1
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Molina GA, Mendes LFS, Fuzo CA, Costa-Filho AJ, Ward RJ. Mapping secondary substrate-binding sites on the GH11 xylanase from Bacillus subtilis. FEBS Lett 2024; 598:363-376. [PMID: 38253842 DOI: 10.1002/1873-3468.14799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Xylanases are of significant interest for biomass conversion technologies. Here, we investigated the allosteric regulation of xylan hydrolysis by the Bacillus subtilis GH11 endoxylanase. Molecular dynamics simulations (MDS) in the presence of xylobiose identified binding to the active site and two potential secondary binding sites (SBS) around surface residues Asn54 and Asn151. Arabinoxylan titration experiments with single cysteine mutants N54C and N151C labeled with the thiol-reactive fluorophore acrylodan or the ESR spin-label MTSSL validated the MDS results. Ligand binding at the SBS around Asn54 confirms previous reports, and analysis of the second SBS around N151C discovered in the present study includes residues Val98/Ala192/Ser155/His156. Understanding the regulation of xylanases contributes to efforts for industrial decarbonization and to establishing a sustainable energy matrix.
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Affiliation(s)
- Gustavo Avelar Molina
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis Felipe Santos Mendes
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos Alessandro Fuzo
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonio José Costa-Filho
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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2
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Welfer GA, Borin VA, Cortez LM, Opresko PL, Agarwal PK, Freudenthal BD. Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants. Genes (Basel) 2023; 14:281. [PMID: 36833208 PMCID: PMC9957172 DOI: 10.3390/genes14020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Telomere biology disorders (TBDs) are a spectrum of diseases that arise from mutations in genes responsible for maintaining telomere integrity. Human telomerase reverse transcriptase (hTERT) adds nucleotides to chromosome ends and is frequently mutated in individuals with TBDs. Previous studies have provided insight into how relative changes in hTERT activity can lead to pathological outcomes. However, the underlying mechanisms describing how disease-associated variants alter the physicochemical steps of nucleotide insertion remain poorly understood. To address this, we applied single-turnover kinetics and computer simulations to the Tribolium castaneum TERT (tcTERT) model system and characterized the nucleotide insertion mechanisms of six disease-associated variants. Each variant had distinct consequences on tcTERT's nucleotide insertion mechanism, including changes in nucleotide binding affinity, rates of catalysis, or ribonucleotide selectivity. Our computer simulations provide insight into how each variant disrupts active site organization, such as suboptimal positioning of active site residues, destabilization of the DNA 3' terminus, or changes in nucleotide sugar pucker. Collectively, this work provides a holistic characterization of the nucleotide insertion mechanisms for multiple disease-associated TERT variants and identifies additional functions of key active site residues during nucleotide insertion.
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Affiliation(s)
- Griffin A. Welfer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103, USA
- University of Kansas Cancer Center, Kansas City, KS 66103, USA
| | - Veniamin A. Borin
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74077, USA
| | - Luis M. Cortez
- University of Kansas Cancer Center, Kansas City, KS 66103, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Patricia L. Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74077, USA
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66103, USA
- University of Kansas Cancer Center, Kansas City, KS 66103, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66103, USA
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3
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Sensitivity of family GH11 Bacillus amyloliquefaciens xylanase A (BaxA) and the T33I mutant to Oryza sativa xylanase inhibitor protein (OsXIP): An experimental and computational study. Enzyme Microb Technol 2022; 156:109998. [DOI: 10.1016/j.enzmictec.2022.109998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022]
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4
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology University College London and Birkbeck College London WC1E 6BT UK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology Pleinlaan 2 1050 Brussels Belgium
- Jean Jeener NMR Centre VUB Pleinlaan 2 1050 Brussels Belgium
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Eiso AB
- ZoBio BV BioPartner 2 building J.H. Oortweg 19 2333 CH Leiden The Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hugo Ingen
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
- Present address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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5
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, van Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase*. Angew Chem Int Ed Engl 2020; 59:20508-20514. [PMID: 32533782 PMCID: PMC7693232 DOI: 10.1002/anie.202003236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Indexed: 11/09/2022]
Abstract
The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College London and Birkbeck CollegeLondonWC1E 6BTUK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural BiologyPleinlaan 21050BrusselsBelgium
- Jean Jeener NMR CentreVUBPleinlaan 21050BrusselsBelgium
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Eiso AB
- ZoBio BVBioPartner 2 buildingJ.H. Oortweg 192333 CHLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hugo van Ingen
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
- Present address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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6
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Visualizing Rev1 catalyze protein-template DNA synthesis. Proc Natl Acad Sci U S A 2020; 117:25494-25504. [PMID: 32999062 DOI: 10.1073/pnas.2010484117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on the Saccharomyces cerevisiae Rev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.
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7
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Dhruw C, Husain K, Kumar V, Sonawane VC. Novel xylanase producing Bacillus strain X2: molecular phylogenetic analysis and its application for production of xylooligosaccharides. 3 Biotech 2020; 10:328. [PMID: 32656061 PMCID: PMC7334322 DOI: 10.1007/s13205-020-02322-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
A Bacillus strain X2 that produced extracellular endo-xylanase (GH 11) (EC: 3.2.1.8) was isolated from the soil of the Northeast India region. This aerobic culture was Gram positive and endospore forming. Chemotaxonomic characterization showed variance with the fatty acid profile of related species in the Bacillus subtilis group. In Bacillus strain X2, distinct occurrence of iso-C14:0 lipids is absent in other related species. The 16S rRNA gene sequence homology showed 99% similarity with Bacillus subtilis subsp. inaquosorum. The phylogenetic analysis by the multilocus sequence analysis (MLSA) of the nucleotide sequence of six concatenated genes (16S rRNA, groEL, gyrA, polC, purH and rpoB) resolved the taxonomic position of the Bacillus strain X2 in the Bacillus subtilis subsp. group. The MLSA showed that it is a member of a clade that includes Bacillus subtilis subsp. stercoris. In in silico DNA-DNA hybridization (DDH), the highest matching score was obtained with Bacillus subtilis subsp. stercoris (87%). The in silico DDH of the genome (G + C 43.7 mol %) shared 48.5%, with Bacillus subtilis subsp. inaquosorum. The MLSA phylogenetic tree and the highest degree of DNA hybridization, indicating that it belongs to the Bacillus subtilis subspecies stercoris.
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Affiliation(s)
- Chandrabhan Dhruw
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Khadim Husain
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Vyas Kumar
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
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8
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Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal P, 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] [Abstract] [MESH Headings] [Grants] [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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9
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Zheng H, Zheng YC, Cui Y, Zhu JJ, Zhong JY. Study on effects of co-solvents on the structure of DhaA by molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:5999-6007. [PMID: 32696722 DOI: 10.1080/07391102.2020.1796801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
With the increasing application of enzymes in various research fields, the choices of co-solvents in enzymatic preparations which directly related to the catalytic activity have been attracted attention. Thus, researching on the stabilization or destabilization behaviors of enzymes in different solvents is extremely essential. In this study, the structural changes of DhaA in two typical aprotic co-solvents (acetonitrile and tetrahydrofuran) were firstly investigated by molecular dynamics (MD) simulation. The simulation results revealed the strong van der Waals force between co-solvents and DhaA which could induce the structural change of enzyme. Interestingly, the differences of molecular size and the electrostatic force with enzyme of two co-solvents led to quite different influences on DhaA. As for acetonitrile, solvent molecules could penetrate into the catalytic site of DhaA which promoted by the electrostatic interaction. On the contrary, tetrahydrofuran molecules were mainly distributed around the catalytic site due to the relative weak electrostatic interaction and steric resistance effect. It can be concluded that different co-solvent can affect the key domains, substrate pathway and catalytic pocket of DhaA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- He Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Yong-Chao Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Yan Cui
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Jian-Jun Zhu
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Jin-Yi Zhong
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
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10
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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] [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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11
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The critical roles of exposed surface residues for the thermostability and halotolerance of a novel GH11 xylanase from the metagenomic library of a saline-alkaline soil. Int J Biol Macromol 2019; 133:316-323. [DOI: 10.1016/j.ijbiomac.2019.04.090] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 01/06/2023]
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12
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Pandya MJ, Schiffers S, Hounslow AM, Baxter NJ, Williamson MP. Why the Energy Landscape of Barnase Is Hierarchical. Front Mol Biosci 2018; 5:115. [PMID: 30619881 PMCID: PMC6306431 DOI: 10.3389/fmolb.2018.00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023] Open
Abstract
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s−1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10−9−10−6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (i.e., 750 s−1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-μs timescale.
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Affiliation(s)
- Maya J Pandya
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Schiffers
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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13
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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] [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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14
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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] [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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15
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Knox R, Lento C, Wilson DJ. Mapping Conformational Dynamics to Individual Steps in the TEM-1 β-Lactamase Catalytic Mechanism. J Mol Biol 2018; 430:3311-3322. [PMID: 29964048 DOI: 10.1016/j.jmb.2018.06.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
Conformational dynamics are increasingly recognized as being essential for enzyme function. However, there is virtually no direct experimental evidence to support the notion that individual dynamic modes are required for specific catalytic processes, apart from the initial step of substrate binding. In this work, we use a unique approach based on millisecond hydrogen-deuterium exchange mass spectrometry to identify dynamic modes linked to individual catalytic processes in the antibiotic resistance enzyme TEM-1 β-lactamase. Using a "good" substrate (ampicillin), a poorly hydrolyzed substrate (cephalexin) and a covalent inhibitor (clavulanate), we are able to isolate dynamic modes that are specifically linked to substrate binding, productive lactam ring hydrolysis and deacylation. These discoveries are ultimately translated into specific targets for allosteric TEM-1 inhibitor development.
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Affiliation(s)
- Ruth Knox
- Department of Chemistry, York University, Toronto, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Canada M3J 1P3
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Canada M3J 1P3; Center for Research in Mass Spectrometry, York University, Toronto, Canada M3J 1P3.
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16
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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] [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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17
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Li Q, Sun B, Jia H, Hou J, Yang R, Xiong K, Xu Y, Li X. Engineering a xylanase from Streptomyce rochei L10904 by mutation to improve its catalytic characteristics. Int J Biol Macromol 2017; 101:366-372. [PMID: 28356235 DOI: 10.1016/j.ijbiomac.2017.03.135] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 11/18/2022]
Abstract
Protein engineering was performed by N-terminal region replacement and site-directed mutagenesis in the cord of a xylanase (Srxyn) from Streptomyce rochei L10904 to improve its catalytic characteristics. Three mutants SrxynF, SrxynM and SrxynFM displayed 2.1-fold, 3.2-fold and 5.3-fold higher specific activities than that of Srxyn, respectively. Moreover, all of the mutants showed greater substrate affinity and kcat/Km than the native Srxyn. In addition, the enzymes showed improved hydrolysis characteristics, of which the most noteworthy is the enhanced ability of producing xylobiose (X2) and xylotriose (X3) from polymeric substrates. The engineered xylanases have greater potential for applications in oligosaccharide preparation industry.
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Affiliation(s)
- Qin Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China
| | - Baoguo Sun
- School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Huiyong Jia
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Jie Hou
- School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China
| | - Ran Yang
- School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China
| | - Ke Xiong
- School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China
| | - Youqiang Xu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; School of Food and Chemical Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing 100048, China.
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