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A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways. Biophys Chem 2022; 285:106803. [DOI: 10.1016/j.bpc.2022.106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022]
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2
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Shi G, Shaw GX, Zhu F, Tarasov SG, Ji X. Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding. Bioorg Med Chem 2021; 29:115847. [PMID: 33199204 PMCID: PMC7855645 DOI: 10.1016/j.bmc.2020.115847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but absent in mammals; therefore, it is an attractive target for developing novel antimicrobial agents. Previously, based on our studies of the structure and mechanism of HPPK, we created first-generation bisubstrate inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed second-generation inhibitors by replacing the phosphate bridge with a linkage that contains a piperidine moiety. Here, we report third-generation inhibitors designed based on the piperidine-containing inhibitor, mimicking the transition state. We synthesized two such inhibitors, characterized their protein-binding and enzyme inhibition properties, and determined their crystal structures in complex with HPPK, advancing the development of such bisubstrate analog inhibitors.
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Affiliation(s)
- Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary X Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Fengxia Zhu
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA; School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaiyin, Jiangsu Province, China(1)
| | - Sergey G Tarasov
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA.
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3
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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4
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Zhao L, Lu HP, Wang J. Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer. J Phys Chem B 2018; 122:1885-1897. [PMID: 29385349 DOI: 10.1021/acs.jpcb.7b12562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large-scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation. With our model, we have made theoretical predictions that are in good agreement with the experimental measurements. Our results revealed the intrinsic conformational fluctuations between apo and open states without ligand binding. We found that HPPK can switch to the activated holo state upon the ordered binding of the two ligands (ATP and HP). We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis. Additionally, we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions. We further explored the temperature effect on the conformational distributions and pathway weights. It gave strong support that higher temperatures promote population shift, while the induced fit pathway is always the predominant activation route of the HPPK system. These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.
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Affiliation(s)
- Lingci Zhao
- College of Physics, Jilin University , Changchun, Jilin 130012, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, People's Republic of China
| | - H Peter Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Jin Wang
- College of Physics, Jilin University , Changchun, Jilin 130012, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry and Physics, State University of New York , Stony Brook, New York 11794-3400, United States
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5
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Jongkon N, Gleeson D, Gleeson MP. Elucidation of the catalytic mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase using QM/MM calculations. Org Biomol Chem 2018; 16:6239-6249. [DOI: 10.1039/c8ob01428k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This account describes the application of QM/MM calculations to understand the reaction mechanism of HPPK, an important pharmacological target on the folate pathway for the treatment of diseases including anti-microbial resistance, malaria and cancer.
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Affiliation(s)
- Nathjanan Jongkon
- Department of Social and Applied Science
- College of Industrial Technology
- King Mongkut's University of Technology North Bangkok
- Bangkok 10800
- Thailand
| | - Duangkamol Gleeson
- Department of Chemistry
- Faculty of Science
- King Mongkut's Institute of Technology Ladkrabang
- Thailand
| | - M. Paul Gleeson
- Department of Biomedical Engineering
- Faculty of Engineering
- King Mongkut's Institute of Technology Ladkrabang
- Bangkok 10520
- Thailand
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6
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Dennis ML, Pitcher NP, Lee MD, DeBono AJ, Wang ZC, Harjani JR, Rahmani R, Cleary B, Peat TS, Baell JB, Swarbrick JD. Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. J Med Chem 2016; 59:5248-63. [PMID: 27094768 DOI: 10.1021/acs.jmedchem.6b00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a member of the folate biosynthesis pathway found in prokaryotes and lower eukaryotes that catalyzes the pyrophosphoryl transfer from the ATP cofactor to a 6-hydroxymethyl-7,8-dihydropterin substrate. We report the chemical synthesis of a series of S-functionalized 8-mercaptoguanine (8MG) analogues as substrate site inhibitors of HPPK and quantify binding against the E. coli and S. aureus enzymes (EcHPPK and SaHPPK). The results demonstrate that analogues incorporating acetophenone-based substituents have comparable affinities for both enzymes. Preferential binding of benzyl-substituted 8MG derivatives to SaHPPK was reconciled when a cryptic pocket unique to SaHPPK was revealed by X-ray crystallography. Differential chemical shift perturbation analysis confirmed this to be a common mode of binding for this series to SaHPPK. One compound (41) displayed binding affinities of 120 nM and 1.76 μM for SaHPPK and EcHPPK, respectively, and represents a lead for the development of more potent and selective inhibitors of SaHPPK.
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Affiliation(s)
- Matthew L Dennis
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Noel P Pitcher
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Aaron J DeBono
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Zhong-Chang Wang
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, People's Republic of China
| | - Jitendra R Harjani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Raphaël Rahmani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Ben Cleary
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - James D Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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7
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Folate Biosynthesis, Reduction, and Polyglutamylation and the Interconversion of Folate Derivatives. EcoSal Plus 2015; 2. [PMID: 26443588 DOI: 10.1128/ecosalplus.3.6.3.6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many microorganisms and plants possess the ability to synthesize folic acid derivatives de novo, initially forming dihydrofolate. All the folic acid derivatives that serve as recipients and donors of one-carbon units are derivatives of tetrahydrofolate, which is formed from dihydrofolate by an NADPH-dependent reduction catalyzed by dihydrofolate reductase (FolA). This review discusses the biosynthesis of dihydrofolate monoglutamate, its reduction to tetrahydrofolate monoglutamate, and the addition of glutamyl residues to form folylpolyglutamates. Escherichia coli and Salmonella, like many microorganisms that can synthesize folate de novo, appear to lack the ability to transport folate into the cell and are thus highly susceptible to inhibitors of folate biosynthesis. The review includes a brief discussion of the inhibition of folate biosynthesis by sulfa drugs. The folate biosynthetic pathway can be divided into two sections. First, the aromatic precursor chorismate is converted to paminobenzoic acid (PABA) by the action of three proteins. Second, the pteridine portion of folate is made from GTP and coupled to PABA to generate dihydropteroate, and the bifunctional protein specified by folC, dihydrofolate synthetase, or folylpolyglutamate synthetase, adds the initial glutamate molecule to form dihydrofolate (H2PteGlu1, or dihydropteroylmonoglutamate). Bacteriophage T4 infection of E. coli has been shown to cause alterations in the metabolism of folate derivatives. Infection is associated with an increase in the chain lengths in folylpolyglutamates and particularly the accumulation of hexaglutamate derivatives.
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8
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Shaw GX, Li Y, Shi G, Wu Y, Cherry S, Needle D, Zhang D, Tropea JE, Waugh DS, Yan H, Ji X. Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis. FEBS J 2014; 281:4123-37. [PMID: 24975935 PMCID: PMC5600157 DOI: 10.1111/febs.12896] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Two valid targets for antibiotic development, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS), catalyze consecutive reactions in folate biosynthesis. In Francisella tularensis (Ft), these two activities are contained in a single protein, FtHPPK-DHPS. Although Pemble et al. (PLoS One 5, e14165) determined the structure of FtHPPK-DHPS, they were unable to measure the kinetic parameters of the enzyme. In this study, we elucidated the binding and inhibitory activities of two HPPK inhibitors (HP-18 and HP-26) against FtHPPK-DHPS, determined the structure of FtHPPK-DHPS in complex with HP-26, and measured the kinetic parameters for the dual enzymatic activities of FtHPPK-DHPS. The biochemical analyses showed that HP-18 and HP-26 have significant isozyme selectivity, and that FtHPPK-DHPS is unique in that the catalytic efficiency of its DHPS activity is only 1/260,000 of that of Escherichia coli DHPS. Sequence and structural analyses suggest that HP-26 is an excellent lead for developing therapeutic agents for tularemia, and that the very low DHPS activity is due, at least in part, to the lack of a key residue that interacts with the substrate p-aminobenzoic acid (pABA). A BLAST search of the genomes of ten F. tularensis strains indicated that the bacterium contains a single FtHPPK-DHPS. The marginal DHPS activity and the single copy existence of FtHPPK-DHPS in F. tularensis make this bacterium more vulnerable to DHPS inhibitors. Current sulfa drugs are ineffective against tularemia; new inhibitors targeting the unique pABA-binding pocket may be effective and less subject to resistance because any mutations introducing resistance may make the marginal DHPS activity unable to support the growth of F. tularensis. DATABASE The coordinates and structure factors have been deposited in the Protein Data Bank under accession code 4PZV.
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Affiliation(s)
- Gary X. Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Danielle Needle
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Di Zhang
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
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9
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Yun MK, Hoagland D, Kumar G, Waddell MB, Rock CO, Lee RE, White SW. The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Bioorg Med Chem 2014; 22:2157-65. [PMID: 24613625 DOI: 10.1016/j.bmc.2014.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 01/19/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is an essential enzyme in the microbial folate biosynthetic pathway. This pathway has proven to be an excellent target for antimicrobial development, but widespread resistance to common therapeutics including the sulfa drugs has stimulated interest in HPPK as an alternative target in the pathway. A screen of a pterin-biased compound set identified several HPPK inhibitors that contain an aryl substituted 8-thioguanine scaffold, and structural analyses showed that these compounds engage the HPPK pterin-binding pocket and an induced cryptic pocket. A preliminary structure activity relationship profile was developed from biophysical and biochemical characterizations of derivative molecules. Also, a similarity search identified additional scaffolds that bind more tightly within the HPPK pterin pocket. These inhibitory scaffolds have the potential for rapid elaboration into novel lead antimicrobial agents.
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Affiliation(s)
- Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel Hoagland
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gyanendra Kumar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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10
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Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery. Antibiotics (Basel) 2014; 3:1-28. [PMID: 27025730 PMCID: PMC4790348 DOI: 10.3390/antibiotics3010001] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 01/07/2023] Open
Abstract
The need for new antimicrobials is great in face of a growing pool of resistant pathogenic organisms. This review will address the potential for antimicrobial therapy based on polypharmacological activities within the currently utilized bacterial biosynthetic folate pathway. The folate metabolic pathway leads to synthesis of required precursors for cellular function and contains a critical node, dihydrofolate reductase (DHFR), which is shared between prokaryotes and eukaryotes. The DHFR enzyme is currently targeted by methotrexate in anti-cancer therapies, by trimethoprim for antibacterial uses, and by pyrimethamine for anti-protozoal applications. An additional anti-folate target is dihyropteroate synthase (DHPS), which is unique to prokaryotes as they cannot acquire folate through dietary means. It has been demonstrated as a primary target for the longest standing antibiotic class, the sulfonamides, which act synergistically with DHFR inhibitors. Investigations have revealed most DHPS enzymes possess the ability to utilize sulfa drugs metabolically, producing alternate products that presumably inhibit downstream enzymes requiring the produced dihydropteroate. Recent work has established an off-target effect of sulfonamide antibiotics on a eukaryotic enzyme, sepiapterin reductase, causing alterations in neurotransmitter synthesis. Given that inhibitors of both DHFR and DHPS are designed to mimic their cognate substrate, which contain shared substructures, it is reasonable to expect such “off-target” effects. These inhibitors are also likely to interact with the enzymatic neighbors in the folate pathway that bind products of the DHFR or DHPS enzymes and/or substrates of similar substructure. Computational studies designed to assess polypharmacology reiterate these conclusions. This leads to hypotheses exploring the vast utility of multiple members of the folate pathway for modulating cellular metabolism, and includes an appealing capacity for prokaryotic-specific polypharmacology for antimicrobial applications.
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11
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Guo Q, He Y, Lu HP. Manipulating and probing enzymatic conformational fluctuations and enzyme–substrate interactions by single-molecule FRET-magnetic tweezers microscopy. Phys Chem Chem Phys 2014; 16:13052-8. [DOI: 10.1039/c4cp01454e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the critical role of the enzyme–substrate interactions in enzymatic reactions, the enzymatic conformation and enzyme–substrate interaction at a single-molecule level are manipulated by magnetic tweezers, and the impact of the manipulation on enzyme–substrate interactions are simultaneously probed by single-molecule FRET spectroscopy.
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Affiliation(s)
- Qing Guo
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
| | - Yufan He
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
| | - H. Peter Lu
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
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12
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13
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He Y, Lu M, Lu HP. Single-molecule photon stamping FRET spectroscopy study of enzymatic conformational dynamics. Phys Chem Chem Phys 2013; 15:770-5. [PMID: 23085845 PMCID: PMC3657739 DOI: 10.1039/c2cp42944f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescence resonant energy transfer (FRET) from a donor to an acceptor via transition dipole-dipole interactions decreases the donor's fluorescent lifetime. The donor's fluorescent lifetime decreases as the FRET efficiency increases, following the equation: E(FRET) = 1 - τ(DA)/τ(D), where τ(D) and τ(DA) are the donor fluorescence lifetime without FRET and with FRET. Accordingly, the FRET time trajectories associated with single-molecule conformational dynamics can be recorded by measuring the donor's lifetime fluctuations. In this article, we report our work on the use of a Cy3/Cy5-labeled enzyme, HPPK to demonstrate probing single-molecule conformational dynamics in an enzymatic reaction by measuring single-molecule FRET donor lifetime time trajectories. Compared with single-molecule fluorescence intensity-based FRET measurements, single-molecule lifetime-based FRET measurements are independent of fluorescence intensity. The latter has an advantage in terms of eliminating the analysis background noise from the acceptor fluorescence detection leak through noise, excitation light intensity noise, or light scattering noise due to local environmental factors, for example, in a AFM-tip correlated single-molecule FRET measurements. Furthermore, lifetime-based FRET also supports simultaneous single-molecule fluorescence anisotropy.
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Affiliation(s)
- Yufan He
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
| | - Maolin Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
| | - H. Peter Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
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14
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He Y, Lu M, Cao J, Lu HP. Manipulating protein conformations by single-molecule AFM-FRET nanoscopy. ACS NANO 2012; 6:1221-9. [PMID: 22276737 PMCID: PMC3662055 DOI: 10.1021/nn2038669] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area and simultaneously monitoring the conformational changes of the targeted protein by recording single-molecule FRET time trajectories. We have further demonstrated an application of using this nanoscopy on manipulation of single-molecule protein conformation and simultaneous single-molecule FRET measurement of a Cy3-Cy5-labeled kinase enzyme, HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase). By analyzing time-resolved FRET trajectories and correlated AFM force pulling curves of the targeted single-molecule enzyme, we are able to observe the protein conformational changes of a specific coordination by AFM mechanic force pulling.
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15
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Chhabra S, Dolezal O, Collins BM, Newman J, Simpson JS, Macreadie IG, Fernley R, Peat TS, Swarbrick JD. Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor. PLoS One 2012; 7:e29444. [PMID: 22276115 PMCID: PMC3261883 DOI: 10.1371/journal.pone.0029444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/28/2011] [Indexed: 12/17/2022] Open
Abstract
The first structural and biophysical data on the folate biosynthesis pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK), from the pathogen Staphylococcus aureus is presented. HPPK is the second essential enzyme in the pathway catalysing the pyrophosphoryl transfer from cofactor (ATP) to the substrate (6-hydroxymethyl-7,8-dihydropterin, HMDP). In-silico screening identified 8-mercaptoguanine which was shown to bind with an equilibrium dissociation constant, Kd, of ∼13 µM as measured by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR). An IC50 of ∼41 µM was determined by means of a luminescent kinase assay. In contrast to the biological substrate, the inhibitor has no requirement for magnesium or the ATP cofactor for competitive binding to the substrate site. The 1.65 Å resolution crystal structure of the inhibited complex showed that it binds in the pterin site and shares many of the key intermolecular interactions of the substrate. Chemical shift and 15N heteronuclear NMR measurements reveal that the fast motion of the pterin-binding loop (L2) is partially dampened in the SaHPPK/HMDP/α,β-methylene adenosine 5′-triphosphate (AMPCPP) ternary complex, but the ATP loop (L3) remains mobile on the µs-ms timescale. In contrast, for the SaHPPK/8-mercaptoguanine/AMPCPP ternary complex, the loop L2 becomes rigid on the fast timescale and the L3 loop also becomes more ordered – an observation that correlates with the large entropic penalty associated with inhibitor binding as revealed by ITC. NMR data, including 15N-1H residual dipolar coupling measurements, indicate that the sulfur atom in the inhibitor is important for stabilizing and restricting important motions of the L2 and L3 catalytic loops in the inhibited ternary complex. This work describes a comprehensive analysis of a new HPPK inhibitor, and may provide a foundation for the development of novel antimicrobials targeting the folate biosynthetic pathway.
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Affiliation(s)
- Sandeep Chhabra
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Olan Dolezal
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Australia
| | - Janet Newman
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Jamie S. Simpson
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ian G. Macreadie
- School of Applied Sciences, RMIT University, Bundoora, Australia
| | - Ross Fernley
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Thomas S. Peat
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - James D. Swarbrick
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- * E-mail:
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16
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He Y, Li Y, Mukherjee S, Wu Y, Yan H, Lu HP. Probing single-molecule enzyme active-site conformational state intermittent coherence. J Am Chem Soc 2011; 133:14389-95. [PMID: 21823644 PMCID: PMC3198842 DOI: 10.1021/ja204644y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule fluorescence resonance energy transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single-molecule intensity-time trajectories of enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multistep conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.
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Affiliation(s)
- Yufan He
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Saptarshi Mukherjee
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - H. Peter Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
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17
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Yan H, Ji X. Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Protein Pept Lett 2011; 18:328-35. [PMID: 21222642 DOI: 10.2174/092986611794654003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 12/15/2010] [Indexed: 11/22/2022]
Abstract
Enzymatic catalysis has conflicting structural requirements of the enzyme. In order for the enzyme to form a Michaelis complex, the enzyme must be in an open conformation so that the substrate can get into its active center. On the other hand, in order to maximize the stabilization of the transition state of the enzymatic reaction, the enzyme must be in a closed conformation to maximize its interactions with the transition state. The conflicting structural requirements can be resolved by a flexible active center that can sample both open and closed conformational states. For a bisubstrate enzyme, the Michaelis complex consists of two substrates in addition to the enzyme. The enzyme must remain flexible upon the binding of the first substrate so that the second substrate can get into the active center. The active center is fully assembled and stabilized only when both substrates bind to the enzyme. However, the side-chain positions of the catalytic residues in the Michaelis complex are still not optimally aligned for the stabilization of the transition state, which lasts only approximately 10(-13) s. The instantaneous and optimal alignment of catalytic groups for the transition state stabilization requires a dynamic enzyme, not an enzyme which undergoes a large scale of movements but an enzyme which permits at least a small scale of adjustment of catalytic group positions. This review will summarize the structure, catalytic mechanism, and dynamic properties of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase and examine the role of protein conformational dynamics in the catalysis of a bisubstrate enzymatic reaction.
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Affiliation(s)
- Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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18
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Pemble CW, Mehta PK, Mehra S, Li Z, Nourse A, Lee RE, White SW. Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis. PLoS One 2010; 5:e14165. [PMID: 21152407 PMCID: PMC2994781 DOI: 10.1371/journal.pone.0014165] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/09/2010] [Indexed: 11/30/2022] Open
Abstract
The 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) enzymes catalyze sequential metabolic reactions in the folate biosynthetic pathway of bacteria and lower eukaryotes. Both enzymes represent validated targets for the development of novel anti-microbial therapies. We report herein that the genes which encode FtHPPK and FtDHPS from the biowarfare agent Francisella tularensis are fused into a single polypeptide. The potential of simultaneously targeting both modules with pterin binding inhibitors prompted us to characterize the molecular details of the multifunctional complex. Our high resolution crystallographic analyses reveal the structural organization between FtHPPK and FtDHPS which are tethered together by a short linker. Additional structural analyses of substrate complexes reveal that the active sites of each module are virtually indistinguishable from those of the monofunctional enzymes. The fused bifunctional enzyme therefore represents an excellent vehicle for finding inhibitors that engage the pterin binding pockets of both modules that have entirely different architectures. To demonstrate that this approach has the potential of producing novel two-hit inhibitors of the folate pathway, we identify and structurally characterize a fragment-like molecule that simultaneously engages both active sites. Our study provides a molecular framework to study the enzyme mechanisms of HPPK and DHPS, and to design novel and much needed therapeutic compounds to treat infectious diseases.
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Affiliation(s)
- Charles W. Pemble
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Perdeep K. Mehta
- Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Smriti Mehra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Amanda Nourse
- The Hartwell Center, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Richard E. Lee
- Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
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19
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Janowski R, Panjikar S, Eddine AN, Kaufmann SHE, Weiss MS. Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2009; 10:137-50. [PMID: 19184528 PMCID: PMC2758359 DOI: 10.1007/s10969-009-9060-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 01/14/2009] [Indexed: 01/07/2023]
Abstract
Tuberculosis (TB) is a major global health threat caused by Mycobacterium tuberculosis (Mtb). It is further fueled by the HIV pandemic and by increasing incidences of multidrug resistant Mtb-strains. Rv2827c, a hypothetical protein from Mtb, has been implicated in the survival of Mtb in the macrophages of the host. The three-dimensional structure of Rv2827c has been determined by the three-wavelength anomalous diffraction technique using bromide-derivatized crystals and refined to a resolution of 1.93 A. The asymmetric unit of the orthorhombic crystals contains two independent protein molecules related by a non-crystallographic translation. The tertiary structure of Rv2827c comprises two domains: an N-terminal domain displaying a winged helix topology and a C-terminal domain, which appears to constitute a new and unique fold. Based on structural homology considerations and additional biochemical evidence, it could be established that Rv2827c is a DNA-binding protein. Once the understanding of the structure-function relationship of Rv2827c extends to the function of Rv2827c in vivo, new clues for the rational design of novel intervention strategies may be obtained.
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Affiliation(s)
- Robert Janowski
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
- IBMB (CSIC), Parc Científic de Barcelona, Baldiri Riexac 10–12, 08028 Barcelona, Spain
| | - Santosh Panjikar
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
| | - Ali Nasser Eddine
- Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Manfred S. Weiss
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
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20
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Lescop E, Lu Z, Liu Q, Xu H, Li G, Xia B, Yan H, Jin C. Dynamics of the conformational transitions in the assembling of the Michaelis complex of a bisubstrate enzyme: a (15)N relaxation study of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 2009; 48:302-12. [PMID: 19108643 DOI: 10.1021/bi8016262] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), which follows an ordered bi-bi kinetic mechanism with ATP binding to the enzyme first. HPPK undergoes dramatic conformational changes during its catalytic cycle as revealed by X-ray crystallography, and the conformational changes are essential for the enzymatic catalysis as shown by site-directed mutagenesis and biochemical and crystallographic analysis of the mutants. However, the dynamic properties of the enzyme have not been measured experimentally. Here, we report a (15)N NMR relaxation study of the dynamic properties of Escherichia coli HPPK from the apo form to the binary substrate complex with MgATP (represented by MgAMPCPP, an ATP analogue) to the Michaelis complex (ternary substrate complex) with MgATP (represented by MgAMPCPP) and HP (represented by 7,7-dimethyl-6-hydroxypterin, an HP analogue). The results show that the binding of the nucleotide to HPPK does not cause major changes in the dynamic properties of the enzyme. Whereas enzymes are often more rigid when bound to the ligand or the substrate, the internal mobility of HPPK is not reduced and is even moderately increased in the binary complex, particularly in the catalytic loops. The internal mobility of the catalytic loops is significantly quenched upon the formation of the ternary complex, but some mobility remains. The enhanced motions in the catalytic loops of the binary substrate complex may be required for the assembling of the ternary complex. On the other hand, some degrees of mobility in the catalytic loops of the ternary complex may be required for the optimal stabilization of the transition state, which may need the instantaneous adjustment and alignment of the side-chain positions of catalytic residues. Such dynamic behaviors may be characteristic of bisubstrate enzymes.
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Affiliation(s)
- Ewen Lescop
- Beijing NMR Center, College of Life Sciences, Peking University, Beijing 100871, China
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21
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Brylinski M, Skolnick J. What is the relationship between the global structures of apo and holo proteins? Proteins 2008; 70:363-77. [PMID: 17680687 DOI: 10.1002/prot.21510] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
It is well known that ligand binding and release may induce a wide range of structural changes in a receptor protein, varying from small movements of loops or side chains in the binding pocket to large-scale domain hinge-bending and shear motions or even partial unfolding that facilitates the capture and release of a ligand. An interesting question is what in general are the conformational changes triggered by ligand binding? The aim of this work is analyze the magnitude of structural changes in a protein resulting from ligand binding to assess if the state of ligand binding needs to be included in template-based protein structure prediction algorithms. To address this issue, a nonredundant dataset of 521 paired protein structures in the ligand-free and ligand-bound form was created and used to estimate the degree of both local and global structure similarity between the apo and holo forms. In most cases, the proteins undergo relatively small conformational rearrangements of their tertiary structure upon ligand binding/release (most root-mean-square-deviations from native, RMSD, are <1 A). However, a clear difference was observed between single- and multiple-domain proteins. For the latter, RMSD changes greater than 1 A and sometimes larger were found for almost 1/3 of the cases; these are mainly associated with large-scale hinge-bending movements of entire domains. The changes in the mutual orientation of individual domains in multiple-domain proteins upon ligand binding were investigated using a mechanistic model based on mass-weighted principal axes as well as interface buried surface calculations. Some preferences toward the anticipated mechanism of protein domain movements are predictable based on the examination of just the ligand-free structural form. These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited.
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Affiliation(s)
- Michal Brylinski
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
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22
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Chapter 15 The Structure and Mechanism of 6‐Hydroxymethyl‐7,8‐Dihydropterin Pyrophosphokinase. VITAMINS AND HORMONES 2008. [DOI: 10.1016/s0083-6729(08)00415-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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23
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Zhao WN, Jiang YJ, Yu QS, Zou JW, Zhang N. Molecular dynamics simulation on complex of HPPK and substrate HP. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.03.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Lawrence MC, Iliades P, Fernley RT, Berglez J, Pilling PA, Macreadie IG. The three-dimensional structure of the bifunctional 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase/dihydropteroate synthase of Saccharomyces cerevisiae. J Mol Biol 2005; 348:655-70. [PMID: 15826662 DOI: 10.1016/j.jmb.2005.03.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/03/2005] [Accepted: 03/04/2005] [Indexed: 11/16/2022]
Abstract
In Saccharomyces cerevisiae and other fungi, the enzymes dihydroneopterin aldolase, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) are encoded by a polycistronic gene that is translated into a single polypeptide having all three functions. These enzymatic functions are essential to both prokaryotes and lower eukaryotes, and catalyse sequential reactions in folate biosynthesis. Deletion or disruption of either function leads to cell death. These enzymes are absent from mammals and thus make ideal antimicrobial targets. DHPS is currently the target of antifolate therapy for a number of infectious diseases, and its activity is inhibited by sulfonamides and sulfones. These drugs are typically used as part of a synergistic cocktail with the 2,4-diaminopyrimidines that inhibit dihydrofolate reductase. A gene encoding the S.cerevisiae HPPK and DHPS enzymes has been cloned and expressed in Escherichia coli. A complex of the purified bifunctional polypeptide with a pterin monophosphate substrate analogue has been crystallized, and its structure solved by molecular replacement and refined to 2.3A resolution. The polypeptide consists of two structural domains, each of which closely resembles its respective monofunctional bacterial HPPK and DHPS counterpart. The mode of ligand binding is similar to that observed in the bacterial enzymes. The association between the domains within the polypeptide as well as the quaternary association of the polypeptide via its constituent DHPS domains provide insight into the assembly of the trifunctional enzyme in S.cerevisiae and probably other fungal species.
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Affiliation(s)
- Michael C Lawrence
- CSIRO Health Sciences and Nutrition, 343 Royal Parade, Parkville, Victoria 3052, Australia.
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25
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Yang R, Lee MC, Yan H, Duan Y. Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP. Biophys J 2005; 89:95-106. [PMID: 15821168 PMCID: PMC1366583 DOI: 10.1529/biophysj.105.061556] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.
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Affiliation(s)
- Rong Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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