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Ramos-Gonzalez N, Paul B, Majumdar S. IUPHAR themed review: Opioid efficacy, bias, and selectivity. Pharmacol Res 2023; 197:106961. [PMID: 37844653 DOI: 10.1016/j.phrs.2023.106961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
Drugs acting at the opioid receptor family are clinically used to treat chronic and acute pain, though they represent the second line of treatment behind GABA analogs, antidepressants and SSRI's. Within the opioid family mu and kappa opioid receptor are commonly targeted. However, activation of the mu opioid receptor has side effects of constipation, tolerance, dependence, euphoria, and respiratory depression; activation of the kappa opioid receptor leads to dysphoria and sedation. The side effects of mu opioid receptor activation have led to mu receptor drugs being widely abused with great overdose risk. For these reasons, newer safer opioid analgesics are in high demand. For many years a focus within the opioid field was finding drugs that activated the G protein pathway at mu opioid receptor, without activating the β-arrestin pathway, known as biased agonism. Recent advances have shown that this may not be the way forward to develop safer analgesics at mu opioid receptor, though there is still some promise at the kappa opioid receptor. Here we discuss recent novel approaches to develop safer opioid drugs including efficacy vs bias and fine-tuning receptor activation by targeting sub-pockets in the orthosteric site, we explore recent works on the structural basis of bias, and we put forward the suggestion that Gα subtype selectivity may be an exciting new area of interest.
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Affiliation(s)
- Nokomis Ramos-Gonzalez
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA
| | - Barnali Paul
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA
| | - Susruta Majumdar
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA.
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Kifayat S, Yele V, Ashames A, Sigalapalli DK, Bhandare RR, Shaik AB, Nasipireddy V, Sanapalli BKR. Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance. RSC Adv 2023; 13:11368-11384. [PMID: 37057268 PMCID: PMC10089256 DOI: 10.1039/d3ra00013c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.
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Affiliation(s)
- Sumaiya Kifayat
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
| | - Vidyasrilekha Yele
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India
| | - Akram Ashames
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Dilep Kumar Sigalapalli
- Department of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University Vadlamudi 522213 Andhra Pradesh India
| | - Richie R Bhandare
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada Chebrolu Guntur 522212 Andhra Pradesh India
| | | | - Bharat Kumar Reddy Sanapalli
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
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Kibou Z, Aissaoui N, Daoud I, Seijas JA, Vázquez-Tato MP, Klouche Khelil N, Choukchou-Braham N. Efficient Synthesis of 2-Aminopyridine Derivatives: Antibacterial Activity Assessment and Molecular Docking Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113439. [PMID: 35684377 PMCID: PMC9182143 DOI: 10.3390/molecules27113439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
A new and suitable multicomponent one-pot reaction was developed for the synthesis of 2-amino-3-cyanopyridine derivatives. BACKGROUND This synthesis was demonstrated by the efficient and easy access to a variety of substituted 2-aminopyridines using enaminones as key precursors under solvent-free conditions. METHODS A range of spectroscopic techniques was used to determine and confirm the chemical structures (FTIR, 1H NMR, 13C NMR). The antimicrobial potency of synthesized compounds (2a-d) was tested using disk diffusion assays, and the Minimum Inhibitory Concentration (MIC) for the active compounds was determined against a panel of microorganisms, including Gram-positive and Gram-negative bacteria and yeasts. Moreover, a docking analysis was conducted by Molecular Operating Environment (MOE) software to provide supplementary information about the potential, as well as an ADME-T prediction to describe the pharmacokinetic properties of the best compound and its toxicity. RESULTS The results of the antimicrobial activity indicated that compound 2c showed the highest activity against Gram-positive bacteria, particularly S. aureus and B. subtilis whose MIC values were 0.039 ± 0.000 µg·mL-1. The results of the theoretical study of compound 2c were in line with the experimental data and exhibited excellent antibacterial potential. CONCLUSIONS On the basis of the obtained results, compound 2c can be used as an antibacterial agent model with high antibacterial potency.
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Affiliation(s)
- Zahira Kibou
- Laboratoire de Catalyse et Synthèse en Chimie Organique, Faculté des Sciences, Université de Tlemcen, BP 119, Tlemcen 13000, Algeria;
- Faculté des Sciences et de la Technologie, Université de Ain Témouchent, BP 284, Ain Témouchent 46000, Algeria
- Correspondence: (Z.K.); (J.A.S.)
| | - Nadia Aissaoui
- Laboratory of the Sustainable Management of Natural Resources in Arid and Semi Aridareas, University Center Salhi Ahmed Naama, BP 66, Naama 45000, Algeria;
- Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, Tlemcen 13000, Algeria
| | - Ismail Daoud
- Département des Sciences de la Matière, Université de Mohamed Khider, BP 145 RP, Biskra 07000, Algerie;
- Laboratory of Natural and Bio-Active Substances, Faculty of Sciences, University of Tlemcen, BP 119, Tlemcen 13000, Algeria
| | - Julio A. Seijas
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Santiago de Compostela, A da, Alfonso X El Sabio s/n, 27002 Lugo, Spain;
- Correspondence: (Z.K.); (J.A.S.)
| | - María Pilar Vázquez-Tato
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Santiago de Compostela, A da, Alfonso X El Sabio s/n, 27002 Lugo, Spain;
| | - Nihel Klouche Khelil
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, Tlemcen 13000, Algeria;
- Laboratory of Experimental Surgery, Medical Faculty, University of Tlemcen, Tlemcen 13000, Algeria
| | - Noureddine Choukchou-Braham
- Laboratoire de Catalyse et Synthèse en Chimie Organique, Faculté des Sciences, Université de Tlemcen, BP 119, Tlemcen 13000, Algeria;
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Structural, molecular docking computational studies and in-vitro evidence for antibacterial activity of mixed ligand complexes. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130481] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lv D, Li J, Ye S. The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models. Front Microbiol 2021; 12:639883. [PMID: 33859629 PMCID: PMC8042166 DOI: 10.3389/fmicb.2021.639883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/05/2021] [Indexed: 01/14/2023] Open
Abstract
Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity.
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Affiliation(s)
- Dashuai Lv
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Institute of Quantitative Biology, Hangzhou, China
| | - Sheng Ye
- Life Sciences Institute, Zhejiang University, Hangzhou, China.,Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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Cell Division Protein FtsZ Is Unfolded for N-Terminal Degradation by Antibiotic-Activated ClpP. mBio 2020; 11:mBio.01006-20. [PMID: 32605984 PMCID: PMC7327170 DOI: 10.1128/mbio.01006-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acyldepsipeptide (ADEP) antibiotics effectively kill multidrug-resistant Gram-positive pathogens, including vancomycin-resistant enterococcus, penicillin-resistant Streptococcus pneumoniae (PRSP), and methicillin-resistant Staphylococcus aureus (MRSA). The antibacterial activity of ADEP depends on a new mechanism of action, i.e., the deregulation of bacterial protease ClpP that leads to bacterial self-digestion. Our data allow new insights into the mode of ADEP action by providing a molecular explanation for the distinct bacterial phenotypes observed at low versus high ADEP concentrations. In addition, we show that ClpP alone, in the absence of any unfoldase or energy-consuming system, and only activated by the small molecule antibiotic ADEP, leads to the unfolding of the cell division protein FtsZ. Antibiotic acyldepsipeptides (ADEPs) deregulate ClpP, the proteolytic core of the bacterial Clp protease, thereby inhibiting its native functions and concomitantly activating it for uncontrolled proteolysis of nonnative substrates. Importantly, although ADEP-activated ClpP is assumed to target multiple polypeptide and protein substrates in the bacterial cell, not all proteins seem equally susceptible. In Bacillus subtilis, the cell division protein FtsZ emerged to be particularly sensitive to degradation by ADEP-activated ClpP at low inhibitory ADEP concentrations. In fact, FtsZ is the only bacterial protein that has been confirmed to be degraded in vitro as well as within bacterial cells so far. However, the molecular reason for this preferred degradation remained elusive. Here, we report the unexpected finding that ADEP-activated ClpP alone, in the absence of any Clp-ATPase, leads to an unfolding and subsequent degradation of the N-terminal domain of FtsZ, which can be prevented by the stabilization of the FtsZ fold via nucleotide binding. At elevated antibiotic concentrations, importantly, the C terminus of FtsZ is notably targeted for degradation in addition to the N terminus. Our results show that different target structures are more or less accessible to ClpP, depending on the ADEP level present. Moreover, our data assign a Clp-ATPase-independent protein unfolding capability to the ClpP core of the bacterial Clp protease and suggest that the protein fold of FtsZ may be more flexible than previously anticipated.
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Silber N, Matos de Opitz CL, Mayer C, Sass P. Cell division protein FtsZ: from structure and mechanism to antibiotic target. Future Microbiol 2020; 15:801-831. [DOI: 10.2217/fmb-2019-0348] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance to virtually all clinically applied antibiotic classes severely limits the available options to treat bacterial infections. Hence, there is an urgent need to develop and evaluate new antibiotics and targets with resistance-breaking properties. Bacterial cell division has emerged as a new antibiotic target pathway to counteract multidrug-resistant pathogens. New approaches in antibiotic discovery and bacterial cell biology helped to identify compounds that either directly interact with the major cell division protein FtsZ, thereby perturbing the function and dynamics of the cell division machinery, or affect the structural integrity of FtsZ by inducing its degradation. The impressive antimicrobial activities and resistance-breaking properties of certain compounds validate the inhibition of bacterial cell division as a promising strategy for antibiotic intervention.
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Affiliation(s)
- Nadine Silber
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Cruz L Matos de Opitz
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Christian Mayer
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen 72076, Germany
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8
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Abstract
The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article, we review what we have learned during the past decade about the Z-ring's structure, function, and dynamics, with a particular focus on insights generated by recent high-resolution imaging and single-molecule analyses. We suggest that the major function of the Z-ring is to govern nascent cell pole morphogenesis by directing the spatiotemporal distribution of septal cell wall remodeling enzymes through the Z-ring's GTP hydrolysis-dependent treadmilling dynamics. In this role, FtsZ functions in cell division as the counterpart of the cell shape-determining actin homolog MreB in cell elongation.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
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Naini R, Pavankumar P, Prabhakar S, Kancha RK, Rao KV, Reddy VD. Evolvement of nutraceutical onion plants engineered for resveratrol biosynthetic pathway. PLANT CELL REPORTS 2019; 38:1127-1137. [PMID: 31154513 DOI: 10.1007/s00299-019-02432-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Genetically engineered onion expressing codon-optimized VvSTS1 gene accumulated stilbenes and extended life span in yeast and can serve as potential nutraceutical. Resveratrol (RV) is a natural polyphenolic compound found in certain plant species including grapes. RV is well known for its nutraceutical properties and to assuage several disease conditions. Onion is the second most consumed vegetable worldwide and contains large quantities of precursor molecules, malonyl-CoA and para-coumaroyl-CoA that are needed for RV biosynthesis. The present study reports the development of nutraceutical onion by engineering RV biosynthetic pathway. A codon-optimized grapevine synthetic stilbene synthase gene (VvSTS1) was synthesized using native grapevine sequence. Six-week-old healthy yellowish compact nodular calli were co-cultivated with Agrobacterium tumefaciens harbouring pCAMBIA1300-hpt II-CaMV35S-VvSTS1-nos. PCR analysis revealed the presence of VvSTS1 and hpt II genes in putative transgenics. Southern blot analysis confirmed the integration of VvSTS1 gene and independent nature of transformants. LC-ESI-HRMS analysis revealed the accumulation of variable quantities of RV (24.98-50.18 µg/g FW) and its glycosylated form polydatin (33.6-67.15 µg/g FW) in both leaves and bulbs, respectively, indicating the successful engineering of RV biosynthetic pathway into onion. The transgenic onion bulb extracts extended the life span in haploid yeast. The transgenic onion accumulating RV and polydatin, developed for the first of its kind, may serve as a potential nutraceutical resource.
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Affiliation(s)
- Raju Naini
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India
| | - P Pavankumar
- Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
- Acadamy of Scientific and Innovative Research, CSIR-IICT, Hyderabad, India
| | - S Prabhakar
- Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
- Acadamy of Scientific and Innovative Research, CSIR-IICT, Hyderabad, India
| | - Rama Krishna Kancha
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India
| | | | - Vudem Dashavantha Reddy
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana, 500007, India.
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Kusuma KD, Griffith R, Harry EJ, Bottomley AL, Ung AT. In silico Analysis of FtsZ Crystal Structures Towards a New Target for Antibiotics. Aust J Chem 2019. [DOI: 10.1071/ch18347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bacterial cell division protein FtsZ is conserved in most bacteria and essential for viability. There have been concerted efforts in developing inhibitors that target FtsZ as potential antibiotics. Key to this is an in-depth understanding of FtsZ structure at the molecular level across diverse bacterial species to ensure inhibitors have high affinity for the FtsZ target in a variety of clinically relevant pathogens. In this study, we show that FtsZ structures differ in three ways: (1) the H7 helix curvature; (2) the dimensions of the interdomain cleft; and (3) the opening/closing mechanism of the interdomain cleft, whereas no differences were observed in the dimensions of the nucleotide-binding pocket and T7 loop. Molecular dynamics simulation may suggest that there are two possible mechanisms for the process of opening and closing of the interdomain cleft on FtsZ structures. This discovery highlights significant differences between FtsZ structures at the molecular level and this knowledge is vital in assisting the design of potent FtsZ inhibitors.
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Fujita J, Harada R, Maeda Y, Saito Y, Mizohata E, Inoue T, Shigeta Y, Matsumura H. Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus. J Struct Biol 2017; 198:65-73. [PMID: 28456664 DOI: 10.1016/j.jsb.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/18/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
The tubulin-homolog protein FtsZ is essential for bacterial cell division. FtsZ polymerizes to form protofilaments that assemble into a contractile ring-shaped structure in the presence of GTP. Recent studies showed that FtsZ treadmilling coupled with the GTPase activity drives cell wall synthesis and bacterial cell division. The treadmilling caused by assembly and disassembly of FtsZ links to a conformational change of the monomer from a tense (T) to a relaxed (R) state, but considerable controversy still remains concerning the mechanism. In this study, we report crystal structures of FtsZ from Staphylococcus aureus corresponding to the T and R state conformations in the same crystal, indicating the structural equilibrium of the two state. The two structures identified a key residue Arg29, whose importance was also confirmed by our modified MD simulations. Crystal structures of the R29A mutant showed T and R state-like conformations with slight but important structural changes compared to those of wild-type. Collectively, these data provide new insights for understanding how intramolecular interactions are related to the structural transition of FtsZ.
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Affiliation(s)
- Junso Fujita
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuhei Harada
- Graduate School of Pure and Applied Sciences/Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Yoko Maeda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Saito
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuteru Shigeta
- Graduate School of Pure and Applied Sciences/Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
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Exploring the possible binding mode of trisubstituted benzimidazoles analogues in silico for novel drug designtargeting Mtb FtsZ. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1734-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC. Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species. PLoS Comput Biol 2015; 11:e1004117. [PMID: 25811761 PMCID: PMC4374959 DOI: 10.1371/journal.pcbi.1004117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/08/2015] [Indexed: 01/28/2023] Open
Abstract
The recent increase in antibiotic resistance in pathogenic bacteria calls for new approaches to drug-target selection and drug development. Targeting the mechanisms of action of proteins involved in bacterial cell division bypasses problems associated with increasingly ineffective variants of older antibiotics; to this end, the essential bacterial cytoskeletal protein FtsZ is a promising target. Recent work on its allosteric inhibitor, PC190723, revealed in vitro activity on Staphylococcus aureus FtsZ and in vivo antimicrobial activities. However, the mechanism of drug action and its effect on FtsZ in other bacterial species are unclear. Here, we examine the structural environment of the PC190723 binding pocket using PocketFEATURE, a statistical method that scores the similarity between pairs of small-molecule binding sites based on 3D structure information about the local microenvironment, and molecular dynamics (MD) simulations. We observed that species and nucleotide-binding state have significant impacts on the structural properties of the binding site, with substantially disparate microenvironments for bacterial species not from the Staphylococcus genus. Based on PocketFEATURE analysis of MD simulations of S. aureus FtsZ bound to GTP or with mutations that are known to confer PC190723 resistance, we predict that PC190723 strongly prefers to bind Staphylococcus FtsZ in the nucleotide-bound state. Furthermore, MD simulations of an FtsZ dimer indicated that polymerization may enhance PC190723 binding. Taken together, our results demonstrate that a drug-binding pocket can vary significantly across species, genetic perturbations, and in different polymerization states, yielding important information for the further development of FtsZ inhibitors.
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Affiliation(s)
- Amanda Miguel
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Jen Hsin
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Tianyun Liu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Grace Tang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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15
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Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2014; 95:142-8. [PMID: 25613812 DOI: 10.1016/j.tube.2014.12.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/10/2014] [Indexed: 01/31/2023]
Abstract
High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brianna Armour
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brandy M Taylor
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Marvin M Muruthi
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - James W Fairman
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David Fox
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Shellie H Dieterich
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Alberto J Napuli
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Janette Myers
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Micah Ferrell
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Elizabeth Mundt
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Katie Thompkins
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ngoc Tran
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Aarthi Sekar
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Dmitri Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Don Lorimer
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States.
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16
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Buske PJ, Mittal A, Pappu RV, Levin PA. An intrinsically disordered linker plays a critical role in bacterial cell division. Semin Cell Dev Biol 2014; 37:3-10. [PMID: 25305578 DOI: 10.1016/j.semcdb.2014.09.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 09/13/2014] [Indexed: 02/07/2023]
Abstract
In bacteria, animals, fungi, and many single celled eukaryotes, division is initiated by the formation of a ring of cytoskeletal protein at the nascent division site. In bacteria, the tubulin-like GTPase FtsZ serves as the foundation for the cytokinetic ring. A conserved feature of FtsZ is an intrinsically disordered peptide known as the C-terminal linker. Chimeric experiments suggest the linker acts as a flexible boom allowing FtsZ to associate with the membrane through a conserved C-terminal domain and also modulates interactions both between FtsZ subunits and between FtsZ and modulatory proteins in the cytoplasm.
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Affiliation(s)
- P J Buske
- Department of Cellular and Molecular Pharmacology and The Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering & Center for Biological Systems Engineering, Saint Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering & Center for Biological Systems Engineering, Saint Louis, MO 63130, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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17
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Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1. Sci Rep 2014; 4:5944. [PMID: 25089892 PMCID: PMC4123200 DOI: 10.1038/srep05944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 12/25/2022] Open
Abstract
Influenza A viruses cause the respiratory illness influenza, which can be mild to fatal depending on the strain and host immune response. The flu polymerase acidic (PA), polymerase basic 1 (PB1), and polymerase basic 2 (PB2) proteins comprise the RNA-dependent RNA polymerase complex responsible for viral genome replication. The first crystal structures of the C-terminal domain of PA (PA-CTD) in the absence of PB1-derived peptides show a number of structural changes relative to the previously reported PB1-peptide bound structures. The human A/WSN/1933 (H1N1) and avian A/Anhui1/2013 (H7N9) strain PA-CTD proteins exhibit the same global topology as other strains in the absence of PB1, but differ extensively in the PB1 binding pocket including a widening of the binding groove and the unfolding of a β-turn. Both PA-CTD proteins exhibited a significant increase in thermal stability in the presence of either a PB1-derived peptide or a previously reported inhibitor in differential scanning fluorimetry assays. These structural changes demonstrate plasticity in the PA-PB1 binding interface which may be exploited in the development of novel therapeutics.
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18
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Singh D, Bhattacharya A, Rai A, Dhaked HPS, Awasthi D, Ojima I, Panda D. SB-RA-2001 inhibits bacterial proliferation by targeting FtsZ assembly. Biochemistry 2014; 53:2979-92. [PMID: 24749867 PMCID: PMC4020581 DOI: 10.1021/bi401356y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
FtsZ
has been recognized as a promising antimicrobial drug target
because of its vital role in bacterial cell division. In this work,
we found that a taxane SB-RA-2001 inhibited the proliferation of Bacillus subtilis 168 and Mycobacterium smegmatis cells with minimal inhibitory concentrations of 38 and 60 μM,
respectively. Cell lengths of these microorganisms increased remarkably
in the presence of SB-RA-2001, indicating that it inhibits bacterial
cytokinesis. SB-RA-2001 perturbed the formation of the FtsZ ring in B. subtilis 168 cells and also affected the localization
of the late cell division protein, DivIVA, at the midcell position.
Flow cytometric analysis of the SB-RA-2001-treated cells indicated
that the compound did not affect the duplication of DNA in B. subtilis 168 cells. Further, SB-RA-2001 treatment did
not affect the localization of the chromosomal partitioning protein,
Spo0J, along the two ends of the nucleoids and also had no discernible
effect on the nucleoid segregation in B. subtilis 168 cells. The agent also did not appear to perturb the membrane
potential of B. subtilis 168 cells. In vitro, SB-RA-2001 bound to FtsZ with modest affinity, promoted the assembly
and bundling of FtsZ protofilaments, and reduced the GTPase activity
of FtsZ. GTP did not inhibit the binding of SB-RA-2001 to FtsZ, suggesting
that it does not bind to the GTP binding site on FtsZ. A computational
analysis indicated that SB-RA-2001 binds to FtsZ in the cleft region
between the C-terminal domain and helix H7, and the binding site of
SB-RA-2001 on FtsZ resembled that of PC190723, a well-characterized
inhibitor of FtsZ. The findings collectively suggested that SB-RA-2001
inhibits bacterial proliferation by targeting the assembly dynamics
of FtsZ, and this can be exploited further to develop potent FtsZ-targeted
antimicrobials.
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Affiliation(s)
- Dipty Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai 400076, India
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19
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A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Antimicrob Agents Chemother 2013; 58:1458-67. [PMID: 24366729 DOI: 10.1128/aac.01875-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis. Crystal structure and nuclear magnetic resonance analyses of BpML1 in complex with known macrocyclics and other derivatives led to the identification of a key chemical scaffold. This scaffold possesses inhibitory potency for BpML1 without the immunosuppressive components of related macrocyclic agents. Biophysical characterization of a compound series with this scaffold allowed binding site specificity in solution and potency determinations for rank ordering the set. The best compounds in this series possessed a low-micromolar affinity for BpML1, bound at the site of enzymatic activity, and inhibited a panel of homologous Mip proteins from other pathogenic bacteria, without demonstrating toxicity in human macrophages. Importantly, the in vitro activity of BpML1 was reduced by these compounds, leading to decreased macrophage infectivity and intracellular growth of Burkholderia pseudomallei. These compounds offer the potential for activity against a new class of antimicrobial targets and present the utility of a structure-based approach for novel antimicrobial drug discovery.
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20
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Matsui T, Han X, Yu J, Yao M, Tanaka I. Structural change in FtsZ Induced by intermolecular interactions between bound GTP and the T7 loop. J Biol Chem 2013; 289:3501-9. [PMID: 24347164 DOI: 10.1074/jbc.m113.514901] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FtsZ is a prokaryotic homolog of tubulin and is a key molecule in bacterial cell division. FtsZ with bound GTP polymerizes into tubulin-like protofilaments. Upon polymerization, the T7 loop of one subunit is inserted into the nucleotide-binding pocket of the second subunit, which results in GTP hydrolysis. Thus, the T7 loop is important for both polymerization and hydrolysis in the tubulin/FtsZ family. Although x-ray crystallography revealed both straight and curved conformations of tubulin, only a curved structure was known for FtsZ. Recently, however, FtsZ from Staphylococcus aureus has been shown to have a very different conformation from the canonical FtsZ structure. The present study was performed to investigate the structure of FtsZ from Staphylococcus aureus by mutagenesis experiments; the effects of amino acid changes in the T7 loop on the structure as well as on GTPase activity were studied. These analyses indicated that FtsZ changes its conformation suitable for polymerization and GTP hydrolysis by movement between N- and C-subdomains via intermolecular interactions between bound nucleotide and residues in the T7 loop.
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Affiliation(s)
- Takashi Matsui
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan and
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21
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Li Y, Hsin J, Zhao L, Cheng Y, Shang W, Huang KC, Wang HW, Ye S. FtsZ protofilaments use a hinge-opening mechanism for constrictive force generation. Science 2013; 341:392-5. [PMID: 23888039 DOI: 10.1126/science.1239248] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The essential bacterial protein FtsZ is a guanosine triphosphatase that self-assembles into a structure at the division site termed the "Z ring". During cytokinesis, the Z ring exerts a constrictive force on the membrane by using the chemical energy of guanosine triphosphate hydrolysis. However, the structural basis of this constriction remains unresolved. Here, we present the crystal structure of a guanosine diphosphate-bound Mycobacterium tuberculosis FtsZ protofilament, which exhibits a curved conformational state. The structure reveals a longitudinal interface that is important for function. The protofilament curvature highlights a hydrolysis-dependent conformational switch at the T3 loop that leads to longitudinal bending between subunits, which could generate sufficient force to drive cytokinesis.
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Affiliation(s)
- Ying Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang, P.R. China
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22
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Jamous C, Basdevant N, Ha-Duong T. Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study. J Biomol Struct Dyn 2013; 32:916-27. [PMID: 23782014 DOI: 10.1080/07391102.2013.799436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present here a structural analysis of ten extensive all-atom molecular dynamics simulations of the monomeric protein FtsZ in various binding states. Since the polymerization and GTPase activities of FtsZ depend on the nature of a bound nucleotide as well as on the presence of a magnesium ion, we studied the structural differences between the average conformations of the following five systems: FtsZ-Apo, FtsZ-GTP, FtsZ-GDP, FtsZ-GTP-Mg, and FtsZ-GDP-Mg. The in silico solvated average structure of FtsZ-Apo significantly differs from the crystallographic structure 1W59 of FtsZ which was crystallized in a dimeric form without nucleotide and magnesium. The simulated Apo form of the protein also clearly differs from the FtsZ structures when it is bound to its ligand, the most important discrepancies being located in the loops surrounding the nucleotide binding pocket. The three average structures of FtsZ-GTP, FtsZ-GDP, and FtsZ-GTP-Mg are overall similar, except for the loop T7 located at the opposite side of the binding pocket and whose conformation in FtsZ-GDP notably differs from the one in FtsZ-GTP and FtsZ-GTP-Mg. The presence of a magnesium ion in the binding pocket has no impact on the FtsZ conformation when it is bound to GTP. In contrast, when the protein is bound to GDP, the divalent cation causes a translation of the nucleotide outwards the pocket, inducing a significant conformational change of the loop H6-H7 and the top of helix H7.
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Affiliation(s)
- Carla Jamous
- a LAMBE - UMR CNRS 8587, Université d'Evry-Val-d'Essonne, Rue du Père André Jarlan , 91025 , Evry Cedex , France
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23
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Buske PJ, Levin PA. A flexible C-terminal linker is required for proper FtsZ assembly in vitro and cytokinetic ring formation in vivo. Mol Microbiol 2013; 89:249-63. [PMID: 23692518 DOI: 10.1111/mmi.12272] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2013] [Indexed: 02/01/2023]
Abstract
Assembly of the cytoskeletal protein FtsZ into a ring-like structure is required for bacterial cell division. Structurally, FtsZ consists of four domains: the globular N-terminal core, a flexible linker, 8-9 conserved residues implicated in interactions with modulatory proteins, and a highly variable set of 4-10 residues at its very C terminus. Largely ignored and distinguished by lack of primary sequence conservation, the linker is presumed to be intrinsically disordered. Here we employ genetics, biochemistry and cytology to dissect the role of the linker in FtsZ function. Data from chimeric FtsZs substituting the native linker with sequences from unrelated FtsZs as well as a helical sequence from human beta-catenin indicate that while variations in the primary sequence are well tolerated, an intrinsically disordered linker is essential for Bacillus subtilis FtsZ assembly. Linker lengths ranging from 25 to 100 residues supported FtsZ assembly, but replacing the B. subtilis FtsZ linker with a 249-residue linker from Agrobacterium tumefaciens FtsZ interfered with cell division. Overall, our results support a model in which the linker acts as a flexible tether allowing FtsZ to associate with the membrane through a conserved C-terminal domain while simultaneously interacting with itself and modulatory proteins in the cytoplasm.
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Affiliation(s)
- P J Buske
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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24
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Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB. Structure and function of a cyanophage-encoded peptide deformylase. THE ISME JOURNAL 2013; 7:1150-60. [PMID: 23407310 PMCID: PMC3660681 DOI: 10.1038/ismej.2013.4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 12/01/2012] [Accepted: 12/07/2012] [Indexed: 12/19/2022]
Abstract
Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.
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Affiliation(s)
- Jeremy A Frank
- Department of Biology, San Diego State University, San Diego, CA 92182-7720, USA.
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25
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Blasios V, Bisson-Filho AW, Castellen P, Nogueira MLC, Bettini J, Portugal RV, Zeri ACM, Gueiros-Filho FJ. Genetic and biochemical characterization of the MinC-FtsZ interaction in Bacillus subtilis. PLoS One 2013; 8:e60690. [PMID: 23577149 PMCID: PMC3618327 DOI: 10.1371/journal.pone.0060690] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 03/01/2013] [Indexed: 11/22/2022] Open
Abstract
Cell division in bacteria is regulated by proteins that interact with FtsZ and modulate its ability to polymerize into the Z ring structure. The best studied of these regulators is MinC, an inhibitor of FtsZ polymerization that plays a crucial role in the spatial control of Z ring formation. Recent work established that E. coli MinC interacts with two regions of FtsZ, the bottom face of the H10 helix and the extreme C-terminal peptide (CTP). Here we determined the binding site for MinC on Bacillus subtilis FtsZ. Selection of a library of FtsZ mutants for survival in the presence of Min overexpression resulted in the isolation of 13 Min-resistant mutants. Most of the substitutions that gave rise to Min resistance clustered around the H9 and H10 helices in the C-terminal domain of FtsZ. In addition, a mutation in the CTP of B. subtilis FtsZ also produced MinC resistance. Biochemical characterization of some of the mutant proteins showed that they exhibited normal polymerization properties but reduced interaction with MinC, as expected for binding site mutations. Thus, our study shows that the overall architecture of the MinC-FtsZ interaction is conserved in E. coli and B. subtilis. Nevertheless, there was a clear difference in the mutations that conferred Min resistance, with those in B. subtilis FtsZ pointing to the side of the molecule rather than to its polymerization interface. This observation suggests that the mechanism of Z ring inhibition by MinC differs in both species.
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Affiliation(s)
- Valdir Blasios
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | | | - Patricia Castellen
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
- Brazilian Biosciences National Laboratory (LNBio), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, Brasil
| | - Maria Luiza C. Nogueira
- Brazilian Biosciences National Laboratory (LNBio), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, Brasil
| | - Jefferson Bettini
- Nanotechnology National Laboratory (LNNano), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, Brasil
| | - Rodrigo V. Portugal
- Nanotechnology National Laboratory (LNNano), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, Brasil
| | - Ana Carolina M. Zeri
- Brazilian Biosciences National Laboratory (LNBio), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, Brasil
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26
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Seguritan V, Alves N, Arnoult M, Raymond A, Lorimer D, Burgin AB, Salamon P, Segall AM. Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput Biol 2012; 8:e1002657. [PMID: 22927809 PMCID: PMC3426561 DOI: 10.1371/journal.pcbi.1002657] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/29/2012] [Indexed: 01/03/2023] Open
Abstract
Phages play critical roles in the survival and pathogenicity of their hosts, via lysogenic conversion factors, and in nutrient redistribution, via cell lysis. Analyses of phage- and viral-encoded genes in environmental samples provide insights into the physiological impact of viruses on microbial communities and human health. However, phage ORFs are extremely diverse of which over 70% of them are dissimilar to any genes with annotated functions in GenBank. Better identification of viruses would also aid in better detection and diagnosis of disease, in vaccine development, and generally in better understanding the physiological potential of any environment. In contrast to enzymes, viral structural protein function can be much more challenging to detect from sequence data because of low sequence conservation, few known conserved catalytic sites or sequence domains, and relatively limited experimental data. We have designed a method of predicting phage structural protein sequences that uses Artificial Neural Networks (ANNs). First, we trained ANNs to classify viral structural proteins using amino acid frequency; these correctly classify a large fraction of test cases with a high degree of specificity and sensitivity. Subsequently, we added estimates of protein isoelectric points as a feature to ANNs that classify specialized families of proteins, namely major capsid and tail proteins. As expected, these more specialized ANNs are more accurate than the structural ANNs. To experimentally validate the ANN predictions, several ORFs with no significant similarities to known sequences that are ANN-predicted structural proteins were examined by transmission electron microscopy. Some of these self-assembled into structures strongly resembling virion structures. Thus, our ANNs are new tools for identifying phage and potential prophage structural proteins that are difficult or impossible to detect by other bioinformatic analysis. The networks will be valuable when sequence is available but in vitro propagation of the phage may not be practical or possible. Bacteriophages are extremely abundant and diverse biological entities. All phage particles are comprised of nucleic acids and structural proteins, with few other packaged proteins. Despite their simplicity and abundance, more than 70% of phage sequences in the viral Reference Sequence database encode proteins with unknown function based on FASTA annotations. As a result, the use of sequence similarity is often insufficient for detecting virus structural proteins among unknown viral sequences. Viral structural protein function is challenging to detect from sequence data because structural proteins possess few known conserved catalytic motifs and sequence domains. To address these issues we investigated the use of Artificial Neural Networks as an alternative means of predicting function. Here, we trained thousands of networks using the amino acid frequency of structural protein sequences and identified the optimal architectures with the highest accuracies. Some hypothetical protein sequences detected by our networks were expressed and visualized by TEM, and produced images that strongly resemble virion structures. Our results support the utility of our neural networks in predicting the functions of unknown viral sequences.
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Affiliation(s)
- Victor Seguritan
- Program of Computational Science, San Diego State University, San Diego, California, United States of America
| | - Nelson Alves
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael Arnoult
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Amy Raymond
- Emerald BioStructures, Seattle, Washington, United States of America
| | - Don Lorimer
- Emerald BioStructures, Seattle, Washington, United States of America
| | - Alex B. Burgin
- Emerald BioStructures, Seattle, Washington, United States of America
| | - Peter Salamon
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, United States of America
| | - Anca M. Segall
- Program of Computational Science, San Diego State University, San Diego, California, United States of America
- Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
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Elsen NL, Lu J, Parthasarathy G, Reid JC, Sharma S, Soisson SM, Lumb KJ. Mechanism of action of the cell-division inhibitor PC190723: modulation of FtsZ assembly cooperativity. J Am Chem Soc 2012; 134:12342-5. [PMID: 22793495 DOI: 10.1021/ja303564a] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cooperative assembly of FtsZ, the prokaryotic homologue of tubulin, plays an essential role in cell division. FtsZ is a potential drug target, as illustrated by the small-molecule cell-cycle inhibitor and antibacterial agent PC190723 that targets FtsZ. We demonstrate that PC190723 negatively modulates Staphylococcus aureus FtsZ polymerization cooperativity as reflected in polymerization at lower concentrations without a defined critical concentration. The crystal structure of the S. aureus FtsZ-PC190723 complex shows a domain movement that would stabilize the FtsZ protofilament over the monomeric state, with the conformational change mediated from the GTP-binding site to the C-terminal domain via helix 7. Together, the results reveal the molecular mechanism of FtsZ modulation by PC190723 and a conformational switch to the high-affinity state that enables polymer assembly.
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Affiliation(s)
- Nathaniel L Elsen
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
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28
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Abstract
The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory β-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory β-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.
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29
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Buske PJ, Levin PA. Extreme C terminus of bacterial cytoskeletal protein FtsZ plays fundamental role in assembly independent of modulatory proteins. J Biol Chem 2012; 287:10945-57. [PMID: 22298780 DOI: 10.1074/jbc.m111.330324] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Bacterial cell division typically requires assembly of the cytoskeletal protein FtsZ into a ring (Z-ring) at the nascent division site that serves as a foundation for assembly of the division apparatus. High resolution imaging suggests that the Z-ring consists of short, single-stranded polymers held together by lateral interactions. Several proteins implicated in stabilizing the Z-ring enhance lateral interactions between FtsZ polymers in vitro. Here we report that residues at the C terminus of Bacillus subtilis FtsZ (C-terminal variable region (CTV)) are both necessary and sufficient for stimulating lateral interactions in vitro in the absence of modulatory proteins. Swapping the 6-residue CTV from B. subtilis FtsZ with the 4-residue CTV from Escherichia coli FtsZ completely abolished lateral interactions between chimeric B. subtilis FtsZ polymers. The E. coli FtsZ chimera readily formed higher order structures normally seen only in the presence of molecular crowding agents. CTV-mediated lateral interactions are important for the integrity of the Z-ring because B. subtilis cells expressing the B. subtilis FtsZ chimera had a low frequency of FtsZ ring formation and a high degree of filamentation relative to wild-type cells. Site-directed mutagenesis of the B. subtilis CTV suggests that electrostatic forces are an important determinant of lateral interaction potential.
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Affiliation(s)
- Paul J Buske
- Department of Biology, Washington University, Saint Louis, Missouri 63130, USA
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30
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Kim Y, Babnigg G, Jedrzejczak R, Eschenfeldt WH, Li H, Maltseva N, Hatzos-Skintges C, Gu M, Makowska-Grzyska M, Wu R, An H, Chhor G, Joachimiak A. High-throughput protein purification and quality assessment for crystallization. Methods 2011; 55:12-28. [PMID: 21907284 DOI: 10.1016/j.ymeth.2011.07.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 12/31/2022] Open
Abstract
The ultimate goal of structural biology is to understand the structural basis of proteins in cellular processes. In structural biology, the most critical issue is the availability of high-quality samples. "Structural biology-grade" proteins must be generated in the quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. With structural genomics emphasizing a genome-based approach in understanding protein structure and function, a number of unique structures covering most of the protein folding space have been determined and new technologies with high efficiency have been developed. At the Midwest Center for Structural Genomics (MCSG), we have developed semi-automated protocols for high-throughput parallel protein expression and purification. A protein, expressed as a fusion with a cleavable affinity tag, is purified in two consecutive immobilized metal affinity chromatography (IMAC) steps: (i) the first step is an IMAC coupled with buffer-exchange, or size exclusion chromatography (IMAC-I), followed by the cleavage of the affinity tag using the highly specific Tobacco Etch Virus (TEV) protease; the second step is IMAC and buffer exchange (IMAC-II) to remove the cleaved tag and tagged TEV protease. These protocols have been implemented on multidimensional chromatography workstations and, as we have shown, many proteins can be successfully produced in large-scale. All methods and protocols used for purification, some developed by MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Diseases (CSGID) purification pipeline, are discussed in this chapter.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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Raymond A, Haffner T, Ng N, Lorimer D, Staker B, Stewart L. Gene design, cloning and protein-expression methods for high-value targets at the Seattle Structural Genomics Center for Infectious Disease. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:992-7. [PMID: 21904039 PMCID: PMC3169391 DOI: 10.1107/s1744309111026698] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 07/04/2011] [Indexed: 01/28/2023]
Abstract
An overview of one salvage strategy for high-value SSGCID targets is given. Any structural genomics endeavor, particularly ambitious ones such as the NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) and Center for Structural Genomics of Infectious Disease (CSGID), face technical challenges at all points of the production pipeline. One salvage strategy employed by SSGCID is combined gene engineering and structure-guided construct design to overcome challenges at the levels of protein expression and protein crystallization. Multiple constructs of each target are cloned in parallel using Polymerase Incomplete Primer Extension cloning and small-scale expressions of these are rapidly analyzed by capillary electrophoresis. Using the methods reported here, which have proven particularly useful for high-value targets, otherwise intractable targets can be resolved.
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Affiliation(s)
- Amy Raymond
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
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Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE. SAD phasing using iodide ions in a high-throughput structural genomics environment. ACTA ACUST UNITED AC 2011; 12:83-95. [PMID: 21359836 PMCID: PMC3123459 DOI: 10.1007/s10969-011-9101-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 02/14/2011] [Indexed: 03/16/2023]
Abstract
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.
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33
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Gurney ME, Burgin AB, Magnusson OT, Stewart LJ. Small molecule allosteric modulators of phosphodiesterase 4. Handb Exp Pharmacol 2011:167-92. [PMID: 21695640 DOI: 10.1007/978-3-642-17969-3_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Phosphodiesterase 4 (PDE4) inhibitors have shown benefit in human clinical trials but dosing is limited by tolerability, particularly because of emesis. Novel cocrystal structures of PDE4 catalytic units with their regulatory domains together with bound inhibitors have revealed three different PDE4 conformers that can be exploited in the design of novel therapeutic agents. The first is an open conformer, which has been employed in the traditional approach to the design of competitive PDE4 inhibitors. The second is an asymmetric dimer in which a UCR2 regulatory helix from one monomer is placed in a closed conformation over the opposite active site in the PDE4 dimer (trans-capping). Only one active site can be closed by an inhibitor at a time with the consequence that compounds exploiting this conformer only partially inhibit PDE4 enzymatic activity while retaining potency in cellular and in vivo models. By placing an intrinsic ceiling on the magnitude of PDE4 inhibition, such compounds may better maintain spatial and temporal patterning of signaling in cAMP microdomains with consequent improved tolerability. The third is a symmetric PDE4 conformer in which helices from the C-terminal portion of the catalytic unit cap both active sites (cis-capping). We propose that dual-gating of PDE4 activity may be further fine tuned by accessory proteins that recognize open or closed conformers of PDE4 regulatory helices.
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34
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Yamada S, Hatta M, Staker BL, Watanabe S, Imai M, Shinya K, Sakai-Tagawa Y, Ito M, Ozawa M, Watanabe T, Sakabe S, Li C, Kim JH, Myler PJ, Phan I, Raymond A, Smith E, Stacy R, Nidom CA, Lank SM, Wiseman RW, Bimber BN, O'Connor DH, Neumann G, Stewart LJ, Kawaoka Y. Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 2010; 6:e1001034. [PMID: 20700447 PMCID: PMC2916879 DOI: 10.1371/journal.ppat.1001034] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack these amino acids. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals. Moreover, a basic amino acid at position 591 of PB2 substantially increased the lethality of an avian H5N1 virus in mice. We also present the X-ray crystallographic structure of the C-terminus of a pandemic H1N1 virus PB2 protein. Arginine at position 591 fills the cleft found in H5N1 PB2 proteins in this area, resulting in differences in surface shape and charge for H1N1 PB2 proteins. These differences may affect the protein's interaction with viral and/or cellular factors, and hence its ability to support virus replication in mammals. Influenza viruses that originate from avian species likely have to acquire adapting amino acid changes to replicate efficiently in mammals. Two amino acid changes in the polymerase PB2 protein—a glutamic acid to lysine change at position 627 or an aspartic acid to asparagine change at position 701—are known to allow influenza viruses of avian origin to replicate efficiently in mammals. Interestingly, the pandemic H1N1 viruses (which possess an avian-like PB2 gene) do not encode the ‘human-type’ amino acids PB2-627K and PB2-701N. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of PB2-627K and allows efficient replication of highly pathogenic H5N1 and pandemic H1N1 viruses in mammalian species. We also present the X-ray crystal structure of the C-terminal portion of a pandemic H1N1 PB2 protein. The basic amino acid at position 591 fills a distinctive cleft found in the PB2 proteins of H5N1 viruses. We also speculate on the biological significance of the altered surface of the H1N1 PB2 protein.
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Affiliation(s)
- Shinya Yamada
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Masato Hatta
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bart L. Staker
- Emerald BioStructures, Inc., Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
| | - Shinji Watanabe
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Masaki Imai
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kyoko Shinya
- Department of Microbiology and Infectious Diseases, Kobe University, Hyogo, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Mutsumi Ito
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Ozawa
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tokiko Watanabe
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saori Sakabe
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- ERATO Infection-Induced Host Responses Project, Saitama, Japan
| | - Chengjun Li
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jin Hyun Kim
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Amy Raymond
- Emerald BioStructures, Inc., Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
| | - Eric Smith
- Emerald BioStructures, Inc., Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Chairul A. Nidom
- Faculty of Veterinary Medicine, Tropical Disease Centre, Airlangga University, Surabaya, Indonesia
- Collaborating Research Center-Emerging and Reemerging Infectious Diseases, Tropical Disease Centre, Airlangga University, Surabaya, Indonesia
| | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Benjamin N. Bimber
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lance J. Stewart
- Emerald BioStructures, Inc., Bainbridge Island, Washington, United States of America
- Seattle Structural Genomics Center for Infectious Disease, Washington, United States of America
- * E-mail: (YK, for virological research aspects); (LJS, for structural research aspects)
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Microbiology and Infectious Diseases, Kobe University, Hyogo, Japan
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- ERATO Infection-Induced Host Responses Project, Saitama, Japan
- Creative Research Initiative, Sousei, Hokkaido University, Sapporo, Japan
- * E-mail: (YK, for virological research aspects); (LJS, for structural research aspects)
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Myler PJ, Stacy R, Stewart L, Staker BL, Van Voorhis WC, Varani G, Buchko GW. The Seattle Structural Genomics Center for Infectious Disease (SSGCID). Infect Disord Drug Targets 2010; 9:493-506. [PMID: 19594426 DOI: 10.2174/187152609789105687] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 03/17/2009] [Indexed: 11/22/2022]
Abstract
The NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium established to apply structural genomics approaches to potential drug targets from NIAID priority organisms for biodefense and emerging and re-emerging diseases. The mission of the SSGCID is to determine approximately 400 protein structures over the next five years. In order to maximize biomedical impact, ligand-based drug-lead discovery campaigns will be pursued for a small number of high-impact targets. Here we review the center's target selection processes, which include pro-active engagement of the infectious disease research and drug therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. This is followed by a brief overview of the SSGCID structure determination pipeline and ligand screening methodology. Finally, specifics of our resources available to the scientific community are presented. Physical materials and data produced by SSGCID will be made available to the scientific community, with the aim that they will provide essential groundwork benefiting future research and drug discovery.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, 307 Westlake Ave N, Seattle, WA 98109-5219, USA.
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36
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Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat Biotechnol 2010; 28:63-70. [DOI: 10.1038/nbt.1598] [Citation(s) in RCA: 301] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 12/04/2009] [Indexed: 12/25/2022]
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Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A, Wallace E, Grice R, Burgin A, Stewart L. Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol 2009; 9:36. [PMID: 19383142 PMCID: PMC2681465 DOI: 10.1186/1472-6750-9-36] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/21/2009] [Indexed: 12/18/2022] Open
Abstract
Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.
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Affiliation(s)
- Don Lorimer
- deCODE biostructures, Inc 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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