1
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Sultanakhmetov G, Kato I, Asada A, Saito T, Ando K. Microtubule-affinity regulating kinase family members distinctively affect tau phosphorylation and promote its toxicity in a Drosophila model. Genes Cells 2024; 29:337-346. [PMID: 38329182 DOI: 10.1111/gtc.13101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
Accumulation of abnormally phosphorylated tau and its aggregation constitute a significant hallmark of Alzheimer's disease (AD). Tau phosphorylation at Ser262 and Ser356 in the KXGS motifs of microtubule-binding repeats plays a critical role in its physiological function and AD disease progression. Major tau kinases to phosphorylate tau at Ser262 and Ser356 belong to the Microtubule Affinity Regulating Kinase family (MARK1-4), which are considered one of the major contributors to tau abnormalities in AD. However, whether and how each member affects tau toxicity in vivo is unclear. We used transgenic Drosophila as a model to compare the effect on tau-induced neurodegeneration among MARKs in vivo. MARK4 specifically promotes tau accumulation and Ser396 phosphorylation, which yields more tau toxicity than was caused by other MARKs. Interestingly, MARK1, 2, and 4 increased tau phosphorylation at Ser262 and Ser356, but only MARK4 caused tau accumulation, indicating that these sites alone did not cause pathological tau accumulation. Our results revealed MARKs are different in their effect on tau toxicity, and also in tau phosphorylation at pathological sites other than Ser262 and Ser356. Understanding the implementation of each MARK into neurodegenerative disease helps to develop more target and safety therapies to overcome AD and related tauopathies.
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Affiliation(s)
- Grigorii Sultanakhmetov
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Iori Kato
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Akiko Asada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Taro Saito
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
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2
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Pathira Kankanamge LS, Ruffner LA, Touch MM, Pina M, Beuning PJ, Ondrechen MJ. Functional annotation of haloacid dehalogenase superfamily structural genomics proteins. Biochem J 2023; 480:1553-1569. [PMID: 37747786 DOI: 10.1042/bcj20230057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
Haloacid dehalogenases (HAD) are members of a large superfamily that includes many Structural Genomics proteins with poorly characterized functionality. This superfamily consists of multiple types of enzymes that can act as sugar phosphatases, haloacid dehalogenases, phosphonoacetaldehyde hydrolases, ATPases, or phosphate monoesterases. Here, we report on predicted functional annotations and experimental testing by direct biochemical assay for Structural Genomics proteins from the HAD superfamily. To characterize the functions of HAD superfamily members, nine representative HAD proteins and 21 structural genomics proteins are analyzed. Using techniques based on computed chemical and electrostatic properties of individual amino acids, the functions of five structural genomics proteins from the HAD superfamily are predicted and validated by biochemical assays. A dehalogenase-like hydrolase, RSc1362 (Uniprot Q8XZN3, PDB 3UMB) is predicted to be a dehalogenase and dehalogenase activity is confirmed experimentally. Four proteins predicted to be sugar phosphatases are characterized as follows: a sugar phosphatase from Thermophilus volcanium (Uniprot Q978Y6) with trehalose-6-phosphate phosphatase and fructose-6-phosphate phosphatase activity; haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron (Uniprot Q8A2F3; PDB 3NIW) with fructose-6-phosphate phosphatase and sucrose-6-phosphate phosphatase activity; putative phosphatase from Eubacterium rectale (Uniprot D0VWU2; PDB 3DAO) as a sucrose-6-phosphate phosphatase; and hypothetical protein from Geobacillus kaustophilus (Uniprot Q5L139; PDB 2PQ0) as a fructose-6-phosphate phosphatase. Most of these sugar phosphatases showed some substrate promiscuity.
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Affiliation(s)
| | - Lydia A Ruffner
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, U.S.A
| | - Mong Mary Touch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, U.S.A
| | - Manuel Pina
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, U.S.A
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, U.S.A
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, U.S.A
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3
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Geddes JW, Bondada V, Croall DE, Rodgers DW, Gal J. Impaired activity and membrane association of most calpain-5 mutants causal for neovascular inflammatory vitreoretinopathy. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166747. [PMID: 37207905 PMCID: PMC10332796 DOI: 10.1016/j.bbadis.2023.166747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/29/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
Neovascular inflammatory vitreoretinopathy (NIV) is a rare eye disease that ultimately leads to complete blindness and is caused by mutations in the gene encoding calpain-5 (CAPN5), with six pathogenic mutations identified. In transfected SH-SY5Y cells, five of the mutations resulted in decreased membrane association, diminished S-acylation, and reduced calcium-induced autoproteolysis of CAPN5. CAPN5 proteolysis of the autoimmune regulator AIRE was impacted by several NIV mutations. R243, L244, K250 and the adjacent V249 are on β-strands in the protease core 2 domain. Conformational changes induced by Ca2+binding result in these β-strands forming a β-sheet and a hydrophobic pocket which docks W286 side chain away from the catalytic cleft, enabling calpain activation based on comparison with the Ca2+-bound CAPN1 protease core. The pathologic variants R243L, L244P, K250N, and R289W are predicted to disrupt the β-strands, β-sheet, and hydrophobic pocket, impairing calpain activation. The mechanism by which these variants impair membrane association is unclear. G376S impacts a conserved residue in the CBSW domain and is predicted to disrupt a loop containing acidic residues which may contribute to membrane binding. G267S did not impair membrane association and resulted in a slight but significant increase in autoproteolytic and proteolytic activity. However, G267S is also identified in individuals without NIV. Combined with the autosomal dominant pattern of NIV inheritance and evidence that CAPN5 may dimerize, the results are consistent with a dominant negative mechanism for the five pathogenic variants which resulted in impaired CAPN5 activity and membrane association and a gain-of-function for the G267S variant.
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Affiliation(s)
- James W Geddes
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA
| | - Dorothy E Croall
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
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4
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Terai H, Hamamoto J, Emoto K, Masuda T, Manabe T, Kuronuma S, Kobayashi K, Masuzawa K, Ikemura S, Nakayama S, Kawada I, Suzuki Y, Takeuchi O, Suzuki Y, Ohtsuki S, Yasuda H, Soejima K, Fukunaga K. SHOC2 Is a Critical Modulator of Sensitivity to EGFR-TKIs in Non-Small Cell Lung Cancer Cells. Mol Cancer Res 2020; 19:317-328. [PMID: 33106373 DOI: 10.1158/1541-7786.mcr-20-0664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/16/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
EGFR mutation-positive patients with non-small cell lung cancer (NSCLC) respond well to treatment with EGFR-tyrosine kinase inhibitors (EGFR-TKI); however, treatment with EGFR-TKIs is not curative, owing to the presence of residual cancer cells with intrinsic or acquired resistance to this class of drugs. Additional treatment targets that may enhance the efficacy of EGFR-TKIs remain elusive. Using a CRISPR/Cas9-based screen, we identified the leucine-rich repeat scaffold protein SHOC2 as a key modulator of sensitivity to EGFR-TKI treatment. On the basis of in vitro assays, we demonstrated that SHOC2 expression levels strongly correlate with the sensitivity to EGFR-TKIs and that SHOC2 affects the sensitivity to EGFR-TKIs in NSCLC cells via SHOC2/MRAS/PP1c and SHOC2/SCRIB signaling. The potential SHOC2 inhibitor celastrol phenocopied SHOC2 depletion. In addition, we confirmed that SHOC2 expression levels were important for the sensitivity to EGFR-TKIs in vivo. Furthermore, IHC showed the accumulation of cancer cells that express high levels of SHOC2 in lung cancer tissues obtained from patients with NSCLC who experienced acquired resistance to EGFR-TKIs. These data indicate that SHOC2 may be a therapeutic target for patients with NSCLC or a biomarker to predict sensitivity to EGFR-TKI therapy in EGFR mutation-positive patients with NSCLC. Our findings may help improve treatment strategies for patients with NSCLC harboring EGFR mutations. IMPLICATIONS: This study showed that SHOC2 works as a modulator of sensitivity to EGFR-TKIs and the expression levels of SHOC2 can be used as a biomarker for sensitivity to EGFR-TKIs.
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Affiliation(s)
- Hideki Terai
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan. .,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan
| | - Katsura Emoto
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadashi Manabe
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keigo Kobayashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Sohei Nakayama
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yusuke Suzuki
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yukio Suzuki
- Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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5
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Debets MF, Tastan OY, Wisnovsky SP, Malaker SA, Angelis N, Moeckl LKR, Choi J, Flynn H, Wagner LJS, Bineva-Todd G, Antonopoulos A, Cioce A, Browne WM, Li Z, Briggs DC, Douglas HL, Hess GT, Agbay AJ, Roustan C, Kjaer S, Haslam SM, Snijders AP, Bassik MC, Moerner WE, Li VSW, Bertozzi CR, Schumann B. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc Natl Acad Sci U S A 2020; 117:25293-25301. [PMID: 32989128 DOI: 10.1101/2020.04.23.057208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.
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Affiliation(s)
- Marjoke F Debets
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Omur Y Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lauren J S Wagner
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Anna Cioce
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - William M Browne
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Zhen Li
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Holly L Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - Anthony J Agbay
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Stuart M Haslam
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Benjamin Schumann
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom;
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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6
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Zook J, Shekhar M, Hansen D, Conrad C, Grant T, Gupta C, White T, Barty A, Basu S, Zhao Y, Zatsepin N, Ishchenko A, Batyuk A, Gati C, Li C, Galli L, Coe J, Hunter M, Liang M, Weierstall U, Nelson G, James D, Stauch B, Craciunescu F, Thifault D, Liu W, Cherezov V, Singharoy A, Fromme P. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure 2020; 28:540-547.e3. [PMID: 32142641 DOI: 10.1016/j.str.2020.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/23/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
Francisella tularensis is the causative agent for the potentially fatal disease tularemia. The lipoprotein Flpp3 has been identified as a virulence determinant of tularemia with no sequence homology outside the Francisella genus. We report a room temperature structure of Flpp3 determined by serial femtosecond crystallography that exists in a significantly different conformation than previously described by the NMR-determined structure. Furthermore, we investigated the conformational space and energy barriers between these two structures by molecular dynamics umbrella sampling and identified three low-energy intermediate states, transitions between which readily occur at room temperature. We have also begun to investigate organic compounds in silico that may act as inhibitors to Flpp3. This work paves the road to developing targeted therapeutics against tularemia and aides in our understanding of the disease mechanisms of tularemia.
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Affiliation(s)
- James Zook
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Mrinal Shekhar
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Center for the Development of TherapeuticsThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Debra Hansen
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie Conrad
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Thomas Grant
- Hauptman Woodward Institute, Jacobs School of Medicine and Biomedical Science, SUNY, Buffalo, NY 14260, USA
| | - Chitrak Gupta
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas White
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Anton Barty
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble, Grenoble Cedex 9 38042, France
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Alex Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Cornelius Gati
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Lorenzo Galli
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Meng Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Garret Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | | | - Felicia Craciunescu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Darren Thifault
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Abhishek Singharoy
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Petra Fromme
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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7
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Schlachter CR, Klapper V, Radford T, Chruszcz M. Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase. Biol Chem 2019; 400:1567-1581. [PMID: 31141475 DOI: 10.1515/hsz-2019-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/15/2019] [Indexed: 11/15/2022]
Abstract
Aspergillus fumigatus is a ubiquitous fungus that is not only a problem in agriculture, but also in healthcare. Aspergillus fumigatus drug resistance is becoming more prominent which is mainly attributed to the widespread use of fungicides in agriculture. The fungi-specific 2-methylcitrate cycle is responsible for detoxifying propionyl-CoA, a toxic metabolite produced as the fungus breaks down proteins and amino acids. The enzyme responsible for this detoxification is 2-methylcitrate synthase (mcsA) and is a potential candidate for the design of new anti-fungals. However, mcsA is very similar in structure to human citrate synthase (hCS) and catalyzes the same reaction. Therefore, both enzymes were studied in parallel to provide foundations for design of mcsA-specific inhibitors. The first crystal structures of citrate synthase from humans and 2-methylcitrate synthase from A. fumigatus are reported. The determined structures capture various conformational states of the enzymes and several inhibitors were identified and characterized. Despite a significant homology, mcsA and hCS display pronounced differences in substrate specificity and cooperativity. Considering that the active sites of the enzymes are almost identical, the differences in reactions catalyzed by enzymes are caused by residues that are in the vicinity of the active site and influence conformational changes of the enzymes.
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Affiliation(s)
- Caleb R Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Vincent Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Taylor Radford
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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8
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Coscia F, Lengyel E, Duraiswamy J, Ashcroft B, Bassani-Sternberg M, Wierer M, Johnson A, Wroblewski K, Montag A, Yamada SD, López-Méndez B, Nilsson J, Mund A, Mann M, Curtis M. Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer. Cell 2019; 175:159-170.e16. [PMID: 30241606 DOI: 10.1016/j.cell.2018.08.065] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/23/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Most high-grade serous ovarian cancer (HGSOC) patients develop resistance to platinum-based chemotherapy and recur, but 15% remain disease free over a decade. To discover drivers of long-term survival, we quantitatively analyzed the proteomes of platinum-resistant and -sensitive HGSOC patients from minute amounts of formalin-fixed, paraffin-embedded tumors. This revealed cancer/testis antigen 45 (CT45) as an independent prognostic factor associated with a doubling of disease-free survival in advanced-stage HGSOC. Phospho- and interaction proteomics tied CT45 to DNA damage pathways through direct interaction with the PP4 phosphatase complex. In vitro, CT45 regulated PP4 activity, and its high expression led to increased DNA damage and platinum sensitivity. CT45-derived HLA class I peptides, identified by immunopeptidomics, activate patient-derived cytotoxic T cells and promote tumor cell killing. This study highlights the power of clinical cancer proteomics to identify targets for chemo- and immunotherapy and illuminate their biological roles.
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Affiliation(s)
- Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
| | | | - Bradley Ashcroft
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Michal Bassani-Sternberg
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alyssa Johnson
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Kristen Wroblewski
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Anthony Montag
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Blanca López-Méndez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Mund
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Marion Curtis
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
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9
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Noguchi K, Dincman TA, Dalton AC, Howley BV, McCall BJ, Mohanty BK, Howe PH. Interleukin-like EMT inducer (ILEI) promotes melanoma invasiveness and is transcriptionally up-regulated by upstream stimulatory factor-1 (USF-1). J Biol Chem 2018; 293:11401-11414. [PMID: 29871931 PMCID: PMC6065179 DOI: 10.1074/jbc.ra118.003616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/22/2018] [Indexed: 12/25/2022] Open
Abstract
Interleukin-like EMT inducer (ILEI, FAM3C) is a secreted factor that contributes to the epithelial-to-mesenchymal transition (EMT), a cell-biological process that confers metastatic properties to a tumor cell. However, very little is known about how ILEI is regulated. Here we demonstrate that ILEI is an in vivo regulator of melanoma invasiveness and is transcriptionally up-regulated by the upstream stimulatory factor-1 (USF-1), an E-box-binding, basic-helix-loop-helix family transcription factor. shRNA-mediated knockdown of ILEI in melanoma cell lines attenuated lung colonization but not primary tumor formation. We also identified the mechanism underlying ILEI transcriptional regulation, which was through a direct interaction of USF-1 with the ILEI promoter. Of note, stimulation of endogenous USF-1 by UV-mediated activation increased ILEI expression, whereas shRNA-mediated USF-1 knockdown decreased ILEI gene transcription. Finally, we report that knocking down USF-1 decreases tumor cell migration. In summary, our work reveals that ILEI contributes to melanoma cell invasiveness in vivo without affecting primary tumor growth and is transcriptionally up-regulated by USF-1.
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Affiliation(s)
- Ken Noguchi
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Toros A Dincman
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425; Division of Hematology and Oncology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Annamarie C Dalton
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Breege V Howley
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Buckley J McCall
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Bidyut K Mohanty
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425; Hollings Cancer Center, Charleston, South Carolina 29425.
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Palanirajan SK, Sivagnanam U, Murugan S, Gummadi SN. In vitro reconstitution and biochemical characterization of human phospholipid scramblase 3: phospholipid specificity and metal ion binding studies. Biol Chem 2018; 399:361-374. [DOI: 10.1515/hsz-2017-0309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 01/11/2023]
Abstract
AbstractHuman phospholipid scramblase 3 (hPLSCR3) is a single pass transmembrane protein that plays a vital role in fat metabolism, mitochondrial function, structure, maintenance and apoptosis. The mechanism of action of scramblases remains still unknown, and the role of scramblases in phospholipid translocation is heavily debated. hPLSCR3 is the only member of scramblase family localized to mitochondria and is involved in cardiolipin translocation at the mitochondrial membrane. Direct biochemical evidence of phospholipid translocation by hPLSCR3 is yet to be reported. Functional assay in synthetic proteoliposomes upon Ca2+and Mg2+revealed that, apart from cardiolipin, recombinant hPLSCR3 translocates aminophospholipids such as NBD-PE and NBD-PS but not neutral phospholipids. Point mutation in hPLSCR3 (F258V) resulted in decreased Ca2+binding affinity. Functional assay with F258V-hPLSCR3 led to ~50% loss in scramblase activity in the presence of Ca2+and Mg2+. Metal ion-induced conformational changes were monitored by intrinsic tryptophan fluorescence, circular dichroism, surface hydrophobicity changes and aggregation studies. Our results revealed that Ca2+and Mg2+bind to hPLSCR3 and trigger conformational changes mediated by aggregation. In summary, we suggest that the metal ion-induced conformational change and the aggregation of the protein are essential for the phospholipid translocation by hPLSCR3.
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11
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Radka CD, Chen D, DeLucas LJ, Aller SG. The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal. Acta Crystallogr D Struct Biol 2017; 73:921-939. [PMID: 29095164 PMCID: PMC5683015 DOI: 10.1107/s2059798317015236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/18/2017] [Indexed: 12/25/2022] Open
Abstract
Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron-siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 Å resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 Å shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs.
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Affiliation(s)
- Christopher D. Radka
- Graduate Biomedical Sciences Microbiology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dongquan Chen
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lawrence J. DeLucas
- Office of the Provost, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Allegrini A, Astegno A, La Verde V, Dominici P. Characterization of C-S lyase from Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 and its potential role in food flavour applications. J Biochem 2017; 161:349-360. [PMID: 28003427 DOI: 10.1093/jb/mvw079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/17/2016] [Indexed: 01/07/2023] Open
Abstract
Volatile thiols have substantial impact on the aroma of many beverages and foods. Thus, the control of their formation, which has been linked to C-S lyase enzymatic activities, is of great significance in industrial applications involving food flavours. Herein, we have carried out a spectroscopic and functional characterization of a putative pyridoxal 5'-phosphate (PLP)-dependent C-S lyase from the lactic acid bacterium Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (LDB C-S lyase). Recombinant LDB C-S lyase exists as a tetramer in solution and shows spectral properties of enzymes containing PLP as cofactor. The enzyme has a broad substrate specificity toward sulphur-containing amino acids with aminoethyl-L-cysteine and L-cystine being the most effective substrates over L-cysteine and L-cystathionine. Notably, the protein also reveals cysteine-S-conjugate β-lyase activity in vitro, and is able to cleave a cysteinylated substrate precursor into the corresponding flavour-contributing thiol, with a catalytic efficiency higher than L-cystathionine. Contrary to similar enzymes of other lactic acid bacteria however, LDB C-S lyase is not capable of α,γ-elimination activity towards L-methionine to produce methanethiol, which is a significant compound in flavour development. Based on our results, future developments can be expected regarding the flavour-forming potential of Lactobacillus C-S lyase and its use in enhancing food flavours.
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Seiler CY, Eschbacher J, Bowser R, LaBaer J. Sustainability in a Hospital-Based Biobank and University-Based DNA Biorepository: Strategic Roadmaps. Biopreserv Biobank 2016; 13:401-9. [PMID: 26697909 DOI: 10.1089/bio.2015.0076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sustainability in the biobanking community has recently become an important and oft-discussed issue as biorepositories struggle to balance limited external funding and complex cost recovery models with high operating costs and the desire to provide the highest quality materials and services to the research community. A multi-faceted view of biobanking sustainability requires consideration of operational and social sustainability in addition to the historical focus exclusively on financial sustainability. Planning and implementing this three pillar model creates a well-rounded biorepository that meets the needs of all the major stakeholders: the funders, the patients/depositors, and the researcher recipients. Often the creation of a detailed business plan is the first step to develop goals and objectives that lead down a path towards sustainability. The definition of sustainability and the complexity of a sustainable business plan may differ for each biorepository. The DNASU Plasmid Repository at Arizona State University stores and distributes DNA plasmids to researchers worldwide, and the Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute consents patients and collects, stores, and distributes human tissue and blood samples. We will discuss these two biorepositories, their similar and different approaches to sustainability and business planning, their challenges in creating and implementing their sustainability plan, and their responses to some of these challenges. From these experiences, the biobanks share lessons learned about planning for sustainability that are applicable to all biorepositories.
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Affiliation(s)
- Catherine Y Seiler
- 1 The Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute , Phoenix, Arizona
| | - Jennifer Eschbacher
- 1 The Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute , Phoenix, Arizona
| | - Robert Bowser
- 2 Divisions of Neurology and Neurobiology, Barrow Neurological Institute , Phoenix, Arizona
| | - Joshua LaBaer
- 3 DNASU Plasmid Repository, Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona
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14
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Drafting biological material transfer agreement: a ready-to-sign model for biobanks and biorepositories. Int J Biol Markers 2016; 31:e211-7. [PMID: 26868333 DOI: 10.5301/jbm.5000190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 01/20/2023]
Abstract
PURPOSE Due to the scarcity of publications, guidelines, and harmonization among national regulations, biobanks and institutions face practical and theoretical issues when drafting a material transfer agreement (MTA), the fundamental tool to regulate the successful exchange of biosamples and information. Frequently researchers do not execute MTAs because of a general lack of knowledge about this topic. It is thus critical to develop new models to prevent loss of traceability and opportunities both for researchers and biobanks, their exposure to various risks, and delays in transferring biomaterials. METHODS Through the involvement of institutional groups and professionals with multidisciplinary expertise, we have drawn up a ready-to-sign MTA for the CRO-Biobank (the biobank of the National Cancer Institute, CRO, Aviano), a standardized template that can be employed as a ready-to-use model agreement. RESULTS The team identified the essential components to be included in the MTA, which comprise i) permissions, liability and representations; ii) custodianship and distribution limitations; iii) appropriate use of materials, including biosafety concerns; iv) confidentiality, non-disclosure, and publications; v) intellectual property protection for both the provider and recipient. CONCLUSIONS This paper aims to be an unabridged report (among the few works in the existing literature) providing a description of the whole process related to the formation of an MTA. Biobanks and institutions may consider adopting our ready-to-sign form as a standard model. The article discusses the most important issues tackled during the drafting of the document, thus proposing an operative approach for other institutions that face the same problems.
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15
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Bian X, Wiktor P, Kahn P, Brunner A, Khela A, Karthikeyan K, Barker K, Yu X, Magee M, Wasserfall CH, Gibson D, Rooney ME, Qiu J, LaBaer J. Antiviral antibody profiling by high-density protein arrays. Proteomics 2015; 15:2136-45. [PMID: 25758251 PMCID: PMC4545592 DOI: 10.1002/pmic.201400612] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/12/2015] [Accepted: 03/07/2015] [Indexed: 12/14/2022]
Abstract
Viral infections elicit antiviral antibodies and have been associated with various chronic diseases. Detection of these antibodies can facilitate diagnosis, treatment of infection, and understanding of the mechanisms of virus-associated diseases. In this work, we assayed antiviral antibodies using a novel high-density nucleic acid programmable protein array (HD-NAPPA) platform. Individual viral proteins were expressed in situ directly from plasmids encoding proteins in an array of microscopic reaction chambers. Quality of protein display and serum response was assured by comparing intra- and inter-array correlation within or between printing batches with average correlation coefficients of 0.91 and 0.96, respectively. HD-NAPPA showed higher signal-to-background ratio compared with standard NAPPA on planar glass slides and ELISA. Antibody responses to 761 antigens from 25 different viruses were profiled among patients with juvenile idiopathic arthritis and type 1 diabetes. Common and unique antibody reactivity patterns were detected between patients and healthy controls. We believe HD-viral-NAPPA will enable the study of host-pathogen interactions at unprecedented dimensions and elucidate the role of pathogen infections in disease development.
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Affiliation(s)
- Xiaofang Bian
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Wiktor
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Kahn
- Engineering Arts LLC, Tempe, AZ, 85281, USA
| | - Al Brunner
- Engineering Arts LLC, Tempe, AZ, 85281, USA
| | - Amritpal Khela
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Kailash Karthikeyan
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Kristi Barker
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaobo Yu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Mitch Magee
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Clive H. Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - David Gibson
- Northern Ireland Centre for Stratified Medicine, Ulster University, C-TRIC, Glenshane Road, Londonderry, BT47 6SB, UK
| | - Madeleine E Rooney
- Arthritis Research Group, Centre for Infection and Immunity, Health Science Building, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Ji Qiu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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16
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Han H, Monroe N, Votteler J, Shakya B, Sundquist WI, Hill CP. Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs). J Biol Chem 2015; 290:13490-9. [PMID: 25833946 DOI: 10.1074/jbc.m115.642355] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 12/21/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) pathway drives reverse topology membrane fission events within multiple cellular pathways, including cytokinesis, multivesicular body biogenesis, repair of the plasma membrane, nuclear membrane vesicle formation, and HIV budding. The AAA ATPase Vps4 is recruited to membrane necks shortly before fission, where it catalyzes disassembly of the ESCRT-III lattice. The N-terminal Vps4 microtubule-interacting and trafficking (MIT) domains initially bind the C-terminal MIT-interacting motifs (MIMs) of ESCRT-III subunits, but it is unclear how the enzyme then remodels these substrates in response to ATP hydrolysis. Here, we report quantitative binding studies that demonstrate that residues from helix 5 of the Vps2p subunit of ESCRT-III bind to the central pore of an asymmetric Vps4p hexamer in a manner that is dependent upon the presence of flexible nucleotide analogs that can mimic multiple states in the ATP hydrolysis cycle. We also find that substrate engagement is autoinhibited by the Vps4p MIT domain and that this inhibition is relieved by binding of either Type 1 or Type 2 MIM elements, which bind the Vps4p MIT domain through different interfaces. These observations support the model that Vps4 substrates are initially recruited by an MIM-MIT interaction that activates the Vps4 central pore to engage substrates and generate force, thereby triggering ESCRT-III disassembly.
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Affiliation(s)
- Han Han
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Nicole Monroe
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Jörg Votteler
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Binita Shakya
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Wesley I Sundquist
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Christopher P Hill
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
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McKay T, Hart K, Horn A, Kessler H, Dodge G, Bardhi K, Bardhi K, Mills JL, Bernstein HJ, Craig PA. Annotation of proteins of unknown function: initial enzyme results. ACTA ACUST UNITED AC 2015; 16:43-54. [PMID: 25630330 DOI: 10.1007/s10969-015-9194-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/16/2015] [Indexed: 01/21/2023]
Abstract
Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having "unknown function". Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.
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18
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Maize KM, Kurbanov EK, De La Mora-Rey T, Geders TW, Hwang DJ, Walters MA, Johnson RL, Amin EA, Finzel BC. Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2813-22. [PMID: 25372673 PMCID: PMC4220970 DOI: 10.1107/s1399004714018161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/07/2014] [Indexed: 12/30/2022]
Abstract
The secreted anthrax toxin consists of three components: the protective antigen (PA), edema factor (EF) and lethal factor (LF). LF, a zinc metalloproteinase, compromises the host immune system primarily by targeting mitogen-activated protein kinase kinases in macrophages. Peptide substrates and small-molecule inhibitors bind LF in the space between domains 3 and 4 of the hydrolase. Domain 3 is attached on a hinge to domain 2 via residues Ile300 and Pro385, and can move through an angular arc of greater than 35° in response to the binding of different ligands. Here, multiple LF structures including five new complexes with co-crystallized inhibitors are compared and three frequently populated LF conformational states termed `bioactive', `open' and `tight' are identified. The bioactive position is observed with large substrate peptides and leaves all peptide-recognition subsites open and accessible. The tight state is seen in unliganded and small-molecule complex structures. In this state, domain 3 is clamped over certain substrate subsites, blocking access. The open position appears to be an intermediate state between these extremes and is observed owing to steric constraints imposed by specific bound ligands. The tight conformation may be the lowest-energy conformation among the reported structures, as it is the position observed with no bound ligand, while the open and bioactive conformations are likely to be ligand-induced.
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Affiliation(s)
- Kimberly M. Maize
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Elbek K. Kurbanov
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Teresa De La Mora-Rey
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Todd W. Geders
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Dong-Jin Hwang
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Michael A. Walters
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Rodney L. Johnson
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, USA
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Heirbaut M, Beelen S, Strelkov SV, Weeks SD. Dissecting the functional role of the N-terminal domain of the human small heat shock protein HSPB6. PLoS One 2014; 9:e105892. [PMID: 25157403 PMCID: PMC4144951 DOI: 10.1371/journal.pone.0105892] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/25/2014] [Indexed: 01/24/2023] Open
Abstract
HSPB6 is a member of the human small heat shock protein (sHSP) family, a conserved group of molecular chaperones that bind partially unfolded proteins and prevent them from aggregating. In vertebrate sHSPs the poorly structured N-terminal domain has been implicated in both chaperone activity and the formation of higher-order oligomers. These two functionally important properties are likely intertwined at the sequence level, complicating attempts to delineate the regions that define them. Differing from the prototypical α-crystallins human HSPB6 has been shown to only form dimers in solution making it more amendable to explore the determinants of chaperoning activity alone. Using a systematic and iterative deletion strategy, we have extensively investigated the role of the N-terminal domain on the chaperone activity of this sHSP. As determined by size-exclusion chromatography and small-angle X-ray scattering, most mutants had a dimeric structure closely resembling that of wild-type HSPB6. The chaperone-like activity was tested using three different substrates, whereby no single truncation, except for complete removal of the N-terminal domain, showed full loss of activity, pointing to the presence of multiple sites for binding unfolding proteins. Intriguingly, we found that the stretch encompassing residues 31 to 35, which is nearly fully conserved across vertebrate sHSPs, acts as a negative regulator of activity, as its deletion greatly enhanced chaperoning capability. Further single point mutational analysis revealed an interplay between the highly conserved residues Q31 and F33 in fine-tuning its function.
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Affiliation(s)
- Michelle Heirbaut
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
| | - Steven Beelen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
- * E-mail: (SVS); (SDW)
| | - Stephen D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
- * E-mail: (SVS); (SDW)
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20
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Cox N, Pilling D, Gomer RH. Distinct Fcγ receptors mediate the effect of serum amyloid p on neutrophil adhesion and fibrocyte differentiation. THE JOURNAL OF IMMUNOLOGY 2014; 193:1701-8. [PMID: 25024390 DOI: 10.4049/jimmunol.1400281] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The plasma protein serum amyloid P (SAP) reduces neutrophil adhesion, inhibits the differentiation of monocytes into fibroblast-like cells called fibrocytes, and promotes phagocytosis of cell debris by macrophages. Together, these effects of SAP reduce key aspects of inflammation and fibrosis, and SAP injections improve lung function in pulmonary fibrosis patients. SAP functions are mediated, in part, by FcγRs, but the contribution of each FcγR is not fully understood. We found that aa Q55 and E126 in human SAP affect human fibrocyte differentiation and SAP binding to FcγRI. E126, K130, and Q128 affect neutrophil adhesion and SAP affinity for FcγRIIa. Q128 also affects phagocytosis by macrophages and SAP affinity for FcγRI. All the identified functionally significant amino acids in SAP form a binding site that is distinct from the previously described SAP-FcγRIIa binding site. Blocking FcγRI with an IgG-blocking Ab reduces the SAP effect on fibrocyte differentiation, and ligating FcγRIIa with Abs reduces neutrophil adhesion. Together, these results suggest that SAP binds to FcγRI on monocytes to inhibit fibrocyte differentiation, and binds to FcγRIIa on neutrophils to reduce neutrophil adhesion.
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Affiliation(s)
- Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Darrell Pilling
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843
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Bruno AE, Ruby AM, Luft JR, Grant TD, Seetharaman J, Montelione GT, Hunt JF, Snell EH. Comparing chemistry to outcome: the development of a chemical distance metric, coupled with clustering and hierarchal visualization applied to macromolecular crystallography. PLoS One 2014; 9:e100782. [PMID: 24971458 PMCID: PMC4074061 DOI: 10.1371/journal.pone.0100782] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/28/2014] [Indexed: 11/18/2022] Open
Abstract
Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields.
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Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, State University of New York (SUNY), Buffalo, New York, United States of America
| | - Amanda M. Ruby
- Center for Computational Research, State University of New York (SUNY), Buffalo, New York, United States of America
| | - Joseph R. Luft
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo Dept. of Structural Biology, Buffalo, New York, United States of America
| | - Thomas D. Grant
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Jayaraman Seetharaman
- Department of Biological Sciences, The Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - John F. Hunt
- Department of Biological Sciences, The Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo Dept. of Structural Biology, Buffalo, New York, United States of America
- * E-mail:
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PHLDA1 expression is controlled by an estrogen receptor-NFκB-miR-181 regulatory loop and is essential for formation of ER+ mammospheres. Oncogene 2014; 34:2309-16. [PMID: 24954507 PMCID: PMC4275416 DOI: 10.1038/onc.2014.180] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/17/2014] [Accepted: 05/16/2014] [Indexed: 12/14/2022]
Abstract
Crosstalk between estrogen receptor (ER) and the inflammatory nuclear factor κB (NFκB) pathway in ER+ breast cancers may contribute to a more aggressive phenotype. Pleckstrin Homology-Like Domain, Family A, member 1 (PHLDA1), a target gene of ER-NFκB crosstalk, has been implicated in cell survival and stem cell properties. 17β-estradiol (E2), acting through ERα, and pro-inflammatory cytokines, acting through NFκB, increase the nascent transcript and PHLDA1 messenger RNA stability, indicating both transcriptional and post-transcriptional control of PHLDA1 expression. We show that PHLDA1 is a direct target of miR-181 and that mature miR-181a and b, as well as their host gene, are synergistically downregulated by E2 and tumor necrosis factor α, also in an ER- and NFκB-dependent manner. Thus, ER and NFκB work together to upregulate PHLDA1 directly through enhanced transcription and indirectly through repression of miR-181a and b. Previous studies have suggested that PHLDA1 may be a stem cell marker in the human intestine that contributes to tumorigenesis. Our findings that PHLDA1 is upregulated in mammospheres (MS) of ER+ breast cancer cells and that PHLDA1 knockdown impairs both MS formation and the expansion of aldehyde dehydrogenase (ALDH)-positive population, suggest that PHLDA1 may play a similar role in breast cancer cells. Upregulation of PHLDA1 in MS is largely dependent on the NFκB pathway, with downregulated miR-181 expression a contributing factor. Over-expression of miR-181 phenocopied PHLDA1 knockdown and significantly impaired MS formation, which was reversed, in part, by protection of the PHLDA1 3' untranslated region (UTR) or overexpression of PHLDA1 lacking the 3'UTR. Furthermore, we find that elevated PHLDA1 expression is associated with a higher risk of distant metastasis in ER+ breast cancer patients. Altogether, these data suggest that high PHLDA1 expression is controlled through an ER-NFκB-miR-181 regulatory axis and may contribute to a poor clinical outcome in patients with ER+ breast tumors by enhancing stem-like properties in these tumors.
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Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Am J Cancer Res 2014; 4:808-22. [PMID: 24955142 PMCID: PMC4063979 DOI: 10.7150/thno.8255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/27/2014] [Indexed: 12/24/2022] Open
Abstract
Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.
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Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative. Proc Natl Acad Sci U S A 2014; 111:3733-8. [PMID: 24567391 DOI: 10.1073/pnas.1321614111] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins--including proteins for which reliable homology models can be generated--on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.
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25
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The oligomeric state of the active Vps4 AAA ATPase. J Mol Biol 2014; 426:510-25. [PMID: 24161953 PMCID: PMC3919030 DOI: 10.1016/j.jmb.2013.09.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 01/07/2023]
Abstract
The cellular ESCRT (endosomal sorting complexes required for transport) pathway drives membrane constriction toward the cytosol and effects membrane fission during cytokinesis, endosomal sorting, and the release of many enveloped viruses, including the human immunodeficiency virus. A component of this pathway, the AAA ATPase Vps4, provides energy for pathway progression. Although it is established that Vps4 functions as an oligomer, subunit stoichiometry and other fundamental features of the functional enzyme are unclear. Here, we report that although some mutant Vps4 proteins form dodecameric assemblies, active wild-type Saccharomyces cerevisiae and Sulfolobus solfataricus Vps4 enzymes can form hexamers in the presence of ATP and ADP, as assayed by size-exclusion chromatography and equilibrium analytical ultracentrifugation. The Vta1p activator binds hexameric yeast Vps4p without changing the oligomeric state of Vps4p, implying that the active Vta1p-Vps4p complex also contains a single hexameric ring. Additionally, we report crystal structures of two different archaeal Vps4 homologs, whose structures and lattice interactions suggest a conserved mode of oligomerization. Disruption of the proposed hexamerization interface by mutagenesis abolished the ATPase activity of archaeal Vps4 proteins and blocked Vps4p function in S. cerevisiae. These data challenge the prevailing model that active Vps4 is a double-ring dodecamer, and argue that, like other type I AAA ATPases, Vps4 functions as a single ring with six subunits.
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26
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Young E, Zheng ZY, Wilkins AD, Jeong HT, Li M, Lichtarge O, Chang EC. Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases. Mol Cell Biol 2014; 34:374-85. [PMID: 24248599 PMCID: PMC3911504 DOI: 10.1128/mcb.01248-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/16/2013] [Accepted: 11/09/2013] [Indexed: 01/06/2023] Open
Abstract
Ras can act on the plasma membrane (PM) to mediate extracellular signaling and tumorigenesis. To identify key components controlling Ras PM localization, we performed an unbiased screen to seek Schizosaccharomyces pombe mutants with reduced PM Ras. Five mutants were found with mutations affecting the same gene, S. pombe erf2 (sp-erf2), encoding sp-Erf2, a palmitoyltransferase, with various activities. sp-Erf2 localizes to the trans-Golgi compartment, a process which is mediated by its third transmembrane domain and the Erf4 cofactor. In fission yeast, the human ortholog zDHHC9 rescues the phenotypes of sp-erf2 null cells. In contrast, expressing zDHHC14, another sp-Erf2-like human protein, did not rescue Ras1 mislocalization in these cells. Importantly, ZDHHC9 is widely overexpressed in cancers. Overexpressing ZDHHC9 promotes, while repressing it diminishes, Ras PM localization and transformation of mammalian cells. These data strongly demonstrate that sp-Erf2/zDHHC9 palmitoylates Ras proteins in a highly selective manner in the trans-Golgi compartment to facilitate PM targeting via the trans-Golgi network, a role that is most certainly critical for Ras-driven tumorigenesis.
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Affiliation(s)
- Evelin Young
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ze-Yi Zheng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Angela D. Wilkins
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- CIBR Center for Computational and Integrative Biomedical Research, Baylor College of Medicine, Houston, Texas, USA
| | - Hee-Tae Jeong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Min Li
- Department of Oncology, Nanjing Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu, China
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- CIBR Center for Computational and Integrative Biomedical Research, Baylor College of Medicine, Houston, Texas, USA
| | - Eric C. Chang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
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27
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Zimmerman MD, Grabowski M, Domagalski MJ, Maclean EM, Chruszcz M, Minor W. Data management in the modern structural biology and biomedical research environment. Methods Mol Biol 2014; 1140:1-25. [PMID: 24590705 PMCID: PMC4086192 DOI: 10.1007/978-1-4939-0354-2_1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Modern high-throughput structural biology laboratories produce vast amounts of raw experimental data. The traditional method of data reduction is very simple-results are summarized in peer-reviewed publications, which are hopefully published in high-impact journals. By their nature, publications include only the most important results derived from experiments that may have been performed over the course of many years. The main content of the published paper is a concise compilation of these data, an interpretation of the experimental results, and a comparison of these results with those obtained by other scientists.Due to an avalanche of structural biology manuscripts submitted to scientific journals, in many recent cases descriptions of experimental methodology (and sometimes even experimental results) are pushed to supplementary materials that are only published online and sometimes may not be reviewed as thoroughly as the main body of a manuscript. Trouble may arise when experimental results are contradicting the results obtained by other scientists, which requires (in the best case) the reexamination of the original raw data or independent repetition of the experiment according to the published description of the experiment. There are reports that a significant fraction of experiments obtained in academic laboratories cannot be repeated in an industrial environment (Begley CG & Ellis LM, Nature 483(7391):531-3, 2012). This is not an indication of scientific fraud but rather reflects the inadequate description of experiments performed on different equipment and on biological samples that were produced with disparate methods. For that reason the goal of a modern data management system is not only the simple replacement of the laboratory notebook by an electronic one but also the creation of a sophisticated, internally consistent, scalable data management system that will combine data obtained by a variety of experiments performed by various individuals on diverse equipment. All data should be stored in a core database that can be used by custom applications to prepare internal reports, statistics, and perform other functions that are specific to the research that is pursued in a particular laboratory.This chapter presents a general overview of the methods of data management and analysis used by structural genomics (SG) programs. In addition to a review of the existing literature on the subject, also presented is experience in the development of two SG data management systems, UniTrack and LabDB. The description is targeted to a general audience, as some technical details have been (or will be) published elsewhere. The focus is on "data management," meaning the process of gathering, organizing, and storing data, but also briefly discussed is "data mining," the process of analysis ideally leading to an understanding of the data. In other words, data mining is the conversion of data into information. Clearly, effective data management is a precondition for any useful data mining. If done properly, gathering details on millions of experiments on thousands of proteins and making them publicly available for analysis-even after the projects themselves have ended-may turn out to be one of the most important benefits of SG programs.
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Affiliation(s)
- Matthew D Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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28
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Makowska-Grzyska M, Kim Y, Maltseva N, Li H, Zhou M, Joachimiak G, Babnigg G, Joachimiak A. Protein production for structural genomics using E. coli expression. Methods Mol Biol 2014; 1140:89-105. [PMID: 24590711 PMCID: PMC4108990 DOI: 10.1007/978-1-4939-0354-2_7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The goal of structural biology is to reveal details of the molecular structure of proteins in order to understand their function and mechanism. X-ray crystallography and NMR are the two best methods for atomic level structure determination. However, these methods require milligram quantities of proteins. In this chapter a reproducible methodology for large-scale protein production applicable to a diverse set of proteins is described. The approach is based on protein expression in E. coli as a fusion with a cleavable affinity tag that was tested on over 20,000 proteins. Specifically, a protocol for fermentation of large quantities of native proteins in disposable culture vessels is presented. A modified protocol that allows for the production of selenium-labeled proteins in defined media is also offered. Finally, a method for the purification of His6-tagged proteins on immobilized metal affinity chromatography columns that generates high-purity material is described in detail.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL, 60557, USA
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29
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Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2013; 42:D336-46. [PMID: 24271400 PMCID: PMC3965011 DOI: 10.1093/nar/gkt1144] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.
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Affiliation(s)
- Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Université Paris Diderot-Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Seiler CY, Park JG, Sharma A, Hunter P, Surapaneni P, Sedillo C, Field J, Algar R, Price A, Steel J, Throop A, Fiacco M, LaBaer J. DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res 2013; 42:D1253-60. [PMID: 24225319 PMCID: PMC3964992 DOI: 10.1093/nar/gkt1060] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external resources that provide additional protein annotations and experimental protocols. Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (Cormier, C.Y., Mohr, S.E., Zuo, D., Hu, Y., Rolfs, A., Kramer, J., Taycher, E., Kelley, F., Fiacco, M., Turnbull, G. et al. (2010) Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res., 38, D743-D749.). In this update we will describe the plasmid collection and highlight the new features in the website redesign, including new browse/search options, plasmid annotations and a dynamic vector mapping feature that was developed in collaboration with LabGenius. Overall, these plasmid resources continue to enable research with the goal of elucidating the role of proteins in both normal biological processes and disease.
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Affiliation(s)
- Catherine Y Seiler
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr. Tempe, AZ 85287-6401, USA and LabGenius, 20-22 Bedford Row, London, WC1R 4JS, UK
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DePietro PJ, Julfayev ES, McLaughlin WA. Quantification of the impact of PSI:Biology according to the annotations of the determined structures. BMC STRUCTURAL BIOLOGY 2013; 13:24. [PMID: 24139526 PMCID: PMC4016320 DOI: 10.1186/1472-6807-13-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/14/2013] [Indexed: 11/23/2022]
Abstract
Background Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. Results One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. Conclusions We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i.e. the numbers of structures and impact of publication records, to monitor the progress of PSI:Biology towards its goals of examining structure to function connections of high biomedical relevance. The metric provides an objective means to quantify the overall impact of PSI:Biology as it uses biomedical annotations from external sources.
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Affiliation(s)
| | | | - William A McLaughlin
- Department of Basic Science, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, USA.
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Goodwin OY, Thomasson MS, Lin AJ, Sweeney MM, Macnaughtan MA. E. coli sabotages the in vivo production of O-linked β-N-acetylglucosamine-modified proteins. J Biotechnol 2013; 168:315-23. [PMID: 24140293 DOI: 10.1016/j.jbiotec.2013.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/20/2013] [Accepted: 10/06/2013] [Indexed: 01/17/2023]
Abstract
The O-linked β-N-acetylglucosamine (O-GlcNAc) post-translational modification is an important, regulatory modification of cytosolic and nuclear enzymes. To date, no 3-dimensional structures of O-GlcNAc-modified proteins exist due to difficulties in producing sufficient quantities with either in vitro or in vivo techniques. Recombinant co-expression of substrate protein and O-GlcNAc transferase in Escherichia coli was used to produce O-GlcNAc-modified domains of human cAMP responsive element-binding protein (CREB1) and Abelson tyrosine-kinase 2 (ABL2). Recombinant expression in E. coli is an advantageous approach, but only small quantities of insoluble O-GlcNAc-modified protein were produced. Adding β-N-acetylglucosaminidase inhibitor, O-(2-acetamido-2-dexoy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), to the culture media provided the first evidence that an E. coli enzyme cleaves O-GlcNAc from proteins in vivo. With the inhibitor present, the yields of O-GlcNAc-modified protein increased. The E. coli β-N-acetylglucosaminidase was isolated and shown to cleave O-GlcNAc from a synthetic O-GlcNAc-peptide in vitro. The identity of the interfering β-N-acetylglucosaminidase was confirmed by testing a nagZ knockout strain. In E. coli, NagZ natively cleaves the GlcNAc-β1,4-N-acetylmuramic acid linkage to recycle peptidoglycan in the cytoplasm and cleaves the GlcNAc-β-O-linkage of foreign O-GlcNAc-modified proteins in vivo, sabotaging the recombinant co-expression system.
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Affiliation(s)
- Octavia Y Goodwin
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, United States
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Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. J Bacteriol 2013; 195:5555-66. [PMID: 24123814 DOI: 10.1128/jb.00900-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase A (LdcA) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of Novosphingobium aromaticivorans DSM 12444 LdcA (NaLdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The NaLdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling.
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Characterization of C-S Lyase from C. diphtheriae: a possible target for new antimicrobial drugs. BIOMED RESEARCH INTERNATIONAL 2013; 2013:701536. [PMID: 24106714 PMCID: PMC3784150 DOI: 10.1155/2013/701536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/16/2013] [Indexed: 12/28/2022]
Abstract
The emergence of antibiotic resistance in microbial pathogens requires the identification of new antibacterial drugs. The biosynthesis of methionine is an attractive target because of its central importance in cellular metabolism. Moreover, most of the steps in methionine biosynthesis pathway are absent in mammals, lowering the probability of unwanted side effects. Herein, detailed biochemical characterization of one enzyme required for methionine biosynthesis, a pyridoxal-5′-phosphate (PLP-) dependent C-S lyase from Corynebacterium diphtheriae, a pathogenic bacterium that causes diphtheria, has been performed. We overexpressed the protein in E. coli and analyzed substrate specificity, pH dependence of steady state kinetic parameters, and ligand-induced spectral transitions of the protein. Structural comparison of the enzyme with cystalysin from Treponema denticola indicates a similarity in overall folding. We used site-directed mutagenesis to highlight the importance of active site residues Tyr55, Tyr114, and Arg351, analyzing the effects of amino acid replacement on catalytic properties of enzyme. Better understanding of the active site of C. diphtheriae C-S lyase and the determinants of substrate and reaction specificity from this work will facilitate the design of novel inhibitors as antibacterial therapeutics.
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Das D, Lee WS, Grant JC, Chiu HJ, Farr CL, Vance J, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Kornfeld S, Wilson IA. Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. J Biol Chem 2013; 288:16789-16799. [PMID: 23572527 DOI: 10.1074/jbc.m112.434977] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DUF2233, a domain of unknown function (DUF), is present in many bacterial and several viral proteins and was also identified in the mammalian transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase ("uncovering enzyme" (UCE)). We report the crystal structure of BACOVA_00430, a 315-residue protein from the human gut bacterium Bacteroides ovatus that is the first structural representative of the DUF2233 protein family. A notable feature of this structure is the presence of a surface cavity that is populated by residues that are highly conserved across the entire family. The crystal structure was used to model the luminal portion of human UCE (hUCE), which is involved in targeting of lysosomal enzymes. Mutational analysis of several residues in a highly conserved surface cavity of hUCE revealed that they are essential for function. The bacterial enzyme (BACOVA_00430) has ∼1% of the catalytic activity of hUCE toward the substrate GlcNAc-P-mannose, the precursor of the Man-6-P lysosomal targeting signal. GlcNAc-1-P is a poor substrate for both enzymes. We conclude that, for at least a subset of proteins in this family, DUF2233 functions as a phosphodiester glycosidase.
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Affiliation(s)
- Debanu Das
- Joint Center for Structural Genomics, Menlo Park, California 94025; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Wang-Sik Lee
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Joanna C Grant
- Joint Center for Structural Genomics, Menlo Park, California 94025; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, Menlo Park, California 94025; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Carol L Farr
- Joint Center for Structural Genomics, Menlo Park, California 94025; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Julie Vance
- Joint Center for Structural Genomics, Menlo Park, California 94025; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121
| | - Heath E Klock
- Joint Center for Structural Genomics, Menlo Park, California 94025; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121
| | - Mark W Knuth
- Joint Center for Structural Genomics, Menlo Park, California 94025; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121
| | - Mitchell D Miller
- Joint Center for Structural Genomics, Menlo Park, California 94025; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, Menlo Park, California 94025; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Ashley M Deacon
- Joint Center for Structural Genomics, Menlo Park, California 94025; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Adam Godzik
- Joint Center for Structural Genomics, Menlo Park, California 94025; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037; Center for Research in Biological Systems, University of California San Diego, La Jolla, California 92093
| | - Scott A Lesley
- Joint Center for Structural Genomics, Menlo Park, California 94025; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110.
| | - Ian A Wilson
- Joint Center for Structural Genomics, Menlo Park, California 94025; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
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Emrick D, Ravichandran A, Gosai J, Lu S, Gordon DM, Smith L. The antifungal occidiofungin triggers an apoptotic mechanism of cell death in yeast. JOURNAL OF NATURAL PRODUCTS 2013; 76:829-838. [PMID: 23672235 DOI: 10.1021/np300678e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Occidiofungin is a nonribosomally synthesized cyclic peptide having a base mass of 1200 Da. It is naturally produced by the soil bacterium Burkholderia contaminans MS14 and possesses potent broad-spectrum antifungal properties. The mechanism of action of occidiofungin is unknown. Viability, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), reactive oxygen species (ROS) detection, membrane and cell wall stability, and membrane mimetic assays were used to characterize the effect of occidiofungin on yeast cells. Confocal and electron microscopy experiments were used to visualize morphological changes within treated cells. TUNEL and ROS detection assays revealed an increase in fluorescence with increasing concentrations of the antifungal. Yeast cells appeared to shrink in size and showed the presence of 'dancing bodies' at low drug concentrations (1 μg/mL). A screen carried out on Saccharomyces cerevisiae gene deletion mutants in the apoptotic and autophagy pathways identified the apoptotic gene for YCA1, as having an important role in occidiofungin response as cells deleted for this gene exhibit a 2-fold increase in resistance. Results from our experiments demonstrate that the mechanism of action for occidiofungin in yeast is different from that of the common classes of antifungals used in the clinic, such as azoles, polyenes, and echinocandins. Our study also indicates that occidiofungin causes cell death in yeast through an apoptotic mechanism of action.
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Affiliation(s)
- Dayna Emrick
- Department of Biological Sciences, Mississippi State University , Mississippi State, MS 39762, United States
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Festa F, Rollins SM, Vattem K, Hathaway M, Lorenz P, Mendoza EA, Yu X, Qiu J, Kilmer G, Jensen P, Webb B, Ryan ET, LaBaer J. Robust microarray production of freshly expressed proteins in a human milieu. Proteomics Clin Appl 2013; 7:372-7. [PMID: 23027544 DOI: 10.1002/prca.201200063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/07/2012] [Accepted: 08/14/2012] [Indexed: 12/14/2022]
Abstract
PURPOSE In vitro transcription/translation (IVTT) systems are widely used in proteomics. For clinical applications, mammalian systems are preferred for protein folding and activity; however, the level of protein obtained is low. A new system extracted from human cells (1-Step Human Coupled IVT (HCIVT)) has the potential to overcome this problem and deliver high yields of protein expressed in a human milieu. EXPERIMENTAL DESIGN Western blots and self-assembled protein microarrays were used to test the efficiency of protein synthesis by HCIVT compared to rabbit reticulocyte lysate (RRL). The arrays were also used to measure the immune response obtained from serum of patients exposed to pathogens or vaccine. RESULTS HCIVT performed better than RRL in all experiments. The yield of protein synthesized in HCIVT is more than ten times higher than RRL, in both Western blot and protein microarrays. Moreover, HCIVT showed a robust lot-to-lot reproducibility. In immune assays, the signals of many antigens were detected only in HCIVT-expressed arrays, mainly due to the reduction in the background signal and the increased levels of protein on the array. CONCLUSION AND CLINICAL RELEVANCE HCIVT is a robust in vitro transcription and translation system that yields high levels of protein produced in a human milieu. It can be used in applications where protein expression in a mammalian system and high yields are needed. The increased immunogenic response of HCIVT-expressed proteins will be critical for biomarker discovery in many diseases, including cancer.
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Affiliation(s)
- Fernanda Festa
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
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Miersch S, Sidhu SS. Synthetic antibodies: concepts, potential and practical considerations. Methods 2012; 57:486-98. [PMID: 22750306 DOI: 10.1016/j.ymeth.2012.06.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 06/18/2012] [Accepted: 06/21/2012] [Indexed: 01/08/2023] Open
Abstract
The last 100 years of enquiry into the fundamental basis of humoral immunity has resulted in the identification of antibodies as key molecular sentinels responsible for the in vivo surveillance, neutralization and clearance of foreign substances. Intense efforts aimed at understanding and exploiting their exquisite molecular specificity have positioned antibodies as a cornerstone supporting basic research, diagnostics and therapeutic applications [1]. More recently, efforts have aimed to circumvent the limitations of developing antibodies in animals by developing wholly in vitro techniques for designing antibodies of tailored specificity. This has been realized with the advent of synthetic antibody libraries that possess diversity outside the scope of natural immune repertoires and are thus capable of yielding specificities not otherwise attainable. This review examines the convergence of technologies that have contributed to the development of combinatorial phage-displayed antibody libraries. It further explores the practical concepts that underlie phage display, antibody diversity and the methods used in the generation of and selection from phage-displayed synthetic antibody libraries, highlighting specific applications in which design approaches gave rise to specificities that could not easily be obtained with libraries based upon natural immune repertories.
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Affiliation(s)
- S Miersch
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2012; 13:57-62. [PMID: 22527514 PMCID: PMC3588887 DOI: 10.1007/s10969-012-9133-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 03/05/2012] [Indexed: 02/01/2023]
Abstract
The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.
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Affiliation(s)
- Lida K. Gifford
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | - Margaret J. Gabanyi
- Department of Chemistry & Chemical Biology, Rutgers – The State University of New Jersey, Piscataway, NJ 08854
| | - Helen M. Berman
- Department of Chemistry & Chemical Biology, Rutgers – The State University of New Jersey, Piscataway, NJ 08854
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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Montelione GT. The Protein Structure Initiative: achievements and visions for the future. F1000 BIOLOGY REPORTS 2012; 4:7. [PMID: 22500193 PMCID: PMC3318194 DOI: 10.3410/b4-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Protein Structure Initiative (PSI) was established in 2000 by the National Institutes of General Medical Sciences with the long-term goal of providing 3D (three-dimensional) structural information for most proteins in nature. As advances in genomic sequencing, bioinformatics, homology modelling, and methods for rapid determination of 3D structures of proteins by X-ray crystallography and nuclear magnetic resonance (NMR) converged, it was proposed that our understanding of the biology of protein structure and evolution could be greatly enabled by ‘genomic-scale’ protein structure determination. Over the past 12 years, the PSI has evolved from a testing bed for new methods of sample and structure production to a core component of a wide range of biology programs.
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Affiliation(s)
- Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
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Bray JE. Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. ACTA ACUST UNITED AC 2012; 13:37-46. [PMID: 22354707 DOI: 10.1007/s10969-012-9130-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/07/2012] [Indexed: 11/29/2022]
Abstract
The objective of this study is to automatically identify regions of the human proteome that are suitable for 3D structure determination by X-ray crystallography and to annotate them according to their likelihood to produce diffraction quality crystals. The results provide a powerful tool for structural genomics laboratories who wish to select human proteins based on the statistical likelihood of crystallisation success. Combining fold recognition and crystallisation prediction algorithms enables the efficient calculation of the crystallisability of the entire human proteome. This novel study estimates that there are approximately 40,000 crystallisable regions in the human proteome. Currently, only 15% of these regions (approx. 6,000 sequences) have been solved to at least 95% sequence identity. The remaining unsolved regions have been categorised into 5 crystallisation classes and an integral membrane protein (IMP) class, based on established structure prediction, crystallisation prediction and transmembrane (TM) helix prediction algorithms. Approximately 750 unsolved regions (2% of the proteome) have been identified as having a PDB fold representative (template) and an 'optimal' likelihood of crystallisation. At the other end of the spectrum, more than 10,500 non-IMP regions with a PDB template are classified as 'very difficult' to crystallise (26%) and almost 2,500 regions (6%) were predicted to contain at least 3 TM helices. The 3D-SPECS (3D Structural Proteomics Explorer with Crystallisation Scores) website contains crystallisation predictions for the entire human proteome and can be found at http://www.bioinformaticsplus.org/3dspecs.
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Affiliation(s)
- James E Bray
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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Griffiths S, Byrne RT, Antson AA, Whelan F. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:333-6. [PMID: 22442237 DOI: 10.1107/s1744309112003831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/29/2012] [Indexed: 11/11/2022]
Abstract
Dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the D-loop and variable loop of tRNA. The human dihydrouridine synthase HsDus2L has been implicated in the development of pulmonary carcinogenesis. Here, the purification, crystallization and preliminary X-ray characterization of the HsDus2L catalytic domain are reported. The crystals belonged to space group P2(1) and contained a single molecule of HsDus2L in the asymmetric unit. A complete data set was collected to 1.9 Å resolution using synchrotron radiation.
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Affiliation(s)
- Sam Griffiths
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, England
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Kim Y, Babnigg G, Jedrzejczak R, Eschenfeldt WH, Li H, Maltseva N, Hatzos-Skintges C, Gu M, Makowska-Grzyska M, Wu R, An H, Chhor G, Joachimiak A. High-throughput protein purification and quality assessment for crystallization. Methods 2011; 55:12-28. [PMID: 21907284 DOI: 10.1016/j.ymeth.2011.07.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 12/31/2022] Open
Abstract
The ultimate goal of structural biology is to understand the structural basis of proteins in cellular processes. In structural biology, the most critical issue is the availability of high-quality samples. "Structural biology-grade" proteins must be generated in the quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. With structural genomics emphasizing a genome-based approach in understanding protein structure and function, a number of unique structures covering most of the protein folding space have been determined and new technologies with high efficiency have been developed. At the Midwest Center for Structural Genomics (MCSG), we have developed semi-automated protocols for high-throughput parallel protein expression and purification. A protein, expressed as a fusion with a cleavable affinity tag, is purified in two consecutive immobilized metal affinity chromatography (IMAC) steps: (i) the first step is an IMAC coupled with buffer-exchange, or size exclusion chromatography (IMAC-I), followed by the cleavage of the affinity tag using the highly specific Tobacco Etch Virus (TEV) protease; the second step is IMAC and buffer exchange (IMAC-II) to remove the cleaved tag and tagged TEV protease. These protocols have been implemented on multidimensional chromatography workstations and, as we have shown, many proteins can be successfully produced in large-scale. All methods and protocols used for purification, some developed by MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Diseases (CSGID) purification pipeline, are discussed in this chapter.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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