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Gajendran C, Fukui S, Sadhu NM, Zainuddin M, Rajagopal S, Gosu R, Gutch S, Fukui S, Sheehy CE, Chu L, Vishwakarma S, Jeyaraj DA, Hallur G, Wagner DD, Sivanandhan D. Alleviation of arthritis through prevention of neutrophil extracellular traps by an orally available inhibitor of protein arginine deiminase 4. Sci Rep 2023; 13:3189. [PMID: 36823444 PMCID: PMC9950073 DOI: 10.1038/s41598-023-30246-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Protein arginine deiminases (PAD) 4 is an enzyme that catalyzes citrullination of protein and its role in autoimmune diseases has been established through clinical genetics and gene knock out studies in mice. Further, studies with PAD4 - deficient mice have shown that PAD4 deficiency does not lead to increased infection or immune suppression, which makes PAD4 an attractive therapeutic target for auto-immune and inflammatory diseases. PAD4 has critical enzymatic role of promoting chromatin decondensation and neutrophil extracellular traps (NETs) formation that is associated with a number of immune-mediated pathological conditions. Here, we present a non-covalent PAD4 inhibitor JBI-589 with high PAD4 isoform selectivity and delineated its binding mode at 2.88 Å resolution by X-ray crystallography. We confirmed its effectiveness in inhibiting NET formation in vitro. Additionally, by using two mouse arthritis models for human rheumatoid arthritis (RA), the well-known disease associated with PAD4 clinically, we established its efficacy in vivo. These results suggest that JBI-589 would be beneficial for both PAD4 and NET-associated pathological conditions.
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Affiliation(s)
| | - Shoichi Fukui
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | | | | | | | | | - Sarah Gutch
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Saeko Fukui
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Casey E Sheehy
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Long Chu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | | | | | | | - Denisa D Wagner
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02125, USA
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2
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Hedin N, Velazquez MB, Barchiesi J, Gomez-Casati DF, Busi MV. CBM20CP, a novel functional protein of starch metabolism in green algae. PLANT MOLECULAR BIOLOGY 2022; 108:363-378. [PMID: 34546521 DOI: 10.1007/s11103-021-01190-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/20/2021] [Indexed: 05/29/2023]
Abstract
Ostreococcus tauri is a picoalga that contains a small and compact genome, which resembles that of higher plants in the multiplicity of enzymes involved in starch synthesis (ADP-glucose pyrophosphorylase, ADPGlc PPase; granule bound starch synthase, GBSS; starch synthases, SSI, SSII, SSIII; and starch branching enzyme, SBE, between others), except starch synthase IV (SSIV). Although its genome is fully sequenced, there are still many genes and proteins to which no function was assigned. Here, we identify the OT_ostta06g01880 gene that encodes CBM20CP, a plastidial protein which contains a central carbohydrate binding domain of the CBM20 family, and a coiled coil domain at the C-terminus that lacks catalytic activity. We demonstrate that CBM20CP has the ability to bind starch, amylose and amylopectin with different affinities. Furthermore, this protein interacts with OsttaSSIII-B, increasing its binding to starch granules, its catalytic efficiency and promoting granule growth. The results allow us to postulate a functional role for CBM20CP in starch metabolism in green algae. KEY MESSAGE: CBM20CP, a plastidial protein that has a modular structure but lacks catalytic activity, regulates the synthesis of starch in Ostreococcus tauri.
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Affiliation(s)
- Nicolas Hedin
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria B Velazquez
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Julieta Barchiesi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria V Busi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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3
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Allert MJ, Hellinga HW. Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation. Biochemistry 2022; 61:276-293. [PMID: 35084821 DOI: 10.1021/acs.biochem.1c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate assignment of protein function from sequence remains a fascinating and difficult challenge. The periplasmic-binding protein (PBP) superfamily present an interesting case of function prediction because they are both ubiquitous in prokaryotes and tend to diversify through gene duplication "explosions" that can lead to large numbers of paralogs in a genome. An engineered version of the moderately thermostable glucose-binding PBP from Escherichia coli has been used successfully as a reagentless fluorescent biosensor both in vitro and in vivo. To develop more robust sensors that meet the challenges of real-world applications, we report the discovery of thermostable homologues that retain a glucose-mediated conformationally coupled fluorescence response. Accurately identifying a glucose-binding PBP homologue among closely related paralogs is challenging. We demonstrate that a structure-based method that filters sequences by residues that bind glucose in an archetype structure is highly effective. Using fully sequenced bacterial genomes, we found that this filter reduced high paralog numbers to single hits in a genome, consistent with the accurate separation of glucose binding from other functions. We expressed engineered proteins for eight homologues, chosen to represent different degrees of sequence identity, and tested their glucose-mediated fluorescence responses. We accurately predicted the presence of glucose binding down to 31% sequence identity. We have also successfully identified suitable candidates for next-generation robust, fluorescent glucose sensors.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
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4
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Bai Y, Wan W, Huang Y, Jin W, Lyu H, Xia Q, Dong X, Gao Z, Liu Y. Quantitative interrogation of protein co-aggregation using multi-color fluorogenic protein aggregation sensors. Chem Sci 2021; 12:8468-8476. [PMID: 34221329 PMCID: PMC8221170 DOI: 10.1039/d1sc01122g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Co-aggregation of multiple pathogenic proteins is common in neurodegenerative diseases but deconvolution of such biochemical process is challenging. Herein, we developed a dual-color fluorogenic thermal shift assay to simultaneously report on the aggregation of two different proteins and quantitatively study their thermodynamic stability during co-aggregation. Expansion of spectral coverage was first achieved by developing multi-color fluorogenic protein aggregation sensors. Orthogonal detection was enabled by conjugating sensors of minimal fluorescence crosstalk to two different proteins via sortase-tag technology. Using this assay, we quantified shifts in melting temperatures in a heterozygous model protein system, revealing that the thermodynamic stability of wild-type proteins was significantly compromised by the mutant ones but not vice versa. We also examined how small molecule ligands selectively and differentially interfere with such interplay. Finally, we demonstrated these sensors are suited to visualize how different proteins exert influence on each other upon their co-aggregation in live cells.
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Affiliation(s)
- Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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5
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Structural basis for a bacterial Pip system plant effector recognition protein. Proc Natl Acad Sci U S A 2021; 118:2019462118. [PMID: 33649224 DOI: 10.1073/pnas.2019462118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A number of plant-associated proteobacteria have LuxR family transcription factors that we refer to as PipR subfamily members. PipR proteins play roles in interactions between bacteria and their plant hosts, and some are important for bacterial virulence of plants. We identified an ethanolamine derivative, N-(2-hydroxyethyl)-2-(2-hydroxyethylamino) acetamide (HEHEAA), as a potent effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas GM79. HEHEAA-dependent PipR activity requires an ATP-binding cassette-type active transport system, and the periplasmic substrate-binding protein (SBP) of that system binds HEHEAA. To begin to understand the molecular basis of PipR system responses to plant factors we crystallized a HEHEAA-responsive SBP in the free- and HEHEAA-bound forms. The SBP, which is similar to peptide-binding SBPs, was in a closed conformation. A narrow cavity at the interface of its two lobes is wide enough to bind HEHEAA, but it cannot accommodate peptides with side chains. The polar atoms of HEHEAA are recognized by hydrogen-bonding interactions, and additional SBP residues contribute to the binding site. This binding mode was confirmed by a structure-based mutational analysis. We also show that a closely related SBP from the plant pathogen Pseudomonas syringae pv tomato DC3000 does not recognize HEHEAA. However, a single amino acid substitution in the presumed effector-binding pocket of the P. syringae SBP converted it to a weak HEHEAA-binding protein. The P. syringae PipR depends on a plant effector for activity, and our findings imply that different PipR-associated SBPs bind different effectors.
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6
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Diep P, Mahadevan R, Yakunin AF. A microplate screen to estimate metal-binding affinities of metalloproteins. Anal Biochem 2020; 609:113836. [PMID: 32750358 DOI: 10.1016/j.ab.2020.113836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/16/2022]
Abstract
Solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters play crucial roles across all forms of life in transporting compounds against chemical gradients. Some SBPs have evolved to scavenge metal substrates from the environment with nanomolar and micromolar affinities (KD). There exist well established techniques like isothermal titration calorimetry for thoroughly studying these metalloprotein interactions with metal ions, but they are low-throughput. For protein libraries comprised of many metalloprotein homologues and mutants, and for collections of buffer conditions and potential ligands, the throughput of these techniques is paramount. In this study, we describe an improved method termed the microITFQ-LTA and validated it using CjNikZ, a well-characterized nickel-specific SBP (Ni-BP) from Campylobacter jejuni. We then demonstrated how the microITFQ-LTA can be designed to screen through a small collection of buffers and ligands to elucidate the binding profile of a putative Ni-BP from Clostridium carboxidivorans that we call CcSBPII. Through this study, we showed CcSBPII can bind to various metal ions with KD ranged over 3 orders of magnitude. In the presence of l-histidine, CcSBPII could bind to Ni2+ over 2000-fold more tightly, which was 11.6-fold tighter than CjNikZ given the same ligand.
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Affiliation(s)
- Patrick Diep
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Radhakrishnan Mahadevan
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, United Kingdom
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7
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Huber AD, Pineda DL, Liu D, Boschert KN, Gres AT, Wolf JJ, Coonrod EM, Tang J, Laughlin TG, Yang Q, Puray-Chavez MN, Ji J, Singh K, Kirby KA, Wang Z, Sarafianos SG. Novel Hepatitis B Virus Capsid-Targeting Antiviral That Aggregates Core Particles and Inhibits Nuclear Entry of Viral Cores. ACS Infect Dis 2019; 5:750-758. [PMID: 30582687 DOI: 10.1021/acsinfecdis.8b00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An estimated 240 million are chronically infected with hepatitis B virus (HBV), which can lead to liver disease, cirrhosis, and hepatocellular carcinoma. Currently, HBV treatment options include only nucleoside reverse transcriptase inhibitors and the immunomodulatory agent interferon alpha, and these treatments are generally not curative. New treatments with novel mechanisms of action, therefore, are highly desired for HBV therapy. The viral core protein (Cp) has gained attention as a possible therapeutic target because of its vital roles in the HBV life cycle. Several classes of capsid assembly effectors (CAEs) have been described in detail, and these compounds all increase capsid assembly rate but inhibit HBV replication by different mechanisms. In this study, we have developed a thermal shift-based screening method for CAE discovery and characterization, filling a much-needed gap in high-throughput screening methods for capsid-targeting molecules. Using this approach followed by cell-based screening, we identified the compound HF9C6 as a CAE with low micromolar potency against HBV replication. HF9C6 caused large multicapsid aggregates when capsids were assembled in vitro and analyzed by transmission electron microscopy. Interestingly, when HBV-expressing cells were treated with HF9C6, Cp was excluded from cell nuclei, suggesting that this compound may inhibit nuclear entry of Cp and capsids. Furthermore, mutational scanning of Cp suggested that HF9C6 binds the known CAE binding pocket, indicating that key Cp-compound interactions within this pocket have a role in determining the CAE mechanism of action.
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Affiliation(s)
- Andrew D. Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
| | - Dallas L. Pineda
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kelsey N. Boschert
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, 204 Gwynn Hall, Columbia, Missouri 65211, United States
| | - Anna T. Gres
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Jennifer J. Wolf
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Emily M. Coonrod
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, Missouri 65211, United States
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Thomas G. Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Qiongying Yang
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Maritza N. Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Juan Ji
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Karen A. Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
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8
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Price MA, Cruz R, Baxter S, Escalettes F, Rosser SJ. CRISPR-Cas9 In Situ engineering of subtilisin E in Bacillus subtilis. PLoS One 2019; 14:e0210121. [PMID: 30615645 PMCID: PMC6322745 DOI: 10.1371/journal.pone.0210121] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/17/2018] [Indexed: 11/18/2022] Open
Abstract
CRISPR-Cas systems have become widely used across all fields of biology as a genome engineering tool. With its recent demonstration in the Gram positive industrial workhorse Bacillus subtilis, this tool has become an attractive option for rapid, markerless strain engineering of industrial production hosts. Previously described strategies for CRISPR-Cas9 genome editing in B. subtilis have involved chromosomal integrations of Cas9 and single guide RNA expression cassettes, or construction of large plasmids for simultaneous transformation of both single guide RNA and donor DNA. Here we use a flexible, co-transformation approach where the single guide RNA is inserted in a plasmid for Cas9 co-expression, and the donor DNA is supplied as a linear PCR product observing an editing efficiency of 76%. This allowed multiple, rapid rounds of in situ editing of the subtilisin E gene to incorporate a salt bridge triad present in the Bacillus clausii thermotolerant homolog, M-protease. A novel subtilisin E variant was obtained with increased thermotolerance and activity.
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Affiliation(s)
- Marcus A. Price
- Department of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
- Ingenza Ltd., Roslin Innovation Centre, Roslin, United Kingdom
- * E-mail: (MAP); (SJR)
| | - Rita Cruz
- Ingenza Ltd., Roslin Innovation Centre, Roslin, United Kingdom
| | - Scott Baxter
- Ingenza Ltd., Roslin Innovation Centre, Roslin, United Kingdom
| | | | - Susan J. Rosser
- Department of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (MAP); (SJR)
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9
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Barchiesi J, Velazquez MB, Palopoli N, Iglesias AA, Gomez-Casati DF, Ballicora MA, Busi MV. Starch Synthesis in Ostreococcus tauri: The Starch-Binding Domains of Starch Synthase III-B Are Essential for Catalytic Activity. FRONTIERS IN PLANT SCIENCE 2018; 9:1541. [PMID: 30410499 PMCID: PMC6210743 DOI: 10.3389/fpls.2018.01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/02/2018] [Indexed: 05/06/2023]
Abstract
Starch is the major energy storage carbohydrate in photosynthetic eukaryotes. Several enzymes are involved in building highly organized semi-crystalline starch granules, including starch-synthase III (SSIII), which is widely conserved in photosynthetic organisms. This enzyme catalyzes the extension of the α-1,4 glucan chain and plays a regulatory role in the synthesis of starch. Interestingly, unlike most plants, the unicellular green alga Ostreococcus tauri has three SSIII isoforms. In the present study, we describe the structure and function of OsttaSSIII-B, which has a similar modular organization to SSIII in higher plants, comprising three putative starch-binding domains (SBDs) at the N-terminal region and a C-terminal catalytic domain (CD). Purified recombinant OsttaSSIII-B displayed a high affinity toward branched polysaccharides such as glycogen and amylopectin, and to ADP-glucose. Lower catalytic activity was detected for the CD lacking the associated SBDs, suggesting that they are necessary for enzyme function. Moreover, analysis of enzyme kinetic and polysaccharide-binding parameters of site-directed mutants with modified conserved aromatic amino acid residues W122, Y124, F138, Y147, W279, and W304, belonging to the SBDs, revealed their importance for polysaccharide binding and SS activity. Our results suggest that OT_ostta13g01200 encodes a functional SSIII comprising three SBD domains that are critical for enzyme function.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Belen Velazquez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and CONICET, Bernal, Argentina
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET- Universidad Nacional del Litoral) and Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Miguel Angel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Maria Victoria Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
- *Correspondence: Maria Victoria Busi,
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10
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Sobe RC, Bond WG, Wotanis CK, Zayner JP, Burriss MA, Fernandez N, Bruger EL, Waters CM, Neufeld HS, Karatan E. Spermine inhibits Vibrio cholerae biofilm formation through the NspS-MbaA polyamine signaling system. J Biol Chem 2017; 292:17025-17036. [PMID: 28827313 PMCID: PMC5641875 DOI: 10.1074/jbc.m117.801068] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/18/2017] [Indexed: 11/06/2022] Open
Abstract
The aquatic bacterium and human intestinal pathogen, Vibrio cholerae, senses and responds to a variety of environment-specific cues to regulate biofilm formation. Specifically, the polyamines norspermidine and spermidine enhance and repress V. cholerae biofilm formation, respectively. These effects are relevant for understanding V. cholerae pathogenicity and are mediated through the periplasmic binding protein NspS and the transmembrane bis-(3'-5') cyclic diguanosine monophosphate (c-di-GMP) phosphodiesterase MbaA. However, the levels of spermidine required to inhibit biofilm formation through this pathway are unlikely to be encountered by V. cholerae in aquatic reservoirs or within the human host during infection. We therefore hypothesized that other polyamines in the gastrointestinal tract may control V. cholerae biofilm formation at physiological levels. The tetramine spermine has been reported to be present at nearly 50 μm concentrations in the intestinal lumen. Here, we report that spermine acts as an exogenous cue that inhibits V. cholerae biofilm formation through the NspS-MbaA signaling system. We found that this effect probably occurs through a direct interaction of spermine with NspS, as purified NspS protein could bind spermine in vitro Spermine also inhibited biofilm formation by altering the transcription of the vps genes involved in biofilm matrix production. Global c-di-GMP levels were unaffected by spermine supplementation, suggesting that biofilm formation may be regulated by variations in local rather than global c-di-GMP pools. Finally, we propose a model illustrating how the NspS-MbaA signaling system may communicate exogenous polyamine content to the cell to control biofilm formation in the aquatic environment and within the human intestine.
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Affiliation(s)
- Richard C Sobe
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Whitney G Bond
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Caitlin K Wotanis
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Josiah P Zayner
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Marybeth A Burriss
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Nicolas Fernandez
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Eric L Bruger
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Christopher M Waters
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Howard S Neufeld
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
| | - Ece Karatan
- From the Department of Biology, Appalachian State University, Boone, North Carolina 28608 and
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11
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Watson MD, Monroe J, Raleigh DP. Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand Interactions. J Phys Chem B 2017; 122:5278-5285. [DOI: 10.1021/acs.jpcb.7b05684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Daniel P. Raleigh
- Research Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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12
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Swaminathan S, Birudukota S, Thakur MK, Parveen R, Kandan S, Juluri S, Shaik S, Anand NN, Burri RR, Kristam R, Hallur MS, Rajagopal S, Schreuder H, Langer T, Rudolph C, Ruf S, Dhakshinamoorthy S, Gosu R, Kannt A. Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide. Biochem Biophys Res Commun 2017; 491:416-422. [PMID: 28720493 DOI: 10.1016/j.bbrc.2017.07.087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 11/26/2022]
Abstract
Nicotinamide N-methyltransferase (NNMT) is a S-adenosyl-l-methionine (SAM)-dependent enzyme that catalyzes N-methylation of nicotinamide (NA) and other pyridines to form N-methyl pyridinium ions. Here we report the first ternary complex X-ray crystal structures of monkey NNMT and mouse NNMT in bound form with the primary endogenous product, 1-methyl nicotinamide (MNA) and demethylated cofactor, S-adenosyl-homocysteine (SAH) determined at 2.30 Å and 1.88 Å respectively. The structural fold of these enzymes is identical to human NNMT. It is known that the primary endogenous product catalyzed by NNMT, MNA is a specific inhibitor of NNMT. Our data clearly indicates that the MNA binds to the active site and it would be trapped in the active site due to the formation of the bridge between the pole (long helix, α3) and long C-terminal loop. This might explain the mechanism of MNA acting as a feedback inhibitor of NNMT.
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Affiliation(s)
| | | | - Manish Kumar Thakur
- Department of Structural Biology, Jubilant Biosys Ltd, Bangalore 560022, India
| | - Reejuana Parveen
- Department of Structural Biology, Jubilant Biosys Ltd, Bangalore 560022, India
| | - Saravanan Kandan
- Department of Structural Biology, Jubilant Biosys Ltd, Bangalore 560022, India
| | - Suresh Juluri
- Department of Biology, Jubilant Biosys Ltd, Bangalore 560022, India
| | - Shama Shaik
- Department of Biology, Jubilant Biosys Ltd, Bangalore 560022, India
| | | | | | - Rajendra Kristam
- Department of Computational Chemistry, Jubilant Biosys Ltd, Bangalore 560022, India
| | | | - Sridharan Rajagopal
- Department of Medicinal Chemistry, Jubilant Biosys Ltd, Bangalore 560022, India
| | - Herman Schreuder
- Sanofi Research and Development, Industriepark Hoechst, H823, D-65926 Frankfurt am Main, Germany
| | - Thomas Langer
- Sanofi Research and Development, Industriepark Hoechst, H823, D-65926 Frankfurt am Main, Germany
| | - Christine Rudolph
- Sanofi Research and Development, Industriepark Hoechst, H823, D-65926 Frankfurt am Main, Germany
| | - Sven Ruf
- Sanofi Research and Development, Industriepark Hoechst, H823, D-65926 Frankfurt am Main, Germany
| | | | - Ramachandraiah Gosu
- Department of Structural Biology, Jubilant Biosys Ltd, Bangalore 560022, India.
| | - Aimo Kannt
- Sanofi Research and Development, Industriepark Hoechst, H823, D-65926 Frankfurt am Main, Germany; Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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13
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Wu R, Wilton R, Cuff ME, Endres M, Babnigg G, Edirisinghe JN, Henry CS, Joachimiak A, Schiffer M, Pokkuluri PR. A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain. Protein Sci 2017; 26:857-869. [PMID: 28168783 DOI: 10.1002/pro.3134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/27/2017] [Accepted: 02/02/2017] [Indexed: 11/07/2022]
Abstract
We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from Lake Retba, in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously, and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.
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Affiliation(s)
- R Wu
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - R Wilton
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - M E Cuff
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, 60439
| | - M Endres
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - G Babnigg
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - J N Edirisinghe
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, 60439.,Computation Institute, University of Chicago, Chicago, Illinois, 60637
| | - C S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, 60439.,Computation Institute, University of Chicago, Chicago, Illinois, 60637
| | - A Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, 60439.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - M Schiffer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - P R Pokkuluri
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
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14
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Zerbs S, Korajczyk PJ, Noirot PH, Collart FR. Transport capabilities of environmental Pseudomonads for sulfur compounds. Protein Sci 2017; 26:784-795. [PMID: 28127814 DOI: 10.1002/pro.3124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 11/11/2022]
Abstract
Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur-containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute-binding proteins from plant-associated Pseudomonads. A high-throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high-quality screening hit for each protein target. Calorimetric and spectroscopic methods were used to validate the best ligand assignments and catalog the thermodynamic properties of the protein-ligand interactions. Two novel high-affinity ligand-binding activities were identified and quantified in this set of solute-binding proteins. Bacteria were cultured in minimal media with screening library components supplied as the sole sulfur sources, demonstrating that these organosulfur compounds can be metabolized and confirming the relevance of ligand assignments. These results expand the set of experimentally validated ligands amenable to transport by this ABC transporter family and demonstrate the complex range of protein-ligand interactions that can be accomplished by solute-binding proteins. Characterizing new nutrient import pathways provides insight into Pseudomonad metabolic capabilities which can be used to further interrogate bacterial survival and participation in soil and rhizosphere communities.
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Affiliation(s)
- Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Frank R Collart
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
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15
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Characterisation of a New Family of Carboxyl Esterases with an OsmC Domain. PLoS One 2016; 11:e0166128. [PMID: 27851780 PMCID: PMC5113044 DOI: 10.1371/journal.pone.0166128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/24/2016] [Indexed: 11/22/2022] Open
Abstract
Proteins in the serine esterase family are widely distributed in bacterial phyla and display activity against a range of biologically produced and chemically synthesized esters. A serine esterase from the psychrophilic bacterium Pseudoalteromonas arctica with a C-terminal OsmC-like domain was recently characterized; here we report on the identification and characterization of further putative esterases with OsmC-like domains constituting a new esterase family that is found in a variety of bacterial species from different environmental niches. All of these proteins contained the Ser-Asp-His motif common to serine esterases and a highly conserved pentapeptide nucleophilic elbow motif. We produced these proteins heterologously in Escherichia coli and demonstrated their activity against a range of esterase substrates. Two of the esterases characterized have activity of over two orders of magnitude higher than other members of the family, and are active over a wide temperature range. We determined the crystal structure of the esterase domain of the protein from Rhodothermus marinus and show that it conforms to the classical α/β hydrolase fold with an extended ‘lid’ region, which occludes the active site of the protein in the crystal. The expansion of characterized members of the esterase family and demonstration of activity over a wide-range of temperatures could be of use in biotechnological applications such as the pharmaceutical, detergent, bioremediation and dairy industries.
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16
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Yadava U, Vetting MW, Al Obaidi N, Carter MS, Gerlt JA, Almo SC. Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine. Acta Crystallogr F Struct Biol Commun 2016; 72:467-72. [PMID: 27303900 PMCID: PMC4909247 DOI: 10.1107/s2053230x16007500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/04/2016] [Indexed: 11/10/2022] Open
Abstract
The uptake of exogenous solutes by prokaryotes is mediated by transport systems embedded in the plasma membrane. In many cases, a solute-binding protein (SBP) is utilized to bind ligands with high affinity and deliver them to the membrane-bound components responsible for translocation into the cytoplasm. In the present study, Avi_5305, an Agrobacterium vitis SBP belonging to Pfam13407, was screened by differential scanning fluorimetry (DSF) and found to be stabilized by D-glucosamine and D-galactosamine. Avi_5305 is the first protein from Pfam13407 shown to be specific for amino sugars, and co-crystallization resulted in structures of Avi_5305 bound to D-glucosamine and D-galactosamine. Typical of Pfam13407, Avi_5305 consists of two α/β domains linked through a hinge region, with the ligand-binding site located in a cleft between the two domains. Comparisons with Escherichia coli ribose-binding protein suggest that a cation-π interaction with Tyr168 provides the specificity for D-glucosamine/D-galactosamine over D-glucose/D-galactose.
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Affiliation(s)
- Umesh Yadava
- Department of Physics, DDU Gorakhpur University, Gorakhpur 273 009, India
| | - Matthew W. Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nawar Al Obaidi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael S. Carter
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John A. Gerlt
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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17
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Bauer WJ, Luthra A, Zhu G, Radolf JD, Malkowski MG, Caimano MJ. Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding. J Struct Biol 2015; 192:48-58. [PMID: 26321039 PMCID: PMC4605270 DOI: 10.1016/j.jsb.2015.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/05/2015] [Accepted: 08/24/2015] [Indexed: 12/15/2022]
Abstract
Two-component signal transduction systems are the primary mechanisms by which bacteria perceive and respond to changes in their environment. The Hk1/Rrp1 two-component system (TCS) in Borrelia burgdorferi consists of a hybrid histidine kinase and a response regulator with diguanylate cyclase activity, respectively. Phosphorylated Rrp1 catalyzes the synthesis of c-di-GMP, a second messenger associated with bacterial life-style control networks. Spirochetes lacking either Hk1 or Rrp1 are virulent in mice but destroyed within feeding ticks. Activation of Hk1 by exogenous stimuli represents the seminal event for c-di-GMP signaling. We reasoned that structural characterization of Hk1's sensor would provide insights into the mechanism underlying signal transduction and aid in the identification of activating ligands. The Hk1 sensor is composed of three ligand-binding domains (D1-3), each with homology to periplasmic solute-binding proteins (PBPs) typically associated with ABC transporters. Herein, we determined the structure for D1, the most N-terminal PBP domain. As expected, D1 displays a bilobed Venus Fly Trap-fold. Similar to the prototypical sensor PBPs HK29S from Geobacter sulfurreducens and VFT2 from Bordetella pertussis, apo-D1 adopts a closed conformation. Using complementary approaches, including SAXS, we established that D1 forms a dimer in solution. The D1 structure enabled us to model the D2 and D3 domains. Differences in the ligand-binding pockets suggest that each PBP recognizes a different ligand. The ability of Hk1 to recognize multiple stimuli provides spirochetes with a means of distinguishing between the acquisition and transmission blood meals and generate a graded output response that is reflective of the perceived environmental threats.
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Affiliation(s)
| | - Amit Luthra
- Department of Medicine, University of Connecticut Health, Farmington, CT, 06030
| | - Guangyu Zhu
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203
| | - Justin D. Radolf
- Department of Medicine, University of Connecticut Health, Farmington, CT, 06030
- Department of Pediatrics, University of Connecticut Health, Farmington, CT, 06030
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030
- Department of Genetics and Genomic Sciences, University of Connecticut Health, Farmington, CT, 06030
- Department of Immunology University of Connecticut Health, Farmington, CT, 06030
- Department of Structural Biology, State University of New York at Buffalo, Buffalo, NY 1420
| | - Michael G. Malkowski
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203
- Department of Structural Biology, State University of New York at Buffalo, Buffalo, NY 1420
| | - Melissa J. Caimano
- Department of Medicine, University of Connecticut Health, Farmington, CT, 06030
- Department of Pediatrics, University of Connecticut Health, Farmington, CT, 06030
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030
- Connecticut Children's Medical Center, Hartford, CT 06106
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18
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Deroy A, Saiag F, Kebbi-Benkeder Z, Touahri N, Hecker A, Morel-Rouhier M, Colin F, Dumarcay S, Gérardin P, Gelhaye E. The GSTome Reflects the Chemical Environment of White-Rot Fungi. PLoS One 2015; 10:e0137083. [PMID: 26426695 PMCID: PMC4591263 DOI: 10.1371/journal.pone.0137083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/13/2015] [Indexed: 11/19/2022] Open
Abstract
White-rot fungi possess the unique ability to degrade and mineralize all the different components of wood. In other respects, wood durability, among other factors, is due to the presence of extractives that are potential antimicrobial molecules. To cope with these molecules, wood decay fungi have developed a complex detoxification network including glutathione transferases (GST). The interactions between GSTs from two white-rot fungi, Trametes versicolor and Phanerochaete chrysosporium, and an environmental library of wood extracts have been studied. The results demonstrate that the specificity of these interactions is closely related to the chemical composition of the extracts in accordance with the tree species and their localization inside the wood (sapwood vs heartwood vs knotwood). These data suggest that the fungal GSTome could reflect the chemical environment encountered by these fungi during wood degradation and could be a way to study their adaptation to their way of life.
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Affiliation(s)
- Aurélie Deroy
- Université de Lorraine, Interactions Arbres—Microorganismes, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France
- INRA, Interactions Arbres—Microorganismes, UMR1136, F-54280, Champenoux, France
| | - Fanny Saiag
- Université de Lorraine, Interactions Arbres—Microorganismes, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France
- INRA, Interactions Arbres—Microorganismes, UMR1136, F-54280, Champenoux, France
| | - Zineb Kebbi-Benkeder
- Laboratoire d’Etudes et de Recherches sur le Matériau Bois, EA4370 Université de Lorraine USC INRA, Faculté des Sciences et Technologies, 54506, Vandoeuvre-les-Nancy, France
- AgroParisTech, UMR 1092 LERFOB, F-54000, Nancy, France
- INRA, UMR 1092 LERFOB, F-54280, Champenoux, France
| | - Nassim Touahri
- Laboratoire d’Etudes et de Recherches sur le Matériau Bois, EA4370 Université de Lorraine USC INRA, Faculté des Sciences et Technologies, 54506, Vandoeuvre-les-Nancy, France
- AgroParisTech, UMR 1092 LERFOB, F-54000, Nancy, France
- INRA, UMR 1092 LERFOB, F-54280, Champenoux, France
| | - Arnaud Hecker
- Université de Lorraine, Interactions Arbres—Microorganismes, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France
- INRA, Interactions Arbres—Microorganismes, UMR1136, F-54280, Champenoux, France
| | - Mélanie Morel-Rouhier
- Université de Lorraine, Interactions Arbres—Microorganismes, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France
- INRA, Interactions Arbres—Microorganismes, UMR1136, F-54280, Champenoux, France
| | - Francis Colin
- AgroParisTech, UMR 1092 LERFOB, F-54000, Nancy, France
- INRA, UMR 1092 LERFOB, F-54280, Champenoux, France
| | - Stephane Dumarcay
- Laboratoire d’Etudes et de Recherches sur le Matériau Bois, EA4370 Université de Lorraine USC INRA, Faculté des Sciences et Technologies, 54506, Vandoeuvre-les-Nancy, France
| | - Philippe Gérardin
- Laboratoire d’Etudes et de Recherches sur le Matériau Bois, EA4370 Université de Lorraine USC INRA, Faculté des Sciences et Technologies, 54506, Vandoeuvre-les-Nancy, France
| | - Eric Gelhaye
- Université de Lorraine, Interactions Arbres—Microorganismes, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France
- INRA, Interactions Arbres—Microorganismes, UMR1136, F-54280, Champenoux, France
- * E-mail:
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19
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Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015; 10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.
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Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics , 1340 Jefferson Park Avenue, Charlottesville, VA 22908 , USA +1 434 243 6865 ; +1 434 243 2981 ;
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20
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McKellar JLO, Minnell JJ, Gerth ML. A high‐throughput screen for ligand binding reveals the specificities of three amino acid chemoreceptors from
P
seudomonas syringae
pv.
actinidiae. Mol Microbiol 2015; 96:694-707. [DOI: 10.1111/mmi.12964] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2015] [Indexed: 11/30/2022]
Affiliation(s)
- James L. O. McKellar
- Department of Biochemistry University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Jordan J. Minnell
- Department of Biochemistry University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Monica L. Gerth
- Department of Biochemistry University of Otago PO Box 56 Dunedin 9054 New Zealand
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21
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Hai Y, Kerkhoven E, Barrett MP, Christianson DW. Crystal structure of an arginase-like protein from Trypanosoma brucei that evolved without a binuclear manganese cluster. Biochemistry 2015; 54:458-71. [PMID: 25536859 PMCID: PMC4303290 DOI: 10.1021/bi501366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/09/2014] [Indexed: 11/28/2022]
Abstract
The X-ray crystal structure of an arginase-like protein from the parasitic protozoan Trypanosoma brucei, designated TbARG, is reported at 1.80 and 2.38 Å resolution in its reduced and oxidized forms, respectively. The oxidized form of TbARG is a disulfide-linked hexamer that retains the overall architecture of a dimer of trimers in the reduced form. Intriguingly, TbARG does not contain metal ions in its putative active site, and amino acid sequence comparisons indicate that all but one of the residues required for coordination to the catalytically obligatory binuclear manganese cluster in other arginases are substituted here with residues incapable of metal ion coordination. Therefore, the structure of TbARG is the first of a member of the arginase/deacetylase superfamily that is not a metalloprotein. Although we show that metal binding activity is easily reconstituted in TbARG by site-directed mutagenesis and confirmed in X-ray crystal structures, it is curious that this protein and its parasitic orthologues evolved away from metal binding function. Knockout of the TbARG gene from the genome demonstrated that its function is not essential to cultured bloodstream-form T. brucei, and metabolomics analysis confirmed that the enzyme has no role in the conversion of l-arginine to l-ornithine in these cells. While the molecular function of TbARG remains enigmatic, the fact that the T. brucei genome encodes only this protein and not a functional arginase indicates that the parasite must import l-ornithine from its host to provide a source of substrate for ornithine decarboxylase in the polyamine biosynthetic pathway, an active target for the development of antiparasitic drugs.
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Affiliation(s)
- Yang Hai
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Eduard
J. Kerkhoven
- Department
of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Michael P. Barrett
- Wellcome
Trust Centre of Molecular Parasitology and Glasgow Polyomics, Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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22
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Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius. Biosci Rep 2014; 34:e00154. [PMID: 25311310 PMCID: PMC4242081 DOI: 10.1042/bsr20140088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Gram-positive bacterium Staphylococcus pseudintermedius is a leading cause of canine bacterial pyoderma, resulting in worldwide morbidity in dogs. S. pseudintermedius also causes life-threatening human infections. Furthermore, methicillin-resistant S. pseudintermedius is emerging, resembling the human health threat of methicillin-resistant Staphylococcus aureus. Therefore it is increasingly important to characterize targets for intervention strategies to counteract S. pseudintermedius infections. Here we used biophysical methods, mutagenesis, and X-ray crystallography, to define the ligand-binding properties and structure of SitA, an S. pseudintermedius surface lipoprotein. SitA was strongly and specifically stabilized by Mn2+ and Zn2+ ions. Crystal structures of SitA complexed with Mn2+ and Zn2+ revealed a canonical class III solute-binding protein with the metal cation bound in a cavity between N- and C-terminal lobes. Unexpectedly, one crystal contained both apo- and holo-forms of SitA, revealing a large side-chain reorientation of His64, and associated structural differences accompanying ligand binding. Such conformational changes may regulate fruitful engagement of the cognate ABC (ATP-binding cassette) transporter system (SitBC) required for metal uptake. These results provide the first detailed characterization and mechanistic insights for a potential therapeutic target of the major canine pathogen S. pseudintermedius, and also shed light on homologous structures in related staphylococcal pathogens afflicting humans.
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23
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Biochemical characterization of mutants in the active site residues of the β-galactosidase enzyme of Bacillus circulans ATCC 31382. FEBS Open Bio 2014; 4:1015-20. [PMID: 25473598 PMCID: PMC4250540 DOI: 10.1016/j.fob.2014.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 11/21/2022] Open
Abstract
Active site characteristics of the β-galactosidase enzyme of Bacillus circulans ATCC 31382. Residues essential for catalysis were identified by structure-based alignments. Mutational analysis identified two catalytic glutamate amino acid residues.
The Bacillus circulans ATCC 31382 β-galactosidase (BgaD) is a retaining-type glycosidase of glycoside hydrolase family 2 (GH2). Its commercial enzyme preparation, Biolacta N5, is used for commercial-scale production of galacto-oligosaccharides (GOS). The BgaD active site and catalytic amino acid residues have not been studied. Using bioinformatic routines we identified two putative catalytic glutamates and two highly conserved active site histidines. The site-directed mutants E447N, E532Q, and H345F, H379F had lost (almost) all catalytic activity. This confirmed their essential role in catalysis, as general acid/base catalyst (E447) and nucleophile (E532), and as transition state stabilizers (H345, H379), respectively.
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24
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Cockerell SR, Rutkovsky AC, Zayner JP, Cooper RE, Porter LR, Pendergraft SS, Parker ZM, McGinnis MW, Karatan E. Vibrio cholerae NspS, a homologue of ABC-type periplasmic solute binding proteins, facilitates transduction of polyamine signals independent of their transport. MICROBIOLOGY-SGM 2014; 160:832-843. [PMID: 24530989 DOI: 10.1099/mic.0.075903-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The polyamines norspermidine and spermidine are among the environmental signals that regulate Vibrio cholerae biofilm formation. The effects of these polyamines are mediated by NspS, a member of the bacterial periplasmic solute binding protein superfamily. Almost all members of this superfamily characterized to date are components of ATP-binding cassette-type transporters involved in nutrient uptake. Consequently, in the current annotation of the V. cholerae genome, NspS has been assigned a function in transport. The objective of this study was to further characterize NspS and investigate its potential role in transport. Our results support a role for NspS in signal transduction in response to norspermidine and spermidine, but not their transport. In addition, we provide evidence that these polyamine signals are processed by c-di-GMP signalling networks in the cell. Furthermore, we present comparative genomics analyses which reveal the presence of NspS-like proteins in a variety of bacteria, suggesting that periplasmic ligand binding proteins may be widely utilized for sensory transduction.
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Affiliation(s)
| | - Alex C Rutkovsky
- Biomedical Sciences, The Medical University of South Carolina, Charleston, SC 29425, USA
| | - Josiah P Zayner
- Department of Biochemistry and Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Rebecca E Cooper
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Sam S Pendergraft
- Biomedical Sciences, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Zach M Parker
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | | | - Ece Karatan
- Appalachian State University, Department of Biology, 572 Rivers St., Boone, NC 28608, USA
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25
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Luan CH, Light SH, Dunne SF, Anderson WF. Ligand screening using fluorescence thermal shift analysis (FTS). Methods Mol Biol 2014; 1140:263-89. [PMID: 24590724 DOI: 10.1007/978-1-4939-0354-2_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The fluorescence thermal shift (FTS) method is a biophysical technique that can improve productivity in a structural genomics pipeline and provide a fast and easy platform for identifying ligands in protein function or drug discovery screening. The technique has gained widespread popularity in recent years due to its broad-scale applicability, throughput, and functional relevance. FTS is based on the principle that a protein unfolds at a critical temperature that depends upon its intrinsic stability. A probe that will fluoresce when bound to hydrophobic surfaces is used to monitor protein unfolding as temperature is increased. In this manner, conditions or small molecules that affect the thermal stability of a protein can be identified. Herein, principles, protocols, data analysis, and special considerations of FTS screening as performed for the Center for Structural Genomics of Infectious Diseases (CSGID) pipeline are described in detail. The CSGID FTS screen is designed as a high-throughput 384-well assay to be performed on a robotic platform; however, all protocols can be adapted to a 96-well format that can be assembled manually. Data analysis can be performed using a simple curve fitting of the fluorescent signal using a Boltzmann or double Boltzmann equation. A case study of 100 proteins screened against Emerald Biosystem's ADDit™ library is included as discussion.
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Affiliation(s)
- Chi-Hao Luan
- High-Throughput Analysis Laboratory, Department of Molecular Biosciences, Center for Structural Genomics of Infectious Diseases, Northwestern University, Evanston, IL, 60208, USA
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26
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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27
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Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR. Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids. Proteins 2013; 81:1709-26. [PMID: 23606130 DOI: 10.1002/prot.24305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/12/2013] [Accepted: 03/28/2013] [Indexed: 11/10/2022]
Abstract
Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.
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Affiliation(s)
- Kemin Tan
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, 60439; The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, Illinois, 60439; Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, 60439
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28
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Gautam S, Gupta MN. WITHDRAWN: Smart polymer-coated microplate wells: Applications in protein purification, protein refolding, and sensing of analytes. Anal Biochem 2013:S0003-2697(13)00221-2. [PMID: 23685053 DOI: 10.1016/j.ab.2013.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/07/2013] [Accepted: 05/05/2013] [Indexed: 11/25/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Saurabh Gautam
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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29
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Structural and functional characterization of the Staphylococcus aureus virulence factor and vaccine candidate FhuD2. Biochem J 2013; 449:683-93. [PMID: 23113737 DOI: 10.1042/bj20121426] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Staphylococcus aureus is a human pathogen causing globally significant morbidity and mortality. The development of antibiotic resistance in S. aureus highlights the need for a preventive vaccine. In the present paper we explore the structure and function of FhuD2 (ferric-hydroxamate uptake D2), a staphylococcal surface lipoprotein mediating iron uptake during invasive infection, recently described as a promising vaccine candidate. Differential scanning fluorimetry and calorimetry studies revealed that FhuD2 is stabilized by hydroxamate siderophores. The FhuD2-ferrichrome interaction was of nanomolar affinity in surface plasmon resonance experiments and fully iron(III)-dependent. We determined the X-ray crystallographic structure of ligand-bound FhuD2 at 1.9 Å (1 Å=0.1 nm) resolution, revealing the bilobate fold of class III SBPs (solute-binding proteins). The ligand, ferrichrome, occupies a cleft between the FhuD2 N- and C-terminal lobes. Many FhuD2-siderophore interactions enable the specific recognition of ferrichrome. Biochemical data suggest that FhuD2 does not undergo significant conformational changes upon siderophore binding, supporting the hypothesis that the ligand-bound complex is essential for receptor engagement and uptake. Finally, immunizations with FhuD2 alone or FhuD2 formulated with hydroxamate siderophores were equally protective in a murine staphylococcal infection model, confirming the suitability and efficacy of apo-FhuD2 as a protective antigen, and suggesting that other class III SBPs might also be exploited as vaccine candidates.
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30
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Dubey P, Gautam S, Kumar PPP, Sadanandan S, Haridas V, Gupta MN. Dendrons and dendrimers as pseudochaperonins for refolding of proteins. RSC Adv 2013. [DOI: 10.1039/c3ra00061c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Pershad K, Kay BK. Generating thermal stable variants of protein domains through phage display. Methods 2012; 60:38-45. [PMID: 23276752 DOI: 10.1016/j.ymeth.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES-MC 066, Chicago, IL 60607-7060, USA
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32
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Michalska K, Chang C, Mack JC, Zerbs S, Joachimiak A, Collart FR. Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins. J Mol Biol 2012; 423:555-75. [PMID: 22925578 PMCID: PMC3836681 DOI: 10.1016/j.jmb.2012.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/27/2012] [Accepted: 08/20/2012] [Indexed: 10/28/2022]
Abstract
In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein-ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure-function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequence-based methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.
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Affiliation(s)
- Karolina Michalska
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changsoo Chang
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jamey C. Mack
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Frank R. Collart
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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33
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Pershad K, Wypisniak K, Kay BK. Directed evolution of the forkhead-associated domain to generate anti-phosphospecific reagents by phage display. J Mol Biol 2012; 424:88-103. [PMID: 22985966 DOI: 10.1016/j.jmb.2012.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/10/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022]
Abstract
While affinity reagents are valuable tools for monitoring protein phosphorylation and studying signaling events in cells, generating them through immunization of animals with phosphopeptides is expensive, laborious, and time-consuming. An attractive alternative is to use protein evolution techniques and isolate new anti-phosphopeptide binding specificities from a library of variants of a phosphopeptide-binding domain. To explore this strategy, we attempted to display on the surface of bacteriophage M13 the N-terminal Forkhead-associated (FHA1) domain of yeast Rad53p, which is a naturally occurring phosphothreonine (pT)-binding domain, and found it to be nonfunctional due to misfolding in the bacterial periplasm. To overcome this limitation, we constructed a library of FHA1 variants by mutagenic PCR and isolated functional variants after three rounds of affinity selection with its pT peptide ligand. A hydrophobic residue at position 34 in the β1 strand was discovered to be essential for phage display of a functional FHA1 domain. Additionally, by heating the phage library to 50°C prior to affinity selection with its cognate pT peptide, we identified a variant (G2) that was ~8°C more thermally stable than the wild-type domain. Using G2 as a scaffold, we constructed phage-displayed libraries of FHA1 variants and affinity selected for variants that bound selectively to five pT peptides. These reagents are renewable and have high protein yields (~20-25mg/L), when expressed in Escherichia coli. Thus, we have changed the specificity of the FHA1 domain and demonstrated that engineering phosphopeptide-binding domains is an attractive avenue for generating new anti-phosphopeptide binding specificities in vitro by phage display.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, Laboratory for Molecular Biology (M/C 567), University of Illinois at Chicago, Molecular Biology Research Building, Chicago, IL 60607, USA.
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34
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Osborne SE, Tuinema BR, Mok MCY, Lau PS, Bui NK, Tomljenovic-Berube AM, Vollmer W, Zhang K, Junop M, Coombes BK. Characterization of DalS, an ATP-binding cassette transporter for D-alanine, and its role in pathogenesis in Salmonella enterica. J Biol Chem 2012; 287:15242-50. [PMID: 22418438 PMCID: PMC3346123 DOI: 10.1074/jbc.m112.348227] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Expansion into new host niches requires bacterial pathogens to adapt to changes in nutrient availability and to evade an arsenal of host defenses. Horizontal acquisition of Salmonella Pathogenicity Island (SPI)-2 permitted the expansion of Salmonella enterica serovar Typhimurium into the intracellular environment of host cells by allowing it to deliver bacterial effector proteins across the phagosome membrane. This is facilitated by the SsrA-SsrB two-component regulatory system and a type III secretion system encoded within SPI-2. SPI-2 acquisition was followed by evolution of existing regulatory DNA, creating an expanded SsrB regulon involved in intracellular fitness and host infection. Here, we identified an SsrB-regulated operon comprising an ABC transporter in Salmonella. Biochemical and structural studies determined that the periplasmic solute-binding component, STM1633/DalS, transports D-alanine and that DalS is required for intracellular survival of the bacteria and for fitness in an animal host. This work exemplifies the role of nutrient exchange at the host-pathogen interface as a critical determinant of disease outcome.
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Affiliation(s)
- Suzanne E. Osborne
- From the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada, ,the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Brian R. Tuinema
- From the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada, ,the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Mac C. Y. Mok
- the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Pui Sai Lau
- the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Nhat Khai Bui
- the Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Ana M. Tomljenovic-Berube
- From the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada, ,the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Waldemar Vollmer
- the Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Kun Zhang
- the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Murray Junop
- From the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada, ,the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and
| | - Brian K. Coombes
- From the Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada, ,the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario. L8N 3Z5, Canada, and , CIHR New Investigator and the Canada Research Chair in Infectious Disease Pathogenesis. To whom correspondence should be addressed: Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4K1, Canada. Tel.: 905-525-9140; E-mail:
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Nishitani Y, Maruyama Y, Itoh T, Mikami B, Hashimoto W, Murata K. Recognition of heteropolysaccharide alginate by periplasmic solute-binding proteins of a bacterial ABC transporter. Biochemistry 2012; 51:3622-33. [PMID: 22486720 DOI: 10.1021/bi300194f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alginate is a heteropolysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G). The Gram-negative bacterium Sphingomonas sp. A1 directly incorporates alginate into the cytoplasm through the periplasmic solute-binding protein (AlgQ1 and AlgQ2)-dependent ABC transporter (AlgM1-AlgM2/AlgS-AlgS). Two binding proteins with at least four subsites strongly recognize the nonreducing terminal residue of alginate at subsite 1. Here, we show the broad substrate preference of strain A1 solute-binding proteins for M and G present in alginate and demonstrate the structural determinants in binding proteins for heteropolysaccharide recognition through X-ray crystallography of four AlgQ1 structures in complex with saturated and unsaturated alginate oligosaccharides. Alginates with different M/G ratios were assimilated by strain A1 cells and bound to AlgQ1 and AlgQ2. Crystal structures of oligosaccharide-bound forms revealed that in addition to interaction between AlgQ1 and unsaturated oligosaccharides, the binding protein binds through hydrogen bonds to the C4 hydroxyl group of the saturated nonreducing terminal residue at subsite 1. The M residue of saturated oligosaccharides is predominantly accommodated at subsite 1 because of the strict binding of Ser-273 to the carboxyl group of the residue. In unsaturated trisaccharide (ΔGGG or ΔMMM)-bound AlgQ1, the protein interacts appropriately with substrate hydroxyl groups at subsites 2 and 3 to accommodate M or G, while substrate carboxyl groups are strictly recognized by the specific residues Tyr-129 at subsite 2 and Lys-22 at subsite 3. Because of this substrate recognition mechanism, strain A1 solute-binding proteins can bind heteropolysaccharide alginate with different M/G ratios.
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Affiliation(s)
- Yu Nishitani
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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36
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Venkatraman J, Bhat J, Solapure SM, Sandesh J, Sarkar D, Aishwarya S, Mukherjee K, Datta S, Malolanarasimhan K, Bandodkar B, Das KS. Screening, identification, and characterization of mechanistically diverse inhibitors of the Mycobacterium tuberculosis enzyme, pantothenate kinase (CoaA). ACTA ACUST UNITED AC 2011; 17:293-302. [PMID: 22086722 DOI: 10.1177/1087057111423069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The authors describe the discovery of anti-mycobacterial compounds through identifying mechanistically diverse inhibitors of the essential Mycobacterium tuberculosis (Mtb) enzyme, pantothenate kinase (CoaA). Target-driven drug discovery technologies often work with purified enzymes, and inhibitors thus discovered may not optimally inhibit the form of the target enzyme predominant in the bacterial cell or may not be available at the desired concentration. Therefore, in addition to addressing entry or efflux issues, inhibitors with diverse mechanisms of inhibition (MoI) could be prioritized before hit-to-lead optimization. The authors describe a high-throughput assay based on protein thermal melting to screen large numbers of compounds for hits with diverse MoI. Following high-throughput screening for Mtb CoaA enzyme inhibitors, a concentration-dependent increase in protein thermal stability was used to identify true binders, and the degree of enhancement or reduction in thermal stability in the presence of substrate was used to classify inhibitors as competitive or non/uncompetitive. The thermal shift-based MoI assay could be adapted to screen hundreds of compounds in a single experiment as compared to traditional biochemical approaches for MoI determination. This MoI was confirmed through mechanistic studies that estimated K(ie) and K(ies) for representative compounds and through nuclear magnetic resonance-based ligand displacement assays.
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Senisterra G, Chau I, Vedadi M. Thermal denaturation assays in chemical biology. Assay Drug Dev Technol 2011; 10:128-36. [PMID: 22066913 DOI: 10.1089/adt.2011.0390] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thermal denaturation-based methods are becoming increasingly used to characterize protein stability and interactions. Recent technical advances have made these methods more suitable for high throughput screening. Reasonable throughput and the ability to perform these screens using commonly used instruments, such as RT-PCR machines or simple plate readers equipped with heating devices, facilitate these experiments in almost any laboratory. Introducing an aggregation-based monitoring approach as well as alternative fluorophores has allowed the screening of a wider range of proteins, including membrane proteins, against large chemical libraries. Thermal denaturation-based methods are independent of protein function, which is especially useful for the identification of orphan protein function. Here, we review applications of thermal denaturation-based methods in characterizing protein stability and ligand binding, and also provide information on protocol modifications that may further increase throughput.
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Abstract
Background Transporter proteins are one of an organism’s primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general classification into families. The development of capabilities to map ligands with specific transporters would improve our knowledge of the function of these proteins, improve the annotation of related genomes, and facilitate predictions for their role in cellular responses to environmental changes. Results To improve the utility of the functional annotation for ABC transporters, we expressed and purified the set of solute binding proteins from Rhodopseudomonas palustris and characterized their ligand-binding specificity. Our approach utilized ligand libraries consisting of environmental and cellular metabolic compounds, and fluorescence thermal shift based high throughput ligand binding screens. This process resulted in the identification of specific binding ligands for approximately 64% of the purified and screened proteins. The collection of binding ligands is representative of common functionalities associated with many bacterial organisms as well as specific capabilities linked to the ecological niche occupied by R. palustris. Conclusion The functional screen identified specific ligands that bound to ABC transporter periplasmic binding subunits from R. palustris. These assignments provide unique insight for the metabolic capabilities of this organism and are consistent with the ecological niche of strain isolation. This functional insight can be used to improve the annotation of related organisms and provides a route to evaluate the evolution of this important and diverse group of transporter proteins.
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Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism. Proc Natl Acad Sci U S A 2010; 107:17351-5. [PMID: 20855615 DOI: 10.1073/pnas.1006267107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two-component sensory transduction systems control important bacterial programs. In Bordetella pertussis, expression of the virulence regulon is controlled by the unorthodox BvgAS two-component system. BvgS is the prototype of a family of sensor-kinases that harbor periplasmic domains homologous to bacterial solute-binding proteins. Although BvgAS is active under laboratory conditions, no activating signal has been identified, only negative modulators. Here we show that the second periplasmic domain of BvgS interacts with modulators and adopts a Venus flytrap (VFT) fold. X-ray crystallography reveals that the two lobes of VFT2 delimitate a ligand-binding cavity enclosing fortuitous ligands. Most substitutions of putative ligand-binding residues in the VFT2 cavity keep BvgS active, and alteration of the cavity's electrostatic potential affects responsiveness to modulation. The crystal structure of this VFT2 variant conferring constitutive kinase activity to BvgS shows a closed cavity with another nonspecific ligand. Thus, VFT2 is closed and active without a specific agonist ligand, in contrast to typical VFTs. Modulators are antagonists of VFT2 that interrupt signaling. BvgAS is active for most of the B. pertussis infectious cycle, consistent with the proposed mechanism.
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Burns JN, Orwig SD, Harris JL, Watkins JD, Vollrath D, Lieberman RL. Rescue of glaucoma-causing mutant myocilin thermal stability by chemical chaperones. ACS Chem Biol 2010; 5:477-87. [PMID: 20334347 DOI: 10.1021/cb900282e] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mutations in myocilin cause an inherited form of open angle glaucoma, a prevalent neurodegenerative disorder associated with increased intraocular pressure. Myocilin forms part of the trabecular meshwork extracellular matrix presumed to regulate intraocular pressure. Missense mutations, clustered in the olfactomedin (OLF) domain of myocilin, render the protein prone to aggregation in the endoplasmic reticulum of trabecular meshwork cells, causing cell dysfunction and death. Cellular studies have demonstrated temperature-sensitive secretion of myocilin mutants, but difficulties in expression and purification have precluded biophysical characterization of wild-type (wt) myocilin and disease-causing mutants in vitro. We have overcome these limitations by purifying wt and select glaucoma-causing mutant (D380A, I477N, I477S, K423E) forms of the OLF domain (228-504) fused to a maltose binding protein (MBP) from E. coli . Monomeric fusion proteins can be isolated in solution. To determine the relative stability of wt and mutant OLF domains, we developed a fluorescence thermal stability assay without removal of MBP and provide the first direct evidence that mutated OLF is folded but less thermally stable than wt. We tested the ability of seven chemical chaperones to stabilize mutant myocilin. Only sarcosine and trimethylamine N-oxide were capable of shifting the melting temperature of all mutants tested to near that of wt OLF. Our work lays the foundation for the identification of tailored small molecules capable of stabilizing mutant myocilin and promoting secretion to the extracellular matrix, to better control intraocular pressure and to ultimately delay the onset of myocilin glaucoma.
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Affiliation(s)
- J. Nicole Burns
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332
| | - Susan D. Orwig
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332
| | - Julia L. Harris
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332
| | - J. Derrick Watkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332
| | - Douglas Vollrath
- Departments of Genetics and Ophthalmology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332
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Crowther GJ, Napuli AJ, Thomas AP, Chung DJ, Kovzun KV, Leibly DJ, Castaneda LJ, Bhandari J, Damman CJ, Hui R, Hol WGJ, Buckner FS, Verlinde CLMJ, Zhang Z, Fan E, van Voorhis WC. Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands. ACTA ACUST UNITED AC 2009; 14:700-7. [PMID: 19470714 DOI: 10.1177/1087057109335749] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the past decade, thermal melt/thermal shift assays have become a common tool for identifying ligands and other factors that stabilize specific proteins. Increased stability is indicated by an increase in the protein's melting temperature (Tm). In optimizing the assays for subsequent screening of compound libraries, it is important to minimize the variability of Tm measurements so as to maximize the assay's ability to detect potential ligands. The authors present an investigation of Tm variability in recombinant proteins from Plasmodium parasites. Ligands of Plasmodium proteins are particularly interesting as potential starting points for drugs for malaria, and new drugs are urgently needed. A single standard buffer (100 mM HEPES [pH 7.5], 150 mM NaCl) permitted estimation of Tm for 58 of 61 Plasmodium proteins tested. However, with several proteins, Tm could not be measured with a consistency suitable for high-throughput screening unless alternative protein-specific buffers were employed. The authors conclude that buffer optimization to minimize variability in Tm measurements increases the success of thermal melt screens involving proteins for which a standard buffer is suboptimal.
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Affiliation(s)
- Gregory J Crowther
- Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA.
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