI: 10.1021/ar400084s] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.
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Affiliation(s)
- Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrej Savol
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Virginia Burger
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S. Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pratul K. Agarwal
- Annavitas Biosciences, 2519 Caspian Drive, Knoxville, Tennessee 37932, United States
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Yang SJ, Min KW, Gupta SK, Park JY, Shivane VK, Pitale SU, Agarwal PK, Sosale A, Gandhi P, Dharmalingam M, Mohan V, Mahesh U, Kim DM, Kim YS, Kim JA, Kim PK, Baik SH. A multicentre, multinational, randomized, placebo-controlled, double-blind, phase 3 trial to evaluate the efficacy and safety of gemigliptin (LC15-0444) in patients with type 2 diabetes. Diabetes Obes Metab 2013; 15:410-6. [PMID: 23170990 DOI: 10.1111/dom.12042] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/27/2012] [Accepted: 11/09/2012] [Indexed: 01/21/2023]
Abstract
AIM This study was designed to assess the efficacy and safety of the dipeptidyl peptidase IV inhibitor gemigliptin (LC15-0444) 50 mg versus placebo in patients with type 2 diabetes. METHODS We conducted a 24-week, randomized, double-blind, placebo-controlled phase III trial in 182 patients (74 from Korea and 108 from India) with type 2 diabetes. After an initial 2 weeks of a diet and exercise programme followed by 2 weeks of a single-blind placebo run-in period, eligible patients were randomized to gemigliptin 50 mg or placebo, receiving the assigned treatment for 24 weeks. HbA1c and fasting plasma glucose (FPG) were measured periodically, and oral glucose tolerance test was performed at baseline and weeks 12 and 24. RESULTS At week 24, gemigliptin treatment led to significant reductions in HbA1c measurements compared to placebo (adjust mean after subtracting the placebo effect size: -0.71%, 95% confidence interval: -1.04 to -0.37%). A significantly greater proportion of patients achieved an HbA1c <7% with gemigliptin than with placebo. The placebo-subtracted FPG change from baseline at week 24 was -19.80 mg/dl. The overall incidence rates for adverse events were similar in the gemigliptin and placebo groups. CONCLUSIONS This study showed the efficacy and safety of gemigliptin 50 mg administered once daily as a monotherapy for type 2 diabetes patients.
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Affiliation(s)
- S J Yang
- Division of Endocrinology, Department of Internal Medicine, Korea University, Guro Hospital, Seoul, Korea
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Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS. Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase. Proteins 2012; 80:2536-51. [PMID: 22733562 DOI: 10.1002/prot.24135] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/08/2012] [Accepted: 06/10/2012] [Indexed: 12/25/2022]
Abstract
Biomolecular simulations at millisecond and longer time-scales can provide vital insights into functional mechanisms. Because post-simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (Ramanathan et al., PLoS One 2011;6:e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this article, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD--a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states, and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on microsecond timescale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three subdomains (LID, CORE, and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate that HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations.
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Affiliation(s)
- Arvind Ramanathan
- Computational Biology Institute & Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Theophilidou E, Waraich N, Raza T, Agarwal PK. Liver metastases, a rare cause of portal hypertension and stoma bleeding. Brief review of literature. Int J Surg Case Rep 2012; 3:173-6. [PMID: 22387413 DOI: 10.1016/j.ijscr.2011.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 11/23/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Portal hypertension is an unusual complication of liver metastases, which is frequently occurring in malignant disease. Portal hypertension may cause oesophageal varices and also stoma varices (colostomy and ileostomy). Oesophageal varices and bleeding from these varices have been frequently reported in literature. Stomal varices have also been reported in literature mostly associated with liver cirrhosis. These stomal varices lead to the massive bleeding causing morbidity and mortality. Portal hypertension is a pathological increase in portal pressure gradient (the difference between pressure in the portal and inferior vena cava veins). It is either due to an increase in portal blood flow or an increase in vascular resistance or combination of both. In liver cirrhosis, the primary factor leading to portal hypertension is increase in portal blood flow resistance and later on development of increased portal blood flow. It has been postulated that in liver metastasis the increase in portal flow resistance occurs at any site within portal venous system as a consequence of mechanical architectural disturbance. PRESENTATION OF CASE We report a case of a 64 year old gentleman who developed portal hypertension due to secondary metastases from colorectal cancer. He subsequently developed bleeding varices in his end colostomy. DISCUSSION We believe that the combination of extensive metastases and chemotherapy induced portal hypertension in our patient. CONCLUSION Our case and other literature review highlight that the recurrent bleeding stoma associated with colorectal cancer should be investigated for portal hypertension.
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Affiliation(s)
- E Theophilidou
- 46 The Quays, Castle Quay Close, Nottingham NG7 1HR, United Kingdom
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Agarwal PK, Schultz C, Kalivretenos A, Ghosh B, Broedel S. Engineering Hyper-Catalytic Enzyme by Photo-Activated Conformation Modulation. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Hellemons ME, Agarwal PK, van der Bij W, Verschuuren EAM, Postmus D, Erasmus ME, Navis GJ, Bakker SJL. Former smoking is a risk factor for chronic kidney disease after lung transplantation. Am J Transplant 2011; 11:2490-8. [PMID: 21883906 DOI: 10.1111/j.1600-6143.2011.03701.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chronic kidney disease (CKD) is a common complication after lung transplantation (LTx). Smoking is a risk factor for many diseases, including CKD. Smoking cessation for >6 months is required for LTx enlistment. However, the impact of smoking history on CKD development after LTx remains unclear. We investigated the effect of former smoking on CKD and mortality after LTx. CKD was based on glomerular filtration rate (GFR) ((125) I-iothalamate measurements). GFR was measured before and repeatedly after LTx. One hundred thirty-four patients never smoked and 192 patients previously smoked for a median of 17.5 pack years. At 5 years after LTx, overall cumulative incidences of CKD-III, CKD-IV and death were 68.5%, 16.3% and 34.6%, respectively. Compared to never smokers, former smokers had a higher risk for CKD-III (hazard ratio [HR] 95% confidence interval [95%CI]= 1.69 [1.27-2.24]) and IV (HR = 1.90 [1.11-3.27]), but not for mortality (HR = 0.99 [0.71-1.38]). Adjustment for potential confounders did not change results. Thus, despite cessation, smoking history remained a risk factor for CKD in LTx recipients. Considering the increasing acceptance for LTx of older recipients with lower baseline renal function and an extensive smoking history, our data suggest that the problem of post-LTx CKD may increase in the future.
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Affiliation(s)
- M E Hellemons
- Department of Internal Medicine, University Medical Center Groningen, Groningen, The Netherlands.
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