1
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Haddad Momeni M, Zitting A, Jäämuru V, Turunen R, Penttilä P, Buchko GW, Hiltunen S, Maiorova N, Koivula A, Sapkota J, Marjamaa K, Master ER. Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils. Biotechnol Biofuels Bioprod 2024; 17:56. [PMID: 38654330 DOI: 10.1186/s13068-024-02500-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp. RESULTS Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20-25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%. CONCLUSION This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
| | - Aleksi Zitting
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Vilma Jäämuru
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Rosaliina Turunen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Paavo Penttilä
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Salla Hiltunen
- NE Research Center, UPM Pulp Research and Innovations, 53200, Lappeenranta, Finland
| | - Natalia Maiorova
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Janak Sapkota
- NE Research Center, UPM Pulp Research and Innovations, 53200, Lappeenranta, Finland
| | - Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Espoo, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
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2
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Tetorya M, Li H, Djami‐Tchatchou AT, Buchko GW, Czymmek KJ, Shah DM. Plant defensin MtDef4-derived antifungal peptide with multiple modes of action and potential as a bio-inspired fungicide. Mol Plant Pathol 2023; 24:896-913. [PMID: 37036170 PMCID: PMC10346373 DOI: 10.1111/mpp.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.
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Affiliation(s)
| | - Hui Li
- Donald Danforth Plant Science CenterSt LouisMissouriUSA
| | | | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National LaboratoryRichlandWashingtonUSA
- School of Molecular BiosciencesWashington State UniversityPullmanWashingtonUSA
| | - Kirk J. Czymmek
- Donald Danforth Plant Science CenterSt LouisMissouriUSA
- Advanced Bioimaging LaboratoryDonald Danforth Plant Science CenterSt LouisMissouriUSA
| | - Dilip M. Shah
- Donald Danforth Plant Science CenterSt LouisMissouriUSA
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3
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Taylor SD, Tao J, Shin Y, Buchko GW, Dohnalkova A, Grimm J, Tarasevich BJ, Ginovska B, Shaw WJ, Devaraj A. Resolving protein-mineral interfacial interactions during in vitro mineralization by atom probe tomography. Mater Today Adv 2023; 18:100378. [PMID: 37324279 PMCID: PMC10262173 DOI: 10.1016/j.mtadv.2023.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.
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Affiliation(s)
- Sandra D. Taylor
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jinhui Tao
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yongsoon Shin
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Alice Dohnalkova
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jack Grimm
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Barbara J. Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Arun Devaraj
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Metallurgical and Materials Engineering Department, Colorado School of Mines, Golden, CO, 80401, USA
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4
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Gu Y, Liu M, Staker BL, Buchko GW, Quinn RJ. Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7. ACS Pharmacol Transl Sci 2023; 6:578-586. [PMID: 37082753 PMCID: PMC10111621 DOI: 10.1021/acsptsci.2c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/09/2023]
Abstract
SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated K d of 15 μM. NMR chemical shift perturbation experiments were used to map the ligand-binding surface of gallic acid on nsp7, indicating that the compound bound to a surface pocket centered on one of the protein's four α-helices (α2). The identification of the gallic acid-binding site on nsp7 may allow development of a SARS-CoV-2 therapeutic via artificial-intelligence-based virtual docking and other strategies.
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Affiliation(s)
- Yushu Gu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Bart L. Staker
- Seattle
Children’s Research Institute, Seattle, Washington 98101, United States
| | - Garry W. Buchko
- Earth
and Biological Sciences Directorate, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
- School of
Molecular Biosciences, Washington State
University, Pullman, Washington 99164, United States
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
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5
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Buchko GW, Zhou M, Vesely CH, Tao J, Shaw WJ, Mehl RA, Cooley RB. High-yield recombinant bacterial expression of 13 C-, 15 N-labeled, serine-16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol. Protein Sci 2023; 32:e4560. [PMID: 36585836 PMCID: PMC9850436 DOI: 10.1002/pro.4560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Amelogenin constitutes ~90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates-enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows 13 C- and 15 N-labeling for detailed structural studies using NMR spectroscopy. However, native amelogenin is phosphorylated at one position, Ser-16 in murine amelogenin, and there is mounting evidence that Ser-16 phosphorylation is important. Using a modified genetic code expansion protocol we have expressed and purified uniformly 13 C-, 15 N-labeled murine amelogenin (pS16M179) with ~95% of the protein being correctly phosphorylated. Homogeneous phosphorylation was achieved using commercially available, enriched, 13 C-, 15 N-labeled media, and protein expression was induced with isopropyl β-D-1-thiogalactopyranoside at 310 K. Phosphoserine incorporation was verified from one-dimensional 31 P NMR spectra, comparison of 1 H-15 N HSQC spectra, Phos-tag SDS PAGE, and mass spectrometry. Phosphorus-31 NMR spectra for pS16M179 under conditions known to trigger amelogenin self-assembly into nanospheres confirm nanosphere models with buried N-termini. Lambda phosphatase treatment of these nanospheres results in the dephosphorylation of pS16M179, confirming that smaller oligomers and monomers with exposed N-termini are in equilibrium with nanospheres. Such 13 C-, 15 N-labeling of amelogenin with accurately encoded phosphoserine incorporation will accelerate biomineralization research to understand amelogenesis and stimulate the expanded use of genetic code expansion protocols to introduce phosphorylated amino acids into proteins.
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Affiliation(s)
- Garry W. Buchko
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA,School of Molecular BiosciencesWashington State UniversityPullmanWashingtonUSA
| | - Mowei Zhou
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Cat Hoang Vesely
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Jinhui Tao
- Physical and Computational Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Wendy J. Shaw
- Physical and Computational Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Ryan A. Mehl
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
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6
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Buchko GW, Mergelsberg ST, Tarasevich BJ, Shaw WJ. Residue-Specific Insights into the Intermolecular Protein–Protein Interfaces Driving Amelogenin Self-Assembly in Solution. Biochemistry 2022; 61:2909-2921. [DOI: 10.1021/acs.biochem.2c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Sebastian T. Mergelsberg
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Barbara J. Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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7
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Tao J, Hanson E, Dohnalkova AC, Buchko GW, Jin B, Shaw WJ, Tarasevich BJ. Changes in the C-terminal, N-terminal, and histidine regions of amelogenin reveal the role of oligomer quaternary structure on adsorption and hydroxyapatite mineralization. Front Physiol 2022; 13:1034662. [PMID: 36523551 PMCID: PMC9746691 DOI: 10.3389/fphys.2022.1034662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 10/29/2023] Open
Abstract
Adsorption interactions between amelogenin and calcium phosphate minerals are believed to be important to amelogenin's function in enamel formation, however, the role of specific amino acid residues and domains within the protein in controlling adsorption is not well known. We synthesized "mechanistic probes" by systematically removing charged regions of amelogenin in order to elucidate their roles. The probes included amelogenin without the charged residues in the N-terminus (SEKR), without two, three, or eight histidines (H) in the central protein region (H2, H3, H8), or without the C-terminal residues (Delta). In-situ atomic force microscopy (AFM) adsorption studies onto hydroxyapatite (HAP) single crystals confirmed that the C-terminus was the dominant domain in promoting adsorption. We propose that subtle changes in protein-protein interactions for proteins with histidines and N-terminal residues removed resulted in changes in the oligomer quaternary size and structure that also affected protein adsorption. HAP mineralization studies revealed that the oligomer-HAP binding energy and protein layer thickness were factors in controlling the amorphous calcium phosphate (ACP) to HAP induction time. Our studies with mechanistic probes reveal the importance of the oligomer quaternary structure in controlling amelogenin adsorption and HAP mineralization.
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Affiliation(s)
- Jinhui Tao
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Emma Hanson
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, WA, United States
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - Biao Jin
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA, United States
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8
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Wu R, Smith CA, Buchko GW, Blaby IK, Paez-Espino D, Kyrpides NC, Yoshikuni Y, McDermott JE, Hofmockel KS, Cort JR, Jansson JK. Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase. Nat Commun 2022; 13:5485. [PMID: 36123347 PMCID: PMC9485262 DOI: 10.1038/s41467-022-32993-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/26/2022] [Indexed: 11/12/2022] Open
Abstract
Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.
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Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Clyde A Smith
- Stanford Synchrotron Radiation Light source, Stanford University, Menlo Park, CA, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Nikos C Kyrpides
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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9
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Mandel C, Yang H, Buchko GW, Abendroth J, Grieshaber N, Chiarelli T, Grieshaber S, Omsland A. Expression and structure of the Chlamydia trachomatis DksA ortholog. Pathog Dis 2022; 80:6564600. [PMID: 35388904 PMCID: PMC9126822 DOI: 10.1093/femspd/ftac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksACt) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksACt in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksACt is similar to the DksA ortholog of Escherichia coli (DksAEc), DksACt did not functionally complement DksAEc. Transcription of dksACt is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksACt and the correlation between dksACt and nrdR expression is consistent with a role for DksACt in the C. trachomatis developmental cycle.
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Affiliation(s)
- Cameron Mandel
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Hong Yang
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Garry W Buchko
- School of Molecular Biosciences, Washington State University, Pullman WA 99164, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Seattle Structural Genomics Center for Infectious Disease, WA, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, WA, USA.,UCB, Bainbridge Island, WA 98110, USA
| | - Nicole Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Travis Chiarelli
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Scott Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Anders Omsland
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
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10
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Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'β-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'β-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'β-Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c'β-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'β-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,UCB Biosciences, Bainbridge Island, Washington 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 98354, United States.,School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Fong Ning Liew
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
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11
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Choi R, Zhou M, Shek R, Wilson JW, Tillery L, Craig JK, Salukhe IA, Hickson SE, Kumar N, James RM, Buchko GW, Wu R, Huff S, Nguyen TT, Hurst BL, Cherry S, Barrett LK, Hyde JL, Van Voorhis WC. High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity. PLoS One 2021; 16:e0250019. [PMID: 33886614 PMCID: PMC8062000 DOI: 10.1371/journal.pone.0250019] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer's therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.
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Affiliation(s)
- Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Roger Shek
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jesse W. Wilson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Logan Tillery
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Justin K. Craig
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Indraneel A. Salukhe
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Sarah E. Hickson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Rhema M. James
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- School of Molecular Bioscience, Washington State University, Pullman, WA, United States of America
| | - Ruilian Wu
- Bioenergy and Biome Sciences, Los Alamos National Laboratory (LANL), Los Alamos, NM, United States of America
| | - Sydney Huff
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Tu-Trinh Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, United States of America
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lynn K. Barrett
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jennifer L. Hyde
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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12
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Buchko GW, Zhou M, Craig JK, Van Voorhis WC, Myler PJ. Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms - μs) dynamics in the C-terminal helix at the dimer interface. Biomol NMR Assign 2021; 15:107-116. [PMID: 33392924 PMCID: PMC7779335 DOI: 10.1007/s12104-020-09992-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein's backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation studies, the backbone 1H, 13C, and 15N NMR chemical shifts for Nsp9 have been extensively assigned. These assignments were assisted by the preparation of an ~ 70% deuterated sample and residue-specific, 15N-labelled samples (V, L, M, F, and K). A major feature of the assignments was the "missing" amide resonances for N96-L106 in the 1H-15N HSQC spectrum, a region that comprises almost the complete C-terminal α-helix that forms a major part of the homodimer interface in the crystal structure of SARS-CoV-2 Nsp9, suggesting this region either undergoes intermediate motion in the ms to μs timescale and/or is heterogenous. These "missing" amide resonances do not unambiguously appear in the 1H-15N HSQC spectrum of SARS-CoV-2 Nsp9 collected at a concentration of 0.0007 mM. At this concentration, at the detection limit, native mass spectrometry indicates the protein is exclusively in the monomeric state, suggesting the intermediate motion in the C-terminal of Nsp9 may be due to intramolecular dynamics. Perhaps this intermediate ms to μs timescale dynamics is the physical basis for a previously suggested "fluidity" of the C-terminal helix that may be responsible for homophilic (Nsp9-Nsp9) and postulated heterophilic (Nsp9-Unknown) protein-protein interactions.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Justin K Craig
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Department of Medical Education and Biomedical Informatics, Department of Global Health, University of Washington, Seattle, Washington, USA
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13
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Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
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Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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14
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Velivelli SLS, Czymmek KJ, Li H, Shaw JB, Buchko GW, Shah DM. Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection. Proc Natl Acad Sci U S A 2020; 117:16043-16054. [PMID: 32571919 PMCID: PMC7354933 DOI: 10.1073/pnas.2003526117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In the indeterminate nodules of a model legume Medicago truncatula, ∼700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.
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Affiliation(s)
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St Louis, MO 63132
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, St Louis, MO 63132
| | - Hui Li
- Donald Danforth Plant Science Center, St Louis, MO 63132
| | - Jared B Shaw
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164
| | - Dilip M Shah
- Donald Danforth Plant Science Center, St Louis, MO 63132;
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15
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Elnaas AR, Grice D, Han J, Feng Y, Capua AD, Mak T, Laureanti JA, Buchko GW, Myler PJ, Cook G, Quinn RJ, Liu M. Discovery of a Natural Product That Binds to the Mycobacterium tuberculosis Protein Rv1466 Using Native Mass Spectrometry. Molecules 2020; 25:molecules25102384. [PMID: 32455540 PMCID: PMC7288112 DOI: 10.3390/molecules25102384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
Elucidation of the mechanism of action of compounds with cellular bioactivity is important for progressing compounds into future drug development. In recent years, phenotype-based drug discovery has become the dominant approach to drug discovery over target-based drug discovery, which relies on the knowledge of a specific drug target of a disease. Still, when targeting an infectious disease via a high throughput phenotypic assay it is highly advantageous to identifying the compound’s cellular activity. A fraction derived from the plant Polyalthia sp. showed activity against Mycobacterium tuberculosis at 62.5 μge/μL. A known compound, altholactone, was identified from this fraction that showed activity towards M. tuberculosis at an minimum inhibitory concentration (MIC) of 64 μM. Retrospective analysis of a target-based screen against a TB proteome panel using native mass spectrometry established that the active fraction was bound to the mycobacterial protein Rv1466 with an estimated pseudo-Kd of 42.0 ± 6.1 µM. Our findings established Rv1466 as the potential molecular target of altholactone, which is responsible for the observed in vivo toxicity towards M. tuberculosis.
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Affiliation(s)
- Ali R. Elnaas
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia;
| | - Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Angela Di Capua
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Peter J. Myler
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA;
| | - Gregory Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
- Correspondence: ; Tel.: +61-7-3735-6077
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16
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Laureanti JA, Ginovska B, Buchko GW, Schenter GK, Hebert M, Zadvornyy OA, Peters JW, Shaw WJ. A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret Hebert
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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17
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Shaheen S, Barrett KF, Subramanian S, Arnold SLM, Laureanti JA, Myler PJ, Van Voorhis WC, Buchko GW. Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state. Protein Sci 2020; 29:809-817. [PMID: 31912584 DOI: 10.1002/pro.3818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
Encephalitozoon cuniculi is a unicellular, obligate intracellular eukaryotic parasite in the Microsporidia family and one of the agents responsible for microsporidosis infections in humans. Like most Microsporidia, the genome of E. cuniculi is markedly reduced and the organism contains mitochondria-like organelles called mitosomes instead of mitochondria. Here we report the solution NMR structure for a protein physically associated with mitosome-like organelles in E. cuniculi, the 128-residue, adrenodoxin-like protein Ec-Adx (UniProt ID Q8SV19) in the [2Fe-2S] ferredoxin superfamily. Oxidized Ec-Adx contains a mixed four-strand β-sheet, β2-β1-β4-β3 (↓↑↑↓), loosely encircled by three α-helices and two 310 -helices. This fold is similar to the structure observed in other adrenodoxin and adrenodoxin-like proteins except for the absence of a fifth anti-parallel β-strand next to β3 and the position of α3. Cross peaks are missing or cannot be unambiguously assigned for 20 amide resonances in the 1 H-15 N HSQC spectrum of Ec-Adx. These missing residues are clustered primarily in two regions, G48-V61 and L94-L98, containing the four cysteine residues predicted to ligate the paramagnetic [2Fe-2S] cluster. Missing amide resonances in 1 H-15 N HSQC spectra are detrimental to NMR-based solution structure calculations because 1 H-1 H NOE restraints are absent (glass half-empty) and this may account for the absent β-strand (β5) and the position of α3 in oxidized Ec-Adx. On the other hand, the missing amide resonances unambiguously identify the presence, and immediate environment, of the paramagnetic [2Fe-2S] cluster in oxidized Ec-Adx (glass half-full).
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Affiliation(s)
- Shareef Shaheen
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Samuel L M Arnold
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington
| | - Joseph A Laureanti
- Physical Chemistry Directorate, Pacific Northwest National Laboratory, Richland, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Medical Education and Biomedical Informatics & Department of Global Health, University of Washington, Seattle, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,School of Molecular Biosciences, Washington State University, Pullman, Washington
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18
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Buchko GW, Abendroth J, Robinson JI, Phan IQ, Myler PJ, Edwards TE. Structural diversity in the Mycobacteria DUF3349 superfamily. Protein Sci 2019; 29:670-685. [PMID: 31658388 DOI: 10.1002/pro.3758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/11/2022]
Abstract
A protein superfamily with a "Domain of Unknown Function,", DUF3349 (PF11829), is present predominately in Mycobacterium and Rhodococcus bacterial species suggesting that these proteins may have a biological function unique to these bacteria. We previously reported the inaugural structure of a DUF3349 superfamily member, Mycobacterium tuberculosis Rv0543c. Here, we report the structures determined for three additional DUF3349 proteins: Mycobacterium smegmatis MSMEG_1063 and MSMEG_1066 and Mycobacterium abscessus MAB_3403c. Like Rv0543c, the NMR solution structure of MSMEG_1063 revealed a monomeric five α-helix bundle with a similar overall topology. Conversely, the crystal structure of MSMEG_1066 revealed a five α-helix protein with a strikingly different topology and a tetrameric quaternary structure that was confirmed by size exclusion chromatography. The NMR solution structure of a fourth member of the DUF3349 superfamily, MAB_3403c, with 18 residues missing at the N-terminus, revealed a monomeric α-helical protein with a folding topology similar to the three C-terminal helices in the protomer of the MSMEG_1066 tetramer. These structures, together with a GREMLIN-based bioinformatics analysis of the DUF3349 primary amino acid sequences, suggest two subfamilies within the DUF3349 family. The division of the DUF3349 into two distinct subfamilies would have been lost if structure solution had stopped with the first structure in the DUF3349 family, highlighting the insights generated by solving multiple structures within a protein superfamily. Future studies will determine if the structural diversity at the tertiary and quaternary levels in the DUF3349 protein superfamily have functional roles in Mycobacteria and Rhodococcus species with potential implications for structure-based drug discovery.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,School of Molecular Biosciences, Washington State University, Pullman, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - John I Robinson
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington.,Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
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19
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Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD. Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Protein Sci 2019; 27:1611-1623. [PMID: 30152054 DOI: 10.1002/pro.3453] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Disulfide-rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide-rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C- and 15 N-labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long-time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro, but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352.,School of Molecular Biosciences, Washington State University, Pullman, Washington, 99164
| | | | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Elizabeth A Shaw
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260
| | - Stephen A Rettie
- Institute for Protein Design, University of Washington, Seattle, Washington, 98195
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Center for Infectious Disease Research, Seattle, Washington, 98109.,Department of Global Health, University of Washington, Seattle, Washington, 98165.,Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, 98195
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.,Laboratoire de Chimie Biophysique, ISIS, Universite de Strasbourg, 67000, Strasbourg, France
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington, 98195.,Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195
| | - Christopher D Bahl
- Institute for Protein Design, University of Washington, Seattle, Washington, 98195.,Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Institute for Protein Innovation, Boston, Massachusetts, 02115
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20
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Laureanti JA, Buchko GW, Katipamula S, Su Q, Linehan JC, Zadvornyy OA, Peters JW, O’Hagan M. Protein Scaffold Activates Catalytic CO2 Hydrogenation by a Rhodium Bis(diphosphine) Complex. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02615] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Joseph A. Laureanti
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Sriram Katipamula
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Qiwen Su
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - John C. Linehan
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Molly O’Hagan
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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21
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Mori S, Green KD, Choi R, Buchko GW, Fried MG, Garneau-Tsodikova S. Using MbtH-Like Proteins to Alter the Substrate Profile of a Nonribosomal Peptide Adenylation Enzyme. Chembiochem 2018; 19:2186-2194. [PMID: 30134012 DOI: 10.1002/cbic.201800240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/21/2018] [Indexed: 01/19/2023]
Abstract
MbtH-like proteins (MLPs) are required for soluble expression and/or optimal activity of some adenylation (A) domains of nonribosomal peptide synthetases. Because A domains can interact with noncognate MLP partners, how the function of an A domain, TioK, involved in the biosynthesis of the bisintercalator thiocoraline, is altered by noncognate MLPs has been investigated. Measuring TioK activity with 12 different MLPs from a variety of bacterial species by using a radiometric assay suggested that the A domain substrate promiscuity could be altered by foreign MLPs. Kinetic studies and bioinformatics analysis expanded the complexity of MLP functions and interactions.
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Affiliation(s)
- Shogo Mori
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
| | - Ryan Choi
- University of Washington, Center for Emerging and Re-emerging Infectious Diseases, 750 Republican St., Seattle, WA, 98109, USA.,University of Washington, Seattle Structural Genomics Center for Infectious Diseases, 307 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Garry W Buchko
- University of Washington, Seattle Structural Genomics Center for Infectious Diseases, 307 Westlake Avenue N, Seattle, WA, 98109, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P. O. Box 999, Richmond, WA, 99352, USA.,School of Molecular Biosciences, Washington State University, P. O. Box 647520, Pullman, WA, 99164, USA
| | - Michael G Fried
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Biological Sciences Research Bldg, 741 South Limestone St., Lexington, KY, 40536-0509, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
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22
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Arachchige RJ, Burton SD, Lu JX, Ginovska B, Harding LK, Taylor ME, Tao J, Dohnalkova A, Tarasevich BJ, Buchko GW, Shaw WJ. Solid-State NMR Identification of Intermolecular Interactions in Amelogenin Bound to Hydroxyapatite. Biophys J 2018; 115:1666-1672. [PMID: 30415654 DOI: 10.1016/j.bpj.2018.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 01/01/2023] Open
Abstract
Biomineralization processes govern the formation of hierarchical hard tissues such as bone and teeth in living organisms, and mimicking these processes could lead to the design of new materials with specialized properties. However, such advances require structural characterization of the proteins guiding biomineral formation to understand and mimic their impact. In their "active" form, biomineralization proteins are bound to a solid surface, severely limiting our ability to use many conventional structure characterization techniques. Here, solid-state NMR spectroscopy was applied to study the intermolecular interactions of amelogenin, the most abundant protein present during the early stages of enamel formation, in self-assembled oligomers bound to hydroxyapatite. Intermolecular dipolar couplings were identified that support amelogenin dimer formation stabilized by residues toward the C-termini. These dipolar interactions were corroborated by molecular dynamics simulations. A β-sheet structure was identified in multiple regions of the protein, which is otherwise intrinsically disordered in the absence of hydroxyapatite. To our knowledge, this is the first intermolecular protein-protein interaction reported for a biomineralization protein, representing an advancement in understanding enamel development and a new general strategy toward investigating biomineralization proteins.
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Affiliation(s)
| | - Sarah D Burton
- Pacific Northwest National Laboratory, Richland, Washington
| | - Jun-Xia Lu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | - Megan E Taylor
- Pacific Northwest National Laboratory, Richland, Washington
| | - Jinhui Tao
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | - Garry W Buchko
- Pacific Northwest National Laboratory, Richland, Washington; School of Molecular Biosciences, Washington State University, Pullman, Washington.
| | - Wendy J Shaw
- Pacific Northwest National Laboratory, Richland, Washington.
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23
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Buchko GW, Jayasinha Arachchige R, Tao J, Tarasevich BJ, Shaw WJ. Identification of major matrix metalloproteinase-20 proteolytic processing products of murine amelogenin and tyrosine-rich amelogenin peptide using a nuclear magnetic resonance spectroscopy based method. Arch Oral Biol 2018; 93:187-194. [PMID: 29960917 DOI: 10.1016/j.archoralbio.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/14/2023]
Abstract
OBJECTIVE The aim of this study was to identify major matrix metalloproteinase-20 (MMP20) proteolytic processing products of amelogenin over time and determine if the tyrosine-rich amelogenin peptide (TRAP) was a substrate of MMP20. DESIGN Recombinant15N-labeled murine amelogenin and 13C,15N-labeled TRAP were incubated with MMP20 under conditions where amelogenin self-assembles into nanospheres. Digestion products were fractionated by reverse-phase high-performance liquid chromatography at various time points. Product identification took advantage of the intrinsic disorder property of amelogenin that results in little change to its fingerprint 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectrum in 2% acetic acid upon removing parts of the protein, allowing cleavage site identification by observing which amide cross peaks disappear. RESULTS The primary product in five out of the six major reverse-phase high-performance liquid chromatography bands generated after a 24 h incubation of murine amelogenin with MMP20 were: S55-L163, P2-L147, P2-E162, P2-A167, and P2-R176. After 72 h these products were replaced with five major reverse-phase high-performance liquid chromatography bands containing: L46-A170, P2-S152, P2-F151, P2-W45, and short N-terminal peptides. TRAP was completely digested by MMP20 into multiple small peptides with the initial primary site of cleavage between S16 and Y17. CONCLUSIONS Identification of the major MMP20 proteolytic products of amelogenin confirm a dynamic process, with sites towards the C-terminus more rapidly attacked than sites near the N-terminus. This observation is consistent with nanosphere models where the C-terminus is exposed and the N-terminus more protected. One previously reported end-product of the MMP20 proteolytic processing of amelogenin, TRAP, is shown to be an in vitro substrate for MMP20.
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Affiliation(s)
- Garry W Buchko
- Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
| | | | - Jinhui Tao
- Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | | | - Wendy J Shaw
- Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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24
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Buchko GW, Hewitt SN, Van Voorhis WC, Myler PJ. Solution NMR structures of oxidized and reduced Ehrlichia chaffeensis thioredoxin: NMR-invisible structure owing to backbone dynamics. Acta Crystallogr F Struct Biol Commun 2018; 74:46-56. [PMID: 29372907 PMCID: PMC5947692 DOI: 10.1107/s2053230x1701799x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/16/2017] [Indexed: 11/10/2022] Open
Abstract
Thioredoxins are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site. Here, the NMR solution structures of a reduced and oxidized thioredoxin from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, are described. The overall topology of the calculated structures is similar in both redox states and is similar to those of other thioredoxins: a five-stranded, mixed β-sheet (β1-β3-β2-β4-β5) surrounded by four α-helices. Unlike other thioredoxins studied by NMR in both redox states, the 1H-15N HSQC spectrum of reduced Ec-Trx was missing eight additional amide cross peaks relative to the spectrum of oxidized Ec-Trx. These missing amides correspond to residues Cys35-Glu39 in the active-site-containing helix (α2) and Ser72-Ile75 in a loop near the active site, and suggest a change in backbone dynamics on the millisecond-to-microsecond timescale associated with the breakage of an intramolecular Cys32-Cys35 disulfide bond in a thioredoxin. A consequence of the missing amide resonances is the absence of observable or unambiguous NOEs to provide the distance restraints necessary to define the N-terminal end of the α-helix containing the CPGC active site in the reduced state. This region adopts a well defined α-helical structure in other reported reduced thioredoxin structures, is mostly helical in oxidized Ec-Trx and CD studies of Ec-Trx in both redox states suggests there is no significant difference in the secondary structure of the protein. The NMR solution structure of reduced Ec-Trx illustrates that the absence of canonical structure in a region of a protein may be owing to unfavorable dynamics prohibiting NOE observations or unambiguous NOE assignments.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Infectious Disease Research, Seattle, Washington, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, USA
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25
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Zerfaß C, Buchko GW, Shaw WJ, Hobe S, Paulsen H. Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation. Proteins 2017; 85:2111-2126. [PMID: 28799215 PMCID: PMC5760248 DOI: 10.1002/prot.25366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/08/2022]
Abstract
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.
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Affiliation(s)
- Christian Zerfaß
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Stephan Hobe
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
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26
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Buchko GW, Echols N, Flynn EM, Ng HL, Stephenson S, Kim HB, Myler PJ, Terwilliger TC, Alber T, Kim CY. Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA. Biochemistry 2017; 56:4015-4027. [PMID: 28692281 DOI: 10.1021/acs.biochem.7b00511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has an amino acid sequence that is 36% identical to that of Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomyces genus. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Å, binding properties with neutral red and deoxyadenosine were surveyed, backbone dynamics were measured, and thermal stability was assayed by circular dichroism spectroscopy. The protein is composed of four approximate repeats with a βαβββ topology arranged radially in consecutive pairs to form two continuous eight-strand β-sheets capped on both ends with an α-helix. The two β-sheets intersect in the center at roughly a right angle and form two asymmetric deep "saddles" that may serve to bind ligands. Nuclear magnetic resonance chemical shift perturbation experiments show that neutral red and deoxyadenosine bind to Rv0577. Binding to deoxyadenosine is weaker with an estimated dissociation constants of 4.1 ± 0.3 mM for saddle 1. Heteronuclear steady-state {1H}-15N nuclear Overhauser effect, T1, and T2 values were generally uniform throughout the sequence with only a few modest pockets of differences. Circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94158-2330, United States.,Department of Molecular and Cell Biology, University of California , Berkeley, California 94158-2330, United States
| | - E Megan Flynn
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94158-2330, United States
| | - Ho-Leung Ng
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94158-2330, United States
| | - Samuel Stephenson
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94158-2330, United States
| | - Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Diseases.,Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington , Seattle, Washington 98195, United States.,Center for Infectious Disease Research , Seattle, Washington 98109-5219, United States
| | - Thomas C Terwilliger
- Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | - Tom Alber
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94158-2330, United States.,Department of Molecular and Cell Biology, University of California , Berkeley, California 94158-2330, United States
| | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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27
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Ravanat JL, Berger M, Buchko GW, Bénard JF, van Lier JE, Cadet J. Photooxydation sensibilisée de la désoxy-2’ guanosine par des phtalocyanines et naphtalocyanines. Détermination de l’importance des mécanismes de type I et de type II. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1991881069] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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28
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Buchko GW, Clifton MC, Wallace EG, Atkins KA, Myler PJ. Backbone chemical shift assignments and secondary structure analysis of the U1 protein from the Bas-Congo virus. Biomol NMR Assign 2017; 11:51-56. [PMID: 27981424 PMCID: PMC8457264 DOI: 10.1007/s12104-016-9719-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
The Bas-Congo virus (BASV) is the first rhabdovirus associated with a human outbreak of acute hemorrhagic fever. The single-stranded, negative-sense RNA genome of BASV contains the five core genes present in all rhabdoviral genomes plus an additional three genes, annotated U1, U2, and U3, with weak (<21%) sequence similarity only to a handful of genes observed in a few other rhabdoviral genomes. The function of the rhabdoviral U proteins is unknown, but, they are hypothesized to play a role in viral infection or replication. To better understand this unique family of proteins, a construct containing residues 27-203 of the 216-residue U1 protein (BASV-U1*) was prepared. By collecting data in 0.5 M urea it was possible to eliminate transient association enough to enable the assignment of most of the observable 1HN, 1Hα, 15N, 13Cα, 13Cβ, and 13C´ chemical shifts for BASV-U1* that will provide a foundation to study its solution properties. The analyses of these chemical shifts along with 15N-edited NOESY data enabled the identification of the elements of secondary structure present in BASV-U1*.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
- Nurix Inc., San Francisco, CA, 94158, USA
| | - Ellen G Wallace
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
| | - Kateri A Atkins
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Center for Infectious Disease Research, 307 Westlake Ave. N., Seattle, WA, 98109, USA
- Department of Global Health, University of Washington, Seattle, WA, 98165, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA, 98195, USA
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29
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Boralugodage NP, Arachchige RJ, Dutta A, Buchko GW, Shaw WJ. Evaluating the role of acidic, basic, and polar amino acids and dipeptides on a molecular electrocatalyst for H2 oxidation. Catal Sci Technol 2017. [DOI: 10.1039/c6cy02579j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Outer coordination sphere interactions reduce the overpotential for H2 oxidation catalysts (brown ellipse) compared to those that have –COOH groups but don't have stabilizing interactions (blue ellipse).
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Affiliation(s)
| | | | - Arnab Dutta
- Pacific Northwest National Laboratory
- Richland
- 99352 USA
| | | | - Wendy J. Shaw
- Pacific Northwest National Laboratory
- Richland
- 99352 USA
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30
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Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen P, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D. Accurate de novo design of hyperstable constrained peptides. Nature 2016; 538:329-335. [PMID: 27626386 PMCID: PMC5161715 DOI: 10.1038/nature19791] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/18/2016] [Indexed: 02/06/2023]
Abstract
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.
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Affiliation(s)
- Gaurav Bhardwaj
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Vikram Khipple Mulligan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Christopher D. Bahl
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jason M. Gilmore
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Peta J. Harvey
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Earth, and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | - Quentin Kaas
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Alexander Eletsky
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William A. Johnsen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Per Greisen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark
| | - Gabriel J. Rocklin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Cyrus Biotechnology, Seattle, Washington 98109, USA
| | - Thomas W. Linsky
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Andrew Watkins
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Stephen A. Rettie
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Xianzhong Xu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Lauren P. Carter
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA
- Center for Computational Biology, Simons Foundation, NY, NY 10010
| | - James M. Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Evangelos Coutsias
- Applied Mathematics and Statistics and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Colin E. Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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31
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Staker BL, Buchko GW, Myler PJ. Recent contributions of structure-based drug design to the development of antibacterial compounds. Curr Opin Microbiol 2016; 27:133-8. [PMID: 26458180 DOI: 10.1016/j.mib.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/09/2015] [Accepted: 09/23/2015] [Indexed: 11/28/2022]
Abstract
According to a Pew Research study published in February 2015, there are 37 antibacterial programs currently in clinical trials in the United States. Protein structure-based methods for guiding small molecule design were used in at least 34 of these programs. Typically, this occurred at an early stage (drug discovery and/or lead optimization) prior to an Investigational New Drug (IND) application, although sometimes in retrospective studies to rationalize biological activity. Recognizing that structure-based methods are resource-intensive and often require specialized equipment and training, the NIAID has funded two Structural Genomics Centers to determine structures of infectious disease species proteins with the aim of supporting individual investigators' research programs with structural biology methods.
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Affiliation(s)
- Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Seattle, WA 98195, United States; Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, United States
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32
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Priyadarshani N, Dutta A, Ginovska B, Buchko GW, O’Hagan M, Raugei S, Shaw WJ. Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01433] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nilusha Priyadarshani
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Arnab Dutta
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Molly O’Hagan
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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33
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Buchko GW, Perkins A, Parsonage D, Poole LB, Karplus PA. Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics. Biomol NMR Assign 2016; 10:57-61. [PMID: 26438558 PMCID: PMC4789116 DOI: 10.1007/s12104-015-9637-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/09/2015] [Indexed: 05/11/2023]
Abstract
Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond.
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Affiliation(s)
- Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA.
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34
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Buchko GW, Edwards TE, Hewitt SN, Phan IQH, Van Voorhis WC, Miller SI, Myler PJ. Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface. Biomol NMR Assign 2015; 9:381-5. [PMID: 25957069 PMCID: PMC4569509 DOI: 10.1007/s12104-015-9614-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/28/2015] [Indexed: 05/11/2023]
Abstract
Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 98110, USA
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195-7185, USA
| | - Isabelle Q H Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Center for Infectous Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, 98109-5219, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195-7185, USA
| | - Samuel I Miller
- Department of Medicine, University of Washington, Seattle, WA, 98195-7185, USA
- Department of Microbiology and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Center for Infectous Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, 98109-5219, USA
- Department of Biomedical Informatics and Medical Education and Department of Global Health, University of Washington, Seattle, WA, 98195, USA
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35
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Tao J, Buchko GW, Shaw WJ, De Yoreo JJ, Tarasevich BJ. Sequence-Defined Energetic Shifts Control the Disassembly Kinetics and Microstructure of Amelogenin Adsorbed onto Hydroxyapatite (100). Langmuir 2015; 31:10451-10460. [PMID: 26381243 PMCID: PMC4917396 DOI: 10.1021/acs.langmuir.5b02549] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The interactions between proteins and surfaces are critical to a number of important processes including biomineralization, the biocompatibility of biomaterials, and the function of biosensors. Although many proteins exist as monomers or small oligomers, amelogenin is a unique protein that self-assembles into supramolecular structures called "nanospheres," aggregates of hundreds of monomers that are 20-60 nm in diameter. The nanosphere quaternary structure is observed in solution; however, the quaternary structure of amelogenin adsorbed onto hydroxyapatite (HAP) surfaces is not known even though it may be important to amelogenin's function in forming highly elongated and intricately assembled HAP crystallites during enamel formation. We report studies of the interactions of the enamel protein, amelogenin (rpM179), with a well-defined (100) face prepared by the synthesis of large crystals of HAP. High-resolution in situ atomic force microscopy (AFM) was used to directly observe protein adsorption onto HAP at the molecular level within an aqueous solution environment. Our study shows that the amelogenin nanospheres disassemble onto the HAP surface, breaking down into oligomeric (25-mer) subunits of the larger nanosphere. In some cases, the disassembly event is directly observed by in situ imaging for the first time. Quantification of the adsorbate amounts by size analysis led to the determination of a protein binding energy (17.1k(b)T) to a specific face of HAP (100). The kinetics of disassembly are greatly slowed in aged solutions, indicating that there are time-dependent increases in oligomer-oligomer binding interactions within the nanosphere. A small change in the sequence of amelogenin by the attachment of a histidine tag to the N-terminus of rpM179 to form rp(H)M180 results in the adsorption of a complete second layer on top of the underlying first layer. Our research elucidates how supramolecular protein structures interact and break down at surfaces and how small changes in the primary sequence of amelogenin can affect the disassembly process.
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36
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Buchko GW, Abendroth J, Clifton MC, Robinson H, Zhang Y, Hewitt SN, Staker BL, Edwards TE, Van Voorhis WC, Myler PJ. Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis. Acta Crystallogr F Struct Biol Commun 2015; 71:522-30. [PMID: 25945704 PMCID: PMC4427160 DOI: 10.1107/s2053230x14028210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/29/2014] [Indexed: 11/11/2022] Open
Abstract
Cryptosporidiosis is an infectious disease caused by protozoan parasites of the Cryptosporidium genus. Infection is associated with mild to severe diarrhea that usually resolves spontaneously in healthy human adults, but may lead to severe complications in young children and in immunocompromised patients. The genome of C. parvum contains a gene, CUTA_CRYPI, that may play a role in regulating the intracellular concentration of copper, which is a toxic element in excess. Here, the crystal structure of this CutA1 protein, Cp-CutA1, is reported at 2.0 Å resolution. As observed for other CutA1 structures, the 117-residue protein is a trimer with a core ferrodoxin-like fold. Circular dichroism spectroscopy shows little, in any, unfolding of Cp-CutA1 up to 353 K. This robustness is corroborated by (1)H-(15)N HSQC spectra at 333 K, which are characteristic of a folded protein, suggesting that NMR spectroscopy may be a useful tool to further probe the function of the CutA1 proteins. While robust, Cp-CutA1 is not as stable as the homologous protein from a hyperthermophile, perhaps owing to a wide β-bulge in β2 that protrudes Pro48 and Ser49 outside the β-sheet.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Yanfeng Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
- Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington, Seattle, Washington, USA
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37
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Buchko GW, Yee A, Semesi A, Myler PJ, Arrowsmith CH, Hui R. Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) from Plasmodium falciparum. Acta Crystallogr F Struct Biol Commun 2015; 71:514-21. [PMID: 25945703 DOI: 10.1107/s2053230x1402799x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/23/2014] [Indexed: 12/22/2022]
Abstract
Protozoa of the genus Plasmodium are responsible for malaria, which is perhaps the most important parasitic disease to infect mankind. The emergence of Plasmodium strains resistant to current therapeutics and prophylactics makes the development of new treatment strategies urgent. Among the potential targets for new antimalarial drugs is the BolA-like protein PFE0790c from Plasmodium falciparum (Pf-BolA). While the function of BolA is unknown, it has been linked to cell morphology by regulating transcription in response to stress. Using an NMR-based method, an ensemble of 20 structures of Pf-BolA was determined and deposited in the PDB (PDB entry 2kdn). The overall topology of the Pf-BolA structure, α1-β1-β2-η1-α2/η2-β3-α3, with the β-strands forming a mixed β-sheet, is similar to the fold observed in other BolA structures. A helix-turn-helix motif similar to the class II KH fold associated with nucleic acid-binding proteins is present, but contains an FXGXXXL signature sequence that differs from the GXXG signature sequence present in class II KH folds, suggesting that the BolA family of proteins may use a novel protein-nucleic acid interface. A well conserved arginine residue, Arg50, hypothesized to play a role in governing the formation of the C-terminal α-helix in the BolA family of proteins, is too distant to form polar contacts with any side chains in this α-helix in Pf-BolA, suggesting that this conserved arginine may only serve a role in guiding the orientation of this C-terminal helix in some BolA proteins. A survey of BolA structures suggests that the C-terminal helix may not have a functional role and that the third helix (α2/η2) has a `kink' that appears to be conserved among the BolA protein structures. Circular dichroism spectroscopy shows that Pf-BolA is fairly robust, partially unfolding when heated to 353 K and refolding upon cooling to 298 K.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Adelinda Yee
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anthony Semesi
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Raymond Hui
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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38
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Tarasevich BJ, Philo JS, Maluf NK, Krueger S, Buchko GW, Lin G, Shaw WJ. The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution. J Struct Biol 2015; 190:81-91. [PMID: 25449314 PMCID: PMC4400868 DOI: 10.1016/j.jsb.2014.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 11/23/2022]
Abstract
Amelogenin proteins are critical to the formation of enamel in teeth and may have roles in controlling growth and regulating microstructures of the intricately woven hydroxyapatite (HAP). Leucine-rich amelogenin protein (LRAP) is a 59-residue splice variant of amelogenin and contains the N- and C-terminal charged regions of the full-length protein thought to control crystal growth. Although the quaternary structure of full-length amelogenin in solution has been well studied and can consist of self-assemblies of monomers called nanospheres, there is limited information on the quaternary structure of LRAP. Here, sedimentation velocity analytical ultracentrifugation (SV) and small angle neutron scattering (SANS) were used to study the tertiary and quaternary structure of LRAP at various pH values, ionic strengths, and concentrations. We found that the monomer is the dominant species of phosphorylated LRAP (LRAP(+P)) over a range of solution conditions (pH 2.7-4.1, pH 4.5-8, 50 mmol/L(mM) to 200 mM NaCl, 0.065-2 mg/mL). The monomer is also the dominant species for unphosphorylated LRAP (LRAP(-P)) at pH 7.4 and for LRAP(+P) in the presence of 2.5 mM calcium at pH 7.4. LRAP aggregates in a narrow pH range near the isoelectric point of pH 4.1. SV and SANS show that the LRAP monomer has a radius of ∼2.0 nm and an asymmetric structure, and solution NMR studies indicate that the monomer is largely unstructured. This work provides new insights into the secondary, tertiary, and quaternary structure of LRAP in solution and provides evidence that the monomeric species may be an important functional form of some amelogenins.
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Affiliation(s)
| | - John S Philo
- Alliance Protein Laboratories, Inc., San Diego, CA 92121, United States
| | - Nasib Karl Maluf
- Alliance Protein Laboratories, Inc., San Diego, CA 92121, United States
| | - Susan Krueger
- National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Garry W Buchko
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Genyao Lin
- WSP Chemicals & Technology, LLC, Leetsdale, PA 15056, United States
| | - Wendy J Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
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39
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Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2014; 95:142-8. [PMID: 25613812 DOI: 10.1016/j.tube.2014.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/10/2014] [Indexed: 01/31/2023]
Abstract
High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brianna Armour
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brandy M Taylor
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Marvin M Muruthi
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - James W Fairman
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David Fox
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Shellie H Dieterich
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Alberto J Napuli
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Janette Myers
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Micah Ferrell
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Elizabeth Mundt
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Katie Thompkins
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ngoc Tran
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Aarthi Sekar
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Dmitri Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Don Lorimer
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States.
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Buchko GW, Shaw WJ. Improved protocol to purify untagged amelogenin - Application to murine amelogenin containing the equivalent P70→T point mutation observed in human amelogenesis imperfecta. Protein Expr Purif 2014; 105:14-22. [PMID: 25306873 DOI: 10.1016/j.pep.2014.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/17/2014] [Indexed: 11/16/2022]
Abstract
Amelogenin is the predominant extracellular protein responsible for converting carbonated hydroxyapatite into dental enamel, the hardest and most heavily mineralized tissue in vertebrates. Despite much effort, the precise mechanism by which amelogenin regulates enamel formation is not fully understood. To assist efforts aimed at understanding the biochemical mechanism of enamel formation, more facile protocols to purify recombinantly expressed amelogenin, ideally without any tag to assist affinity purification, are advantageous. Here we describe an improved method to purify milligram quantities of amelogenin that exploits its high solubility in 2% glacial acetic acid under conditions of low ionic strength. The method involves heating the frozen cell pellet for two 15min periods at ∼70°C with 2min of sonication in between, dialysis twice in 2% acetic acid (1:250 v/v), and reverse phase chromatography. A further improvement in yield is obtained by resuspending the frozen cell pellet in 6M guanidine hydrochloride in the first step. The acetic acid heating method is illustrated with a murine amelogenin containing the corresponding P70→T point mutation observed in an human amelogenin associated with amelogenesis imperfecta (P71T), while the guanidine hydrochloride heating method is illustrated with wild type murine amelogenin (M180). The self-assembly properties of P71T were probed by NMR chemical shift perturbation studies as a function of protein (0.1-1.8mM) and NaCl (0-367mM) concentration. Relative to similar studies with wild type murine amelogenin, P71T self-associates at lower protein or salt concentrations with the interactions initiated near the N-terminus.
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Affiliation(s)
- Garry W Buchko
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Wendy J Shaw
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Lu JX, Burton SD, Xu YS, Buchko GW, Shaw WJ. The flexible structure of the K24S28 region of Leucine-Rich Amelogenin Protein (LRAP) bound to apatites as a function of surface type, calcium, mutation, and ionic strength. Front Physiol 2014; 5:254. [PMID: 25071599 PMCID: PMC4092356 DOI: 10.3389/fphys.2014.00254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/17/2014] [Indexed: 12/30/2022] Open
Abstract
Leucine-Rich Amelogenin Protein (LRAP) is a member of the amelogenin family of biomineralization proteins, proteins which play a critical role in enamel formation. Recent studies have revealed the structure and orientation of the N- and C-terminus of LRAP bound to hydroxyapatite (HAP), a surface used as an analog of enamel. The structure of one region, K24 to S28, was found to be sensitive to phosphorylation of S16, the only naturally observed site of serine phosphorylation in LRAP, suggesting that K24S28 may sit at a key region of structural flexibility and play a role in the protein's function. In this work, we investigated the sensitivity of the structure and orientation of this region when bound to HAP as a function of several factors which may vary during enamel formation to influence structure: the ionic strength (0.05, 0.15, 0.2 M), the calcium concentration (0.07 and 0.4 mM), and the surface to which it is binding [HAP and carbonated apatite (CAP), a more direct mimic of enamel]. A naturally occurring mutation found in amelogenin (T21I) was also investigated. The structure in the K24S28 region of the protein was found to be sensitive to these conditions, with the CAP surface and excess Ca(2+) (8:1 [Ca(2+)]:[LRAP-K24S28(+P)]) resulting in a tighter helix, while low ionic strength relaxed the helical structure. Higher ionic strength and the point mutation did not result in any structural change in this region. The distance of the backbone of K24 from the surface was most sensitive to excess Ca(2+) and in the T21I-mutation. Collectively, these data suggest that phosphorylated LRAP is able to accommodate structural changes while maintaining its interaction with the surface, and provides further evidence of the structural sensitivity of the K24S28 region, a sensitivity that may contribute to function in biomineralization.
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Affiliation(s)
| | | | | | | | - Wendy J. Shaw
- Fundamental and Computational Sciences Directorate, Pacific Northwest National LaboratoryRichland, WA, USA
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42
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Reback ML, Buchko GW, Kier BL, Ginovska-Pangovska B, Xiong Y, Lense S, Hou J, Roberts JAS, Sorensen CM, Raugei S, Squier TC, Shaw WJ. Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere. Chemistry 2014; 20:1510-4. [PMID: 24443316 DOI: 10.1002/chem.201303976] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Indexed: 11/07/2022]
Abstract
Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.
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43
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Abstract
Amelogenin is one of the key protein constituents responsible for the exquisite organization of the calcium phosphate crystals in enamel. Amelogenin forms into nanospheres in solution, while its association with hydroxyapatite is also essential to enamel development. Structural information of full-length amelogenin in either of these physiologically important forms has the potential to provide mechanistic information; however, these data are limited because of the difficulty of determining the structure of large protein complexes and proteins bound to surfaces. To obtain structural insights into amelogenin during these early stages of enamel development, we used a lysine-specific (13)C-, (15)N-labeled sample of murine amelogenin to provide insight into the structure of the hydroxyapatite (HAP)-binding domains of the protein. A combination of one-and two-dimensional solid-state NMR experiments was used to obtain molecular-level insights into the secondary structure and dynamics of full-length amelogenin within a nanosphere-gel and on the surface of HAP. Regions of amelogenin that appear to be primarily random coil in the nanosphere-gel adopt a β-strand structure and are less mobile with HAP binding, indicative of a structural switch upon binding that may be important in the role of amelogenin in enamel development.
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Affiliation(s)
- J X Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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44
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Buchko GW, Hewitt SN, Van Voorhis WC, Myler PJ. Solution structure of a putative FKBP-type peptidyl-propyl cis-trans isomerase from Giardia lamblia. J Biomol NMR 2013; 57:369-374. [PMID: 24293257 PMCID: PMC3903135 DOI: 10.1007/s10858-013-9797-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 11/19/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA,
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45
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Buchko GW, Lin G, Tarasevich BJ, Shaw WJ. A solution NMR investigation into the impaired self-assembly properties of two murine amelogenins containing the point mutations T21→I or P41→T. Arch Biochem Biophys 2013; 537:217-24. [PMID: 23896516 PMCID: PMC3788651 DOI: 10.1016/j.abb.2013.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Amelogenesis imperfecta describes a group of inherited disorders that results in defective tooth enamel. Two disorders associated with human amelogenesis imperfecta are the point mutations T21→I or P40→T in amelogenin, the dominant protein present during the early stages of enamel biomineralization. The biophysical properties of wildtype murine amelogenin (M180) and two proteins containing the equivalent mutations in murine amelogenin, T21→I (M180-I) and P41→T (M180-T), were probed by NMR spectroscopy. At low protein concentration (0.1mM), M180, M180-I, and M180-T are predominately monomeric at pH 3.0 in 2% acetic acid and neither mutation produces a major structural change. Chemical shift perturbation studies as a function of protein (0.1-1.8mM) or NaCl (0-400mM) concentrations show that the mutations affect the self-association properties by causing self-assembly at lower protein or salt concentrations, relative to wildtype amelogenin, with the largest effect observed for M180-I. Under both conditions, the premature self-assembly is initiated near the N-terminus, providing further evidence for the importance of this region in the self-assembly process. The self-association of M180-I and M180-T at lower protein concentrations and lower ionic strengths than wildtype M180 may account for the clinical phenotypes of these mutations, defective enamel formation.
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Affiliation(s)
- Garry W. Buchko
- Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Genyao Lin
- Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Barbara J. Tarasevich
- Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wendy J. Shaw
- Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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46
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Buchko GW, Jain A, Reback ML, Shaw WJ. Structural characterization of the model amphipathic peptide Ac-LKKLLKLLKKLLKL-NH2 in aqueous solution and with 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoroisopropanol. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Short-chain amphipathic peptides are promising components in the new generation of engineered biomaterials. The model 14-residue leucine–lysine peptide Ac-LKKLLKLLKKLLKL-NH2 (LKα) is one such amphipathic peptide. In dilute aqueous solution (<0.05 mmol/L), it was previously proposed, using CD spectroscopic data, that LKα existed in a cooperative monomeric (unstructured) – tetrameric (α-helical) equilibrium that shifted towards the tetramer at high NaCl and peptide concentrations. Here, at similar peptide concentrations, CD spectroscopy shows that LKα readily adopts α-helical structure in the presence of 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) with maximal helical character in 20% TFE and ∼10% HFIP (v/v). The helical character in fluorinated alcohols suggested by the CD data at low peptide concentrations (0.06 mmol/L) is corroborated at high peptide concentrations (1.5 mmol/L) by NMR NOE data that also show that 1.5 mmol/L LKα is helical in 100% water. Size exclusion chromatography and estimations of rotational correlation times (τc) showed that the self-assembled LKα complexes contained three to five peptides. Removing the N-terminal acetyl group prevents LKα from forming helices and self-associating at high NaCl and peptide concentrations. This more detailed characterization of the structural and physical properties of LKα over a greater range of peptide concentrations and in the presence of fluorinated alcohols will assist the design of biomaterials containing amphipathic peptides and guide the ability to control self-assembly.
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Affiliation(s)
- Garry W. Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Avijita Jain
- Chemicals & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew L. Reback
- Chemicals & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wendy J. Shaw
- Chemicals & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Buchko GW, Abendroth J, Robinson H, Zhang Y, Hewitt SN, Edwards TE, Van Voorhis WC, Myler PJ. Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia. ACTA ACUST UNITED AC 2013; 14:47-57. [PMID: 23709284 DOI: 10.1007/s10969-013-9155-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/09/2013] [Indexed: 11/29/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with two anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two "gate-keeper" residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y --> R) and 100 (V --> D) and for Gl-MIF it is at position 100 (V --> R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.
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Affiliation(s)
- Garry W Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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48
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Zhang Y, Gardberg AS, Edwards TE, Sankaran B, Robinson H, Varnum SM, Buchko GW. Structural insights into the functional role of the Hcn sub-domain of the receptor-binding domain of the botulinum neurotoxin mosaic serotype C/D. Biochimie 2013; 95:1379-85. [PMID: 23523511 DOI: 10.1016/j.biochi.2013.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/05/2013] [Indexed: 12/13/2022]
Abstract
Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding domain (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell's membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a β-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been identified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) moiety bound in a hydrophobic cleft between β-strands in the β-sheet jelly roll fold of the Hcn sub-domain. The PG4 moiety is completely engulfed in the cleft, making numerous hydrophilic (Y932, S959, W966, and D1042) and hydrophobic (S935, W977, L979, N1013, and I1066) contacts with the protein's side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid molecule was observed bound to the equivalent residues suggesting that residues T1176, D1177, K1196, and R1243 in BoNT/CD may play a role in ganglioside binding.
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Affiliation(s)
- Yanfeng Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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49
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Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013; 8:e53851. [PMID: 23382856 PMCID: PMC3561365 DOI: 10.1371/journal.pone.0053851] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rapatbhorn Patrapuvich
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Anna S. Gardberg
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Brianna Armour
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | | | - David M. Dranow
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - James W. Fairman
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - David Fox
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Angela Gillespie
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Mary Trang Nguyen
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Lynn Barrett
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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50
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Jain A, Buchko GW, Reback ML, O’Hagan M, Ginovska-Pangovska B, Linehan JC, Shaw WJ. Active Hydrogenation Catalyst with a Structured, Peptide-Based Outer-Coordination Sphere. ACS Catal 2012. [DOI: 10.1021/cs3004177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Avijita Jain
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
| | - Matthew L. Reback
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
| | - Molly O’Hagan
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
| | | | - John C. Linehan
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, Washington
99354, United States
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