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Garcia-Maldonado E, Huber AD, Chai SC, Nithianantham S, Li Y, Wu J, Poudel S, Miller DJ, Seetharaman J, Chen T. Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR. Nat Commun 2024; 15:4054. [PMID: 38744881 DOI: 10.1038/s41467-024-48472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.
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Affiliation(s)
- Efren Garcia-Maldonado
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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Singh S, Sutkus L, Li Z, Baker S, Bear J, Dilger RN, Miller DJ. Standardization of a silver stain to reveal mesoscale myelin in histological preparations of the mammalian brain. J Neurosci Methods 2024; 407:110139. [PMID: 38626852 DOI: 10.1016/j.jneumeth.2024.110139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND The brain is built of neurons supported by myelin, a fatty substance that improves cellular communication. Noninvasive magnetic resonance imaging (MRI) is now able to measure brain structure like myelin and requires histological validation. NEW METHOD Here we present work in small and large biomedical model mammals to standardize a silver impregnation method as a high-throughput histological myelin visualization procedure. Specifically, we built a new staining well plate to increase batch size, and then systematically varied the staining and clearing cycles to describe the staining response curve across taxa and conditions. We compared tissues fixed by immersion or perfusion, mounted versus free-floating, and cut as thicker or thinner slices, with two-weeks of post-fixation. RESULTS The staining response curves show optimal staining with a single exposure across taxa when incubation and clearing epochs are held to within 3-9 min. We show that clearing was slower in mounted vs free-floating tissue, and that staining was faster and caused fracturing earlier in thinner sliced and smaller volumes of tissue. COMPARISON WITH EXISTING METHODS We developed a batch processing approach to increase throughput while ensuring reproducibility and demonstrate the optimal conditions for fine myelinated fiber morphology visualization with short cycles (<9 minutes). CONCLUSIONS We present our optimized protocol to reveal mesoscale neuroanatomical myelin content in histology across mammals. This standard staining procedure will facilitate multiscale analyses of myelin content across development as well as in the presence of injury or disease.
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Affiliation(s)
- S Singh
- Department of Evolution, Ecology, and Behavior, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - L Sutkus
- Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - Z Li
- Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - S Baker
- Machine Shop, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - J Bear
- Machine Shop, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - R N Dilger
- Department of Animal Sciences, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - D J Miller
- Department of Evolution, Ecology, and Behavior, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America.
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3
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Gewirtz-Meydan A, Koós M, Nagy L, Kraus SW, Demetrovics Z, Potenza MN, Ballester-Arnal R, Batthyány D, Bergeron S, Billieux J, Burkauskas J, Cárdenas-López G, Carvalho J, Castro-Calvo J, Chen L, Ciocca G, Corazza O, Csako R, Fernandez DP, Fujiwara H, Fernandez EF, Fuss J, Gabrhelík R, Gjoneska B, Gola M, Grubbs JB, Hashim HT, Islam MS, Ismail M, Jiménez-Martínez MC, Jurin T, Kalina O, Klein V, Költő A, Lee SK, Lewczuk K, Lin CY, Lochner C, López-Alvarado S, Lukavská K, Mayta-Tristán P, Miller DJ, Orosová O, Orosz G, Ponce FP, Quintana GR, Quintero Garzola GC, Ramos-Diaz J, Rigaud K, Rousseau A, De Tubino Scanavino M, Schulmeyer MK, Sharan P, Shibata M, Shoib S, Sigre-Leirós V, Sniewski L, Spasovski O, Steibliene V, Stein DJ, Strong C, Ünsal BC, Vaillancourt-Morel MP, Van Hout MC, Bőthe B. Global cross-cultural validation of a brief measure for identifying potential suicide risk in 42 countries. Public Health 2024; 229:13-23. [PMID: 38382177 DOI: 10.1016/j.puhe.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 02/23/2024]
Abstract
OBJECTIVES This study aimed to examine the psychometric properties of the P4 suicide screener in a multinational sample. The primary goal was to evaluate the reliability and validity of the scale and investigate its convergent validity by analyzing its correlation with depression, anxiety, and substance use. STUDY DESIGN The study design is a cross-sectional self-report study conducted across 42 countries. METHODS A cross-sectional, self-report study was conducted in 42 countries, with a total of 82,243 participants included in the final data set. RESULTS The study provides an overview of suicide ideation rates across 42 countries and confirms the structural validity of the P4 screener. The findings indicated that sexual and gender minority individuals exhibited higher rates of suicidal ideation. The P4 screener showed adequate reliability, convergence, and discriminant validity, and a cutoff score of 1 is recommended to identify individuals at risk of suicidal behavior. CONCLUSIONS The study supports the reliability and validity of the P4 suicide screener across 42 diverse countries, highlighting the importance of using a cross-cultural suicide risk assessment to standardize the identification of high-risk individuals and tailoring culturally sensitive suicide prevention strategies.
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Affiliation(s)
- A Gewirtz-Meydan
- School of Social Work, Faculty of Social Welfare and Health Sciences, University of Haifa, Israel. Agewirtz-@univ.haifa.ac.il
| | - M Koós
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Forensic Psychiatry and Sex Research, University of Duisburg-Essen, Essen, Germany
| | - L Nagy
- Doctoral School of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - S W Kraus
- Department of Psychology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Z Demetrovics
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Centre of Excellence in Responsible Gaming, University of Gibraltar, Gibraltar, Gibraltar
| | - M N Potenza
- Yale University School of Medicine, New Haven, CT, USA; Connecticut Council on Problem Gambling, Wethersfield, CT, USA
| | - R Ballester-Arnal
- Departmento de Psicología Básica, Clínica y Psicobiología, University Jaume I of Castellón, Spain
| | - D Batthyány
- Institute for Behavioural Addictions, Sigmund Freud University Vienna, Austria
| | - S Bergeron
- Département de Psychologie, Université de Montréal, Montréal, Canada
| | - J Billieux
- Institute of Psychology, University of Lausanne, Lausanne, Switzerland; Center for Excessive Gambling, Addiction Medicine, Lausanne University Hospitals (CHUV), Lausanne, Switzerland
| | - J Burkauskas
- Laboratory of Behavioral Medicine, Neuroscience Institute, Lithuanian University of Health Sciences, Lithuania
| | - G Cárdenas-López
- Virtual Teaching and Cyberpsychology Laboratory, School of Psychology, National Autonomous University of Mexico, Mexico
| | - J Carvalho
- William James Center for Research, Departamento de Educação e Psicologia, Universidade de Aveiro, Aveiro, Portugal
| | - J Castro-Calvo
- Department of Personality, Assessment, and Psychological Treatments, University of Valencia, Spain
| | - L Chen
- Department of Psychology, College of Humanity and Social Science, Fuzhou University, China
| | - G Ciocca
- Section of Sexual Psychopathology, Department of Dynamic and Clinical Psychology, and Health Studies, Sapienza University of Rome, Rome, Italy
| | - O Corazza
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, UK; Department of Psychology and Cognitive Science, University of Trento, Italy
| | - R Csako
- Department of Psychology and Neuroscience, Auckland University of Technology, Auckland, New Zealand
| | | | - H Fujiwara
- Department of Neuropsychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Decentralized Big Data Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | | | - J Fuss
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Essen, Germany
| | - R Gabrhelík
- Charles University, First Faculty of Medicine, Department of Addictology, Prague, Czech Republic; General University Hospital in Prague, Department of Addictology, Czech Republic
| | - B Gjoneska
- Macedonian Academy of Sciences and Arts, Macedonia
| | - M Gola
- Institute of Psychlogy, Polish Academy of Sciences, Poland; Institute for Neural Computations, University of California San Diego, USA
| | - J B Grubbs
- University of New Mexico, Albuquerque, USA; Center for Alcohol, Substance Use, And Addiction (CASAA), University of New Mexico, Albuquerque, USA
| | - H T Hashim
- University of Baghdad, College of Medicine, Iraq
| | - M S Islam
- Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Centre for Advanced Research Excellence in Public Health, Savar, Dhaka 1342, Bangladesh
| | - M Ismail
- University of Baghdad, College of Medicine, Iraq
| | - M C Jiménez-Martínez
- Universidad Pedagógca y Tecnológica de Colombia, Colombia; Grupo de Investigación Biomédica y de Patología, Colombia
| | - T Jurin
- Department of Psychology, Humanities and Social Sciences, University of Zagreb, Croatia
| | - O Kalina
- Department of Educational Psychology and Psychology of Health, Pavol Jozef Safarik University in Kosice, Slovakia
| | - V Klein
- School of Psychology, University of Southampton, UK
| | - A Költő
- Health Promotion Research Centre, University of Galway, Ireland, UK
| | - S-K Lee
- Department of Psychiatry, Hallym University Chuncheon Sacred Heart Hospital, South Korea; Chuncheon Addiction Management Center, South Korea
| | - K Lewczuk
- Institute of Psychology, Cardinal Stefan Wyszynski University, Warsaw, Poland
| | - C-Y Lin
- Institute of Allied Health Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - C Lochner
- SAMRC Unit on Risk & Resilience in Mental Disorders, Stellenbosch University, South Africa
| | | | - K Lukavská
- Charles University, First Faculty of Medicine, Department of Addictology, Prague, Czech Republic; Charles University, Faculty of Education, Department of Psychology, Prague, Czech Republic
| | - P Mayta-Tristán
- Facultad de Medicina, Universidad Científica del Sur, Lima, Peru
| | - D J Miller
- College of Healthcare Sciences, James Cook University, Australia
| | - O Orosová
- Pavol Jozef Safarik University in Kosice, Department of Educational Psychology and Psychology of Health, Slovakia
| | | | - F P Ponce
- Facultad de Psicología, Universidad de Talca, Chile
| | - G R Quintana
- Departamento de Psicología y Filosofía, Facultad de Ciencias Sociales, Universidad de Tarapacá, Arica, Arica y Parinacota, Chile
| | - G C Quintero Garzola
- Florida State University, Panama; Sistema Nacional de Investigación (SNI), SENACYT, Panama
| | - J Ramos-Diaz
- Facultad de Ciencias de la Salud, Universidad Privada del Norte, Lima, Perú
| | | | - A Rousseau
- Leuven School for Mass Communication, KU Leuven, Leuven, Belgium
| | - M De Tubino Scanavino
- Department of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, Brazil; Experimental Pathophisiology Post Graduation Program, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | | | - P Sharan
- Department of Psychiatry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - M Shibata
- Department of Neuropsychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - S Shoib
- Department of Psychology, Shardha University, India; Department of Health Kashmir, India
| | - V Sigre-Leirós
- Institute of Psychology, University of Lausanne, Lausanne, Switzerland; Institute of Legal Psychiatry, Lausanne University Hospitals (CHUV), Lausanne, Switzerland
| | - L Sniewski
- Auckland University of Technology, New Zealand
| | - O Spasovski
- Faculty of Philosophy, Ss. Cyril and Methodius University in Skopje, Macedonia; Faculty of Philosophy, University of Ss. Cyril and Methodius in Trnava, Slovakia
| | - V Steibliene
- Laboratory of Behavioral Medicine, Neuroscience Institute, Lithuanian University of Health Sciences, Lithuania
| | - D J Stein
- SAMRC Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, South Africa
| | - C Strong
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - B C Ünsal
- Doctoral School of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - M-P Vaillancourt-Morel
- Département de Psychologie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - M C Van Hout
- Public Health Institute, Faculty of Health, Liverpool John Moores University, UK
| | - B Bőthe
- Département de Psychologie, Université de Montréal, Montréal, Canada; Département de Psychologie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
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4
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Huber AD, Poudel S, Wu J, Miller DJ, Lin W, Yang L, Bwayi MN, Rimmer MA, Gee RRF, Seetharaman J, Chai SC, Chen T. A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR. Nucleic Acids Res 2024; 52:1661-1676. [PMID: 38084912 PMCID: PMC10899790 DOI: 10.1093/nar/gkad1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 02/29/2024] Open
Abstract
Bromodomain and extraterminal (BET) proteins are extensively studied in multiple pathologies, including cancer. BET proteins modulate transcription of various genes, including those synonymous with cancer, such as MYC. Thus, BET inhibitors are a major area of drug development efforts. (+)-JQ1 (JQ1) is the prototype inhibitor and is a common tool to probe BET functions. While showing therapeutic promise, JQ1 is not clinically usable, partly due to metabolic instability. Here, we show that JQ1 and the BET-inactive (-)-JQ1 are agonists of pregnane X receptor (PXR), a nuclear receptor that transcriptionally regulates genes encoding drug-metabolizing enzymes such as CYP3A4, which was previously shown to oxidize JQ1. A PXR-JQ1 co-crystal structure identified JQ1's tert-butyl moiety as a PXR anchor and explains binding by (-)-JQ1. Analogs differing at the tert-butyl lost PXR binding, validating our structural findings. Evaluation in liver cell models revealed both PXR-dependent and PXR-independent modulation of CYP3A4 expression by BET inhibitors. We have characterized a non-BET JQ1 target, a mechanism of physiological JQ1 instability, a biological function of (-)-JQ1, and BET-dependent transcriptional regulation of drug metabolism genes.
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Affiliation(s)
- Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Monicah N Bwayi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mary Ashley Rimmer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Rebecca R Florke Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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5
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Nishiguchi G, Mascibroda LG, Young SM, Caine EA, Abdelhamed S, Kooijman JJ, Miller DJ, Das S, McGowan K, Mayasundari A, Shi Z, Barajas JM, Hiltenbrand R, Aggarwal A, Chang Y, Mishra V, Narina S, Thomas M, Loughran AJ, Kalathur R, Yu K, Zhou S, Wang X, High AA, Peng J, Pruett-Miller SM, Daniels DL, Urh M, Shelat AA, Mullighan CG, Riching KM, Zaman GJR, Fischer M, Klco JM, Rankovic Z. Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines. Nat Commun 2024; 15:482. [PMID: 38228616 PMCID: PMC10791743 DOI: 10.1038/s41467-024-44698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.
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Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lauren G Mascibroda
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sarah M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | | | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhe Shi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Juan M Barajas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anup Aggarwal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Melvin Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Memphis, TN, 38105, USA
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Guido J R Zaman
- Oncolines B.V., Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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6
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Huber AD, Poudel S, Li Y, Lin W, Wu J, Miller DJ, Chen T. Ligand flexibility and binding pocket malleability cooperate to allow selective PXR activation by analogs of a promiscuous nuclear receptor ligand. Structure 2023; 31:1545-1555.e9. [PMID: 37729916 PMCID: PMC10872772 DOI: 10.1016/j.str.2023.08.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/01/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
The human nuclear receptor (NR) family of transcription factors contains 48 proteins that bind lipophilic molecules. Approved NR therapies have had immense success treating various diseases, but lack of selectivity has hindered efforts to therapeutically target the majority of NRs due to unpredictable off-target effects. The synthetic ligand T0901317 was originally discovered as a potent agonist of liver X receptors (LXRα/β) but subsequently found to target additional NRs, with activation of pregnane X receptor (PXR) being as potent as that of LXRs. We previously showed that directed rigidity reduces PXR binding by T0901317 derivatives through unfavorable protein remodeling. Here, we use a similar approach to achieve selectivity for PXR over other T0901317-targeted NRs. One molecule, SJPYT-318, accomplishes selectivity by favorably utilizing PXR's flexible binding pocket and surprisingly binding in a new mode distinct from the parental T0901317. Our work provides a structure-guided framework to achieve NR selectivity from promiscuous compounds.
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Affiliation(s)
- Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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7
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Ketzer M, Praeg D, Augustin AH, Rodrigues LF, Steiger AK, Rahmati-Abkenar M, Viana AR, Miller DJ, Malinverno A, Dickens GR, Cupertino JA. Gravity complexes as a focus of seafloor fluid seepage: the Rio Grande Cone, SE Brazil. Sci Rep 2023; 13:4590. [PMID: 36944652 PMCID: PMC10030975 DOI: 10.1038/s41598-023-31815-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Seafloor methane emissions can affect Earth's climate and ocean chemistry. Vast quantities of methane formed by microbial decomposition of organic matter are locked within gas hydrate and free gas on continental slopes, particularly in large areas with high sediment accumulations such as deep-sea fans. The release of methane in slope environments has frequently been associated with dissociation of gas hydrates near the edge of the gas hydrate stability zone on the upper slope, with discharges in greater water depths less understood. Here we show, using data from the Rio Grande Cone (western South Atlantic), that the intrinsic, gravity-induced downslope collapse of thick slope sediment accumulations creates structures that serve as pathways for gas migration, unlocking methane and causing seafloor emissions via giant gas flares in the water column. The observed emissions in the study region (up to 310 Mg year-1) are three times greater than estimates for the entire US North Atlantic margin and reveal the importance of collapsing sediment accumulations for ocean carbon cycling. Similar outgassing systems on the Amazon and Niger fans suggest that gravity tectonics on passive margins is a common yet overlooked mechanism driving massive seafloor methane emissions in sediment-laden continental slopes.
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Affiliation(s)
- M Ketzer
- Department of Biology and Environmental Science, Linnaeus University, 391 81, Kalmar, Sweden.
| | - D Praeg
- Géoazur, 250 Rue Albert Einstein, 06560, Valbonne, France
| | - A H Augustin
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
| | - L F Rodrigues
- Universidade Federal do Rio Grande, Rio Grande, 96203-900, Brazil
| | - A K Steiger
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
| | - M Rahmati-Abkenar
- Department of Biology and Environmental Science, Linnaeus University, 391 81, Kalmar, Sweden
| | - A R Viana
- Petrobras Petroleo Brasileiro SA, Rio de Janeiro, 20031-170, Brazil
| | - D J Miller
- Petrobras Petroleo Brasileiro SA, Rio de Janeiro, 20031-170, Brazil
| | - A Malinverno
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY, 10964, USA
| | | | - J A Cupertino
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
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8
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Lin W, Huber AD, Poudel S, Li Y, Seetharaman J, Miller DJ, Chen T. Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein. Proc Natl Acad Sci U S A 2023; 120:e2217804120. [PMID: 36848571 PMCID: PMC10013835 DOI: 10.1073/pnas.2217804120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/30/2023] [Indexed: 03/01/2023] Open
Abstract
Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR's ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR's ligand-binding pocket and reduce their safety liability due to PXR binding.
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Affiliation(s)
- Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
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9
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Radka CD, Miller DJ, Frank MW, Rock CO. Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii. J Biol Chem 2022; 298:102195. [PMID: 35760102 PMCID: PMC9304779 DOI: 10.1016/j.jbc.2022.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/01/2022] Open
Abstract
Sulfonolipids are unusual lipids found in the outer membranes of Gram-negative bacteria in the phylum Bacteroidetes. Sulfonolipid and its deacylated derivative, capnine, are sulfur analogs of ceramide-1-phosphate and sphingosine-1-phosphate, respectively; thus, sulfonolipid biosynthesis is postulated to be similar to the sphingolipid biosynthetic pathway. Here, we identify the first enzyme in sulfonolipid synthesis in Alistipes finegoldii, an anaerobic gut commensal bacterium, as the product of the alfi_1224 gene, cysteate acyl-acyl carrier protein (ACP) transferase (SulA). We show SulA catalyzes the condensation of acyl-ACP and cysteate (3-sulfo-alanine) to form 3-ketocapnine. Acyl-CoA is a poor substrate. We show SulA has a bound pyridoxal phosphate (PLP) cofactor that undergoes a spectral redshift in the presence of cysteate, consistent with the transition of the lysine-aldimine complex to a substrate-aldimine complex. Furthermore, the SulA crystal structure shows the same prototypical fold found in bacterial serine palmitoyltransferases (Spt), enveloping the PLP cofactor bound to Lys251. We observed the SulA and Spt active sites are identical except for Lys281 in SulA, which is an alanine in Spt. Additionally, SulA(K281A) is catalytically inactive, but binds cysteate and forms the external aldimine normally, highlighting the structural role of the Lys281 side chain in walling off the active site from bulk solvent. Finally, the electropositive groove on the protein surface adjacent to the active site entrance provides a landing pad for the electronegative acyl-ACP surface. Taken together, these data identify the substrates, products, and mechanism of SulA, the PLP-dependent condensing enzyme that catalyzes the first step in sulfonolipid synthesis in a gut commensal bacterium.
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Affiliation(s)
- Christopher D Radka
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA.
| | - Darcie J Miller
- Departments of, Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Matthew W Frank
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Charles O Rock
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
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10
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Wang J, Buchman CD, Seetharaman J, Miller DJ, Huber AD, Wu J, Chai SC, Garcia-Maldonado E, Wright WC, Chenge J, Chen T. Unraveling the structural basis of selective inhibition of human cytochrome p450 3a5. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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11
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Fernando DM, Gee CT, Griffith EC, Meyer CJ, Wilt LA, Tangallapally R, Wallace MJ, Miller DJ, Lee RE. Biophysical analysis of the Mycobacteria tuberculosis peptide binding protein DppA reveals a stringent peptide binding pocket. Tuberculosis (Edinb) 2022; 132:102157. [PMID: 34894561 PMCID: PMC8818035 DOI: 10.1016/j.tube.2021.102157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 01/03/2023]
Abstract
The peptide binding protein DppA is an ABC transporter found in prokaryotes that has the potential to be used as drug delivery tool for hybrid antibiotic compounds. Understanding the motifs and structures that bind to DppA is critical to the development of these bivalent compounds. This study focused on the biophysical analysis of the MtDppA from M. tuberculosis. Analysis of the crystal structure revealed a SVA tripeptide was co-crystallized with the protein. Further peptide analysis demonstrated MtDppA shows very little affinity for dipeptides but rather preferentially binds to peptides that are 3-4 amino acids in length. The structure-activity relationships (SAR) between MtDppA and tripeptides with varied amino acid substitutions were evaluated using thermal shift, SPR, and molecular dynamics simulations. Efforts to identify novel ligands for use as alternative scaffolds through the thermal shift screening of 35,000 compounds against MtDppA were unsuccessful, indicating that the MtDppA binding pocket is highly specialized for uptake of peptides. Future development of compounds that seek to utilize MtDppA as a drug delivery mechanism, will likely require a tri- or tetrapeptide component with a hydrophobic -non-acidic peptide sequence.
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Affiliation(s)
- Dinesh M. Fernando
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Clifford T. Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Christopher J. Meyer
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Laura A. Wilt
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105,Corresponding Author:
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12
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Wang J, Buchman CD, Seetharaman J, Miller DJ, Huber AD, Wu J, Chai SC, Garcia-Maldonado E, Wright WC, Chenge J, Chen T. Unraveling the Structural Basis of Selective Inhibition of Human Cytochrome P450 3A5. J Am Chem Soc 2021; 143:18467-18480. [PMID: 34648292 DOI: 10.1021/jacs.1c07066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human cytochrome P450 (CYP) CYP3A4 and CYP3A5 enzymes metabolize more than one-half of marketed drugs. They share high structural and substrate similarity and are often studied together as CYP3A4/5. However, CYP3A5 preferentially metabolizes several clinically prescribed drugs, such as tacrolimus. Genetic polymorphism in CYP3A5 makes race-based dosing adjustment of tacrolimus necessary to minimize acute rejection after organ transplantation. Moreover, the differential tissue distribution and expression levels of CYP3A4 and CYP3A5 can aggravate toxicity during treatment. Therefore, selective inhibitors of CYP3A5 are needed to distinguish the role of CYP3A5 from that of CYP3A4 and serve as starting points for potential therapeutic development. To this end, we report the crystal structure of CYP3A5 in complex with a previously reported selective inhibitor, clobetasol propionate (CBZ). This is the first CYP3A5 structure with a type I inhibitor, which along with the previously reported substrate-free and type II inhibitor-bound structures, constitute the main CYP3A5 structural modalities. Supported by structure-guided mutagenesis analyses, the CYP3A5-CBZ structure showed that a unique conformation of the F-F' loop in CYP3A5 enables selective binding of CBZ to CYP3A5. Several polar interactions, including hydrogen bonds, stabilize the position of CBZ to interact with this unique F-F' loop conformation. In addition, functional and biophysical assays using CBZ analogs highlight the importance of heme-adjacent moieties for selective CYP3A5 inhibition. Our findings can be used to guide further development of more potent and selective CYP3A5 inhibitors.
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Affiliation(s)
- Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Cameron D Buchman
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Efren Garcia-Maldonado
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - William C Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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13
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Koirala S, Klein J, Zheng Y, Glenn NO, Eisemann T, Fon Tacer K, Miller DJ, Kulak O, Lu M, Finkelstein DB, Neale G, Tillman H, Vogel P, Strand DW, Lum L, Brautigam CA, Pascal JM, Clements WK, Potts PR. Tissue-Specific Regulation of the Wnt/β-Catenin Pathway by PAGE4 Inhibition of Tankyrase. Cell Rep 2021; 32:107922. [PMID: 32698014 DOI: 10.1016/j.celrep.2020.107922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/30/2020] [Accepted: 06/26/2020] [Indexed: 01/10/2023] Open
Abstract
Spatiotemporal control of Wnt/β-catenin signaling is critical for organism development and homeostasis. The poly-(ADP)-ribose polymerase Tankyrase (TNKS1) promotes Wnt/β-catenin signaling through PARylation-mediated degradation of AXIN1, a component of the β-catenin destruction complex. Although Wnt/β-catenin is a niche-restricted signaling program, tissue-specific factors that regulate TNKS1 are not known. Here, we report prostate-associated gene 4 (PAGE4) as a tissue-specific TNKS1 inhibitor that robustly represses canonical Wnt/β-catenin signaling in human cells, zebrafish, and mice. Structural and biochemical studies reveal that PAGE4 acts as an optimal substrate decoy that potently hijacks substrate binding sites on TNKS1 to prevent AXIN1 PARylation and degradation. Consistently, transgenic expression of PAGE4 in mice phenocopies TNKS1 knockout. Physiologically, PAGE4 is selectively expressed in stromal prostate fibroblasts and functions to establish a proper Wnt/β-catenin signaling niche through suppression of autocrine signaling. Our findings reveal a non-canonical mechanism for TNKS1 inhibition that functions to establish tissue-specific control of the Wnt/β-catenin pathway.
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Affiliation(s)
- Sajjan Koirala
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yumei Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole O Glenn
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA; Department of Biology, Belmont University, Nashville, TN, USA
| | - Travis Eisemann
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Klementina Fon Tacer
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ozlem Kulak
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meifen Lu
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David B Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Tillman
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas W Strand
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lawrence Lum
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Pfizer, La Jolla, CA, USA
| | - Chad A Brautigam
- Departments of Biophysics and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Wilson K Clements
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Mason B, Cooke I, Moya A, Augustin R, Lin MF, Satoh N, Bosch TCG, Bourne DG, Hayward DC, Andrade N, Forêt S, Ying H, Ball EE, Miller DJ. AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones. Dev Comp Immunol 2021; 114:103866. [PMID: 32937163 DOI: 10.1016/j.dci.2020.103866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
A candidate antimicrobial peptide (AmAMP1) was identified by searching the whole genome sequence of Acropora millepora for short (<125AA) cysteine-rich predicted proteins with an N-terminal signal peptide but lacking clear homologs in the SwissProt database. It resembled but was not closely related to damicornin, the only other known AMP from a coral, and was shown to be active against both Gram-negative and Gram-positive bacteria. These proteins define a family of AMPs present in corals and their close relatives, the Corallimorpharia, and are synthesised as preproproteins in which the C-terminal mature peptide contains a conserved arrangement of six cysteine residues. Consistent with the idea of a common origin for AMPs and toxins, this Cys motif is shared between the coral AMPs and the Shk neurotoxins of sea anemones. AmAMP1 is expressed at late stages of coral development, in ectodermal cells that resemble the "ganglion neurons" of Hydra, in which it has recently been demonstrated that a distinct AMP known as NDA-1 is expressed.
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Affiliation(s)
- B Mason
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia
| | - I Cooke
- Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - A Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia
| | - R Augustin
- Zoological Institute, Kiel University, Kiel, Germany
| | - M-F Lin
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan
| | - N Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan
| | - T C G Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - D G Bourne
- Department of Marine Ecosystems and Impacts, James Cook University, Townsville, 4811, Queensland, Australia
| | - D C Hayward
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - N Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia
| | - S Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - H Ying
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - E E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - D J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia; Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan.
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15
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Yang SW, Huang X, Lin W, Min J, Miller DJ, Mayasundari A, Rodrigues P, Griffith EC, Gee CT, Li L, Li W, Lee RE, Rankovic Z, Chen T, Potts PR. Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases. Nat Commun 2020; 11:4931. [PMID: 33004795 PMCID: PMC7529893 DOI: 10.1038/s41467-020-18708-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.
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Affiliation(s)
- Seung Wook Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Xin Huang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Patrick Rodrigues
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Elizabeth C Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Lei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California Irvine, 5270 California Ave, Irvine, CA, 92617, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California Irvine, 5270 California Ave, Irvine, CA, 92617, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
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16
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Radka CD, Frank MW, Yao J, Seetharaman J, Miller DJ, Rock CO. The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI). J Biol Chem 2020; 295:7635-7652. [PMID: 32317282 PMCID: PMC7261799 DOI: 10.1074/jbc.ra120.013336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Indexed: 01/07/2023] Open
Abstract
Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1-3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix-helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.
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Affiliation(s)
- Christopher D. Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Matthew W. Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles O. Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, To whom correspondence should be addressed:
262 Danny Thomas Place, Memphis, TN 38105. Tel.:
901-595-3491; E-mail:
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17
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Radka CD, Frank MW, Yao J, Jayaraman S, Miller DJ, Rock CO. Unique Aspects of Lipid Metabolism in the Human Gut Microbiome. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Griffith EC, Zhao Y, Singh AP, Conlon BP, Tangallapally R, Shadrick WR, Liu J, Wallace MJ, Yang L, Elmore JM, Li Y, Zheng Z, Miller DJ, Cheramie MN, Lee RB, LaFleur MD, Lewis K, Lee RE. Ureadepsipeptides as ClpP Activators. ACS Infect Dis 2019; 5:1915-1925. [PMID: 31588734 DOI: 10.1021/acsinfecdis.9b00245] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Acyldepsipeptides are a unique class of antibiotics that act via allosterically dysregulated activation of the bacterial caseinolytic protease (ClpP). The ability of ClpP activators to kill nongrowing bacteria represents a new opportunity to combat deep-seated biofilm infections. However, the acyldepsipeptide scaffold is subject to rapid metabolism. Herein, we explore alteration of the potentially metabolically reactive α,β unsaturated acyl chain. Through targeted synthesis, a new class of phenyl urea substituted depsipeptide ClpP activators with improved metabolic stability is described. The ureadepsipeptides are potent activators of Staphylococcus aureus ClpP and show activity against Gram-positive bacteria, including S. aureus biofilms. These studies demonstrate that a phenyl urea motif can successfully mimic the double bond, maintaining potency equivalent to acyldepsipeptides but with decreased metabolic liability. Although removal of the double bond from acyldepsipeptides generally has a significant negative impact on potency, structural studies revealed that the phenyl ureadepsipeptides can retain potency through the formation of a third hydrogen bond between the urea and the key Tyr63 residue in the ClpP activation domain. Ureadepsipeptides represent a new class of ClpP activators with improved drug-like properties, potent antibacterial activity, and the tractability to be further optimized.
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Affiliation(s)
- Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ying Zhao
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Aman P. Singh
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Brian P. Conlon
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - William R. Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - John M. Elmore
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhong Zheng
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Darcie J. Miller
- Department of Structure Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Martin N. Cheramie
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Robin B. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Michael D. LaFleur
- Arietis Pharma, 650 Albany Street, Suite 114, Boston, Massachusetts 02118, United States
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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19
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Ling T, Miller DJ, Lang WH, Griffith E, Rodriguez-Cortes A, El Ayachi I, Palacios G, Min J, Miranda-Carboni G, Lee RE, Rivas F. Mechanistic Insight on the Mode of Action of Colletoic Acid. J Med Chem 2019; 62:6925-6940. [PMID: 31294974 DOI: 10.1021/acs.jmedchem.9b00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The natural product colletoic acid (CA) is a selective inhibitor of 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), which primarily converts cortisone to the active glucocorticoid (GC) cortisol. Here, CA's mode of action and its potential as a chemical tool to study intracellular GC signaling in adipogenesis are disclosed. 11β-HSD1 biochemical studies of CA indicated that its functional groups at C-1, C-4, and C-9 were important for enzymatic activity; an X-ray crystal structure of 11β-HSD1 bound to CA at 2.6 Å resolution revealed the nature of those interactions, namely, a close-fitting and favorable interactions between the constrained CA spirocycle and the catalytic triad of 11β-HSD1. Structure-activity relationship studies culminated in the development of a superior CA analogue with improved target engagement. Furthermore, we demonstrate that CA selectively inhibits preadipocyte differentiation through 11β-HSD1 inhibition, suppressing other relevant key drivers of adipogenesis (i.e., PPARγ, PGC-1α), presumably by negatively modulating the glucocorticoid signaling pathway. The combined findings provide an in-depth evaluation of the mode of action of CA and its potential as a tool compound to study adipose tissue and its implications in metabolic syndrome.
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Affiliation(s)
| | | | | | | | | | - Ikbale El Ayachi
- Department of Medicine , The University of Tennessee Health Science Center , Memphis , Tennessee 38163 , United States
| | | | | | - Gustavo Miranda-Carboni
- Department of Medicine , The University of Tennessee Health Science Center , Memphis , Tennessee 38163 , United States
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20
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Matar HE, Tripathi S, Miller DJ. Iliac crest apophyseal insufficiency avulsion fractures. Ann R Coll Surg Engl 2018; 100:e4-e6. [PMID: 29046079 PMCID: PMC5838676 DOI: 10.1308/rcsann.2017.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 11/22/2022] Open
Abstract
Iliac crest apophyseal avulsion fractures are rare injuries caused mainly through forceful contraction of attached muscles during high level sporting activities. We present the first case of a spontaneous iliac crest apophyseal avulsion insufficiency fracture in a patient with severe atopic eczema on oral steroids and review the relevant literature.
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Affiliation(s)
- H E Matar
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
| | - S Tripathi
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
| | - D J Miller
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
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21
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Bartol FF, Wiley AA, George AF, Miller DJ, Bagnell CA. PHYSIOLOGY AND ENDOCRINOLOGY SYMPOSIUM: Postnatal reproductive development and the lactocrine hypothesis. J Anim Sci 2017; 95:2200-2210. [PMID: 28727004 DOI: 10.2527/jas.2016.1144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Maternal effects on development can program cell fate and dictate offspring phenotype. Such effects do not end at birth, but extend into postnatal life through signals communicated from mother to offspring in first milk (colostrum). Transmission of bioactive factors from mother to offspring as a specific consequence of nursing defines a lactocrine mechanism. The female reproductive tract is not fully formed at birth (postnatal day = PND 0). Data for ungulates and mice indicate that disruption of development during neonatal life can have lasting effects on the form and function of uterine tissues. Uterine growth and histogenesis proceed in an ovary-independent manner shortly after birth, suggesting that extra-ovarian inputs are important in this process. Data for the pig indicate that lactocrine signals communicated within 12 to 48 h from birth constitute one source of such uterotrophic support. Disruption of lactocrine signaling, either naturally, by limited colostrum consumption, or experimentally, by milk replacer feeding, alters neonatal porcine uterine development and can have negative consequences for reproductive performance in adults. Substantial differences in endometrial and uterine gene expression between colostrum- and replacer-fed gilts were evident by PND 2, when RNA sequencing revealed over 800 differentially expressed, lactocrine-sensitive genes. Lactocrine-sensitive biological processes identified through transcriptomic studies and integrated microRNA-mRNA pathway analyses included those associated with both cell-cell and ESR1 signaling, and tissue development. Evidence for the pig indicates that colostrum consumption and lactocrine signaling are required to establish a normal uterine developmental program and optimal uterine developmental trajectory.
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22
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Zhang C, Miller DJ, Guibao CD, Donato DM, Hanks SK, Zheng JJ. Structural and functional insights into the interaction between the Cas family scaffolding protein p130Cas and the focal adhesion-associated protein paxillin. J Biol Chem 2017; 292:18281-18289. [PMID: 28860193 DOI: 10.1074/jbc.m117.807271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/25/2017] [Indexed: 11/06/2022] Open
Abstract
The Cas family scaffolding protein p130Cas is a Src substrate localized in focal adhesions (FAs) and functions in integrin signaling to promote cell motility, invasion, proliferation, and survival. p130Cas targeting to FAs is essential for its tyrosine phosphorylation and downstream signaling. Although the N-terminal SH3 domain is important for p130Cas localization, it has also been reported that the C-terminal region is involved in p130Cas FA targeting. The C-terminal region of p130Cas or Cas family homology domain (CCHD) has been reported to adopt a structure similar to that of the focal adhesion kinase C-terminal focal adhesion-targeting domain. The mechanism by which the CCHD promotes FA targeting of p130Cas, however, remains unclear. In this study, using a calorimetry approach, we identified the first LD motif (LD1) of the FA-associated protein paxillin as the binding partner of the p130Cas CCHD (in a 1:1 stoichiometry with a Kd ∼4.2 μm) and elucidated the structure of the p130Cas CCHD in complex with the paxillin LD1 motif by X-ray crystallography. Of note, a comparison of the CCHD/LD1 complex with a previously solved structure of CCHD in complex with the SH2-containing protein NSP3 revealed that LD1 had almost identical positioning of key hydrophobic and acidic residues relative to NSP3. Because paxillin is one of the key scaffold molecules in FAs, we propose that the interaction between the p130Cas CCHD and the LD1 motif of paxillin plays an important role in p130Cas FA targeting.
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Affiliation(s)
- Chi Zhang
- From the Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Cristina D Guibao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Dominique M Donato
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232.,Physics of Life Processes, Huygens Kamerlingh-Onnes Laboratory, Leiden University, 2300 RE Leiden, The Netherlands, and
| | - Steven K Hanks
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Jie J Zheng
- From the Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, .,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163.,Molecular Biology Institute, UCLA, Los Angeles, California 90095
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23
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Dove KK, Olszewski JL, Martino L, Duda DM, Wu XS, Miller DJ, Reiter KH, Rittinger K, Schulman BA, Klevit RE. Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1. Structure 2017; 25:890-900.e5. [PMID: 28552575 PMCID: PMC5462532 DOI: 10.1016/j.str.2017.04.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/07/2017] [Accepted: 04/28/2017] [Indexed: 12/02/2022]
Abstract
RING-between-RING (RBR) E3s contain RING1 domains that are structurally similar yet mechanistically distinct from canonical RING domains. Both types of E3 bind E2∼ubiquitin (E2∼Ub) via their RINGs but canonical RING E3s promote closed E2∼Ub conformations required for direct Ub transfer from the E2 to substrate, while RBR RING1s promote open E2∼Ub to favor Ub transfer to the E3 active site. This different RING/E2∼Ub conformation determines its direct target, which for canonical RING E3s is typically a substrate or substrate-linked Ub, but is the E3 active-site cysteine in the case of RBR-type E3s. Here we show that a short extension of HHARI RING1, namely Zn2+-loop II, not present in any RING E3s, acts as a steric wedge to disrupt closed E2∼Ub, providing a structural explanation for the distinctive RING1-dependent conformational restriction mechanism utilized by RBR E3s. HHARI RING1 Zn2+-loop II extension disrupts closed conformation of E2∼Ubs A crystal structure shows open UbcH7∼Ub binding RING1 of auto-inhibited HHARI HHARI UBA-L domain has Ub binding properties
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Affiliation(s)
- Katja K Dove
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | - Jennifer L Olszewski
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Luigi Martino
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David M Duda
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiaoli S Wu
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Katherine H Reiter
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | | | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA.
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24
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Silva E, Frost D, Li L, Bovin N, Miller DJ. Lactadherin is a candidate oviduct Lewis X trisaccharide receptor on porcine spermatozoa. Andrology 2017; 5:589-597. [PMID: 28296340 DOI: 10.1111/andr.12340] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/03/2017] [Accepted: 01/17/2017] [Indexed: 01/21/2023]
Abstract
A recent study has demonstrated that porcine spermatozoa recognize with high affinity carbohydrate structures containing Lewis X motifs. Sperm adhesion to Lewis X is proposed to mediate sperm binding to the oviduct epithelium to form a reservoir. The objective of this study was to identify Lewis X-binding proteins from porcine spermatozoa as candidate receptors for oviduct glycans. To identify low-abundance proteins typically masked by proteins originating from seminal fluid, Lewis X candidate receptors were enriched from cauda epididymal boar spermatozoa. Plasma membrane preparations from cauda epididymal spermatozoa were subjected to RP-HPLC and glycan blotting assays to isolate and detect proteins that bind Lewis X. Following bottom-up LC-MS/MS analysis, among the two bands that bound sulfated Lewis X, ADAM5, which spermatozoa, was confidently identified. ADAM family members have been established as contributors to sperm entry into the oviduct. A second sulfated Lewis X-binding protein identified was the peripheral membrane protein lactadherin (also known as P47, SED1 and MFG-E8 in different species). The interaction between Lewis X and lactadherin was functionally important because competitive inhibition by soluble recombinant lactadherin reduced sperm binding to the oviduct epithelium. Furthermore, far-western blotting demonstrated that purified lactadherin could bind oviduct cells. In summary, these findings reveal that, in addition to the previously reported glycan affinity of accessory gland proteins that adhere to spermatozoa, multiple proteins intrinsic to spermatozoa have affinity for a specific oviduct glycan. Further, in addition to binding to the zona pellucida, lactadherin is now implicated in binding to oviduct glycans to promote formation of the sperm reservoir.
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Affiliation(s)
- E Silva
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - D Frost
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - L Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - N Bovin
- Shemyakin Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - D J Miller
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
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25
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Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell 2016; 165:1440-1453. [PMID: 27259151 DOI: 10.1016/j.cell.2016.05.037] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/16/2016] [Accepted: 05/09/2016] [Indexed: 11/25/2022]
Abstract
Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.
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Affiliation(s)
- Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA
| | - Edmond R Watson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Prakash Dube
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael R Brunner
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Haselbach
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marc A Jarvis
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Yanishevski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Georg Petzold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Holger Stark
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA.
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Capel KCC, Migotto AE, Zilberberg C, Lin MF, Forsman Z, Miller DJ, Kitahara MV. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. Gene 2016; 590:270-7. [PMID: 27234370 DOI: 10.1016/j.gene.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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Affiliation(s)
- K C C Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A E Migotto
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - C Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M F Lin
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Z Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, USA
| | - D J Miller
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - M V Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil; Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
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Broussard TC, Miller DJ, Jackson P, Nourse A, White SW, Rock CO. Biochemical Roles for Conserved Residues in the Bacterial Fatty Acid-binding Protein Family. J Biol Chem 2016; 291:6292-303. [PMID: 26774272 PMCID: PMC4813577 DOI: 10.1074/jbc.m115.706820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
Fatty acid kinase (Fak) is a ubiquitous Gram-positive bacterial enzyme consisting of an ATP-binding protein (FakA) that phosphorylates the fatty acid bound to FakB. In Staphylococcus aureus, Fak is a global regulator of virulence factor transcription and is essential for the activation of exogenous fatty acids for incorporation into phospholipids. The 1.2-Å x-ray structure of S. aureus FakB2, activity assays, solution studies, site-directed mutagenesis, and in vivo complementation were used to define the functions of the five conserved residues that define the FakB protein family (Pfam02645). The fatty acid tail is buried within the protein, and the exposed carboxyl group is bound by a Ser-93-fatty acid carboxyl-Thr-61-His-266 hydrogen bond network. The guanidinium of the invariant Arg-170 is positioned to potentially interact with a bound acylphosphate. The reduced thermal denaturation temperatures of the T61A, S93A, and H266A FakB2 mutants illustrate the importance of the hydrogen bond network in protein stability. The FakB2 T61A, S93A, and H266A mutants are 1000-fold less active in the Fak assay, and the R170A mutant is completely inactive. All FakB2 mutants form FakA(FakB2)2 complexes except FakB2(R202A), which is deficient in FakA binding. Allelic replacement shows that strains expressing FakB2 mutants are defective in fatty acid incorporation into phospholipids and virulence gene transcription. These conserved residues are likely to perform the same critical functions in all bacterial fatty acid-binding proteins.
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Affiliation(s)
| | - Darcie J Miller
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | | | - Amanda Nourse
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Stephen W White
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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Vanarotti MS, Finkelstein DB, Guibao CD, Nourse A, Miller DJ, Zheng JJ. Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats. Biochemistry 2016; 55:1332-45. [PMID: 26866573 PMCID: PMC4843776 DOI: 10.1021/acs.biochem.5b01274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Proline-rich
tyrosine kinase 2 (Pyk2) is a nonreceptor tyrosine
kinase and belongs to the focal adhesion kinase (FAK) family. Like
FAK, the C-terminal focal adhesion-targeting (FAT) domain of Pyk2
binds to paxillin, a scaffold protein in focal adhesions; however,
the interaction between the FAT domain of Pyk2 and paxillin is dynamic
and unstable. Leupaxin is another member in the paxillin family and
was suggested to be the native binding partner of Pyk2; Pyk2 gene
expression is strongly correlated with that of leupaxin in many tissues
including primary breast cancer. Here, we report that leupaxin interacts
with Pyk2-FAT. Leupaxin has four leucine–aspartate (LD) motifs.
The first and third LD motifs of leupaxin preferably target the two
LD-binding sites on the Pyk2-FAT domain, respectively. Moreover, the
full-length leupaxin binds to Pyk2-FAT as a stable one-to-one complex.
Together, we propose that there is an underlying selectivity between
leupaxin and paxillin for Pyk2, which may influence the differing
behavior of the two proteins at focal adhesion sites.
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Affiliation(s)
| | | | | | | | | | - Jie J Zheng
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA , Los Angeles, California 90095, United States
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29
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Miller DJ. Increasing the yield of atrial fibrillation detection in cryptogenic stroke using risk factor stratification: a more satisfying approach. Eur J Neurol 2015; 23:239-40. [PMID: 26662867 DOI: 10.1111/ene.12900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D J Miller
- Department of Neurology, Henry Ford Hospital, Stroke Division, Detroit, MI, USA.
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Adams SE, Robinson EJ, Miller DJ, Rizkallah PJ, Hallett MB, Allemann RK. Conformationally restricted calpain inhibitors. Chem Sci 2015; 6:6865-6871. [PMID: 28757975 PMCID: PMC5508670 DOI: 10.1039/c5sc01158b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
Oxidised α-mercaptoacrylic acid derivatives are potent conformationally restricted calpain-I inhibitors that mimic the endogenous inhibitor calpastatin.
The cysteine protease calpain-I is linked to several diseases and is therefore a valuable target for inhibition. Selective inhibition of calpain-I has proved difficult as most compounds target the active site and inhibit a broad spectrum of cysteine proteases as well as other calpain isoforms. Selective inhibitors might not only be potential drugs but should act as tools to explore the physiological and pathophysiological roles of calpain-I. α-Mercaptoacrylic acid based calpain inhibitors are potent, cell permeable and selective inhibitors of calpain-I and calpain-II. These inhibitors target the calcium binding domain PEF(S) of calpain-I and -II. Here X-ray diffraction analysis of co-crystals of PEF(S) revealed that the disulfide form of an α-mercaptoacrylic acid bound within a hydrophobic groove that is also targeted by a calpastatin inhibitory region and made a greater number of favourable interactions with the protein than the reduced sulfhydryl form. Measurement of the inhibitory potency of the α-mercaptoacrylic acids and X-ray crystallography revealed that the IC50 values decreased significantly on oxidation as a consequence of the stereo-electronic properties of disulfide bonds that restrict rotation around the S–S bond. Consequently, thioether analogues inhibited calpain-I with potencies similar to those of the free sulfhydryl forms of α-mercaptoacrylic acids.
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Affiliation(s)
- S E Adams
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , UK CF10 3AT . ; ; Tel: +44 (0) 29 2087 9014
| | - E J Robinson
- Institute of Infection & Immunology , School of Medicine , Heath Campus , Cardiff , UK CF14 4XN
| | - D J Miller
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , UK CF10 3AT . ; ; Tel: +44 (0) 29 2087 9014
| | - P J Rizkallah
- Institute of Infection & Immunology , School of Medicine , Heath Campus , Cardiff , UK CF14 4XN
| | - M B Hallett
- Institute of Infection & Immunology , School of Medicine , Heath Campus , Cardiff , UK CF14 4XN
| | - R K Allemann
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , UK CF10 3AT . ; ; Tel: +44 (0) 29 2087 9014
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Bertucci A, Forêt S, Ball EE, Miller DJ. Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals. Mol Ecol 2015. [PMID: 26198296 DOI: 10.1111/mec.13328] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
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Affiliation(s)
- A Bertucci
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
| | - S Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - E E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - D J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
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Miller DJ. Regulation of Sperm Function by Oviduct Fluid and the Epithelium: Insight into the Role of Glycans. Reprod Domest Anim 2015; 50 Suppl 2:31-9. [DOI: 10.1111/rda.12570] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 01/18/2023]
Affiliation(s)
- DJ Miller
- Department of Animal Sciences; University of Illinois; Urbana-Champaign IL USA
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Daigneault BW, McNamara KA, Purdy PH, Krisher RL, Knox RV, Rodriguez-Zas SL, Miller DJ. Enhanced fertility prediction of cryopreserved boar spermatozoa using novel sperm function assessment. Andrology 2015; 3:558-68. [PMID: 25914302 DOI: 10.1111/andr.12035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/14/2015] [Accepted: 03/02/2015] [Indexed: 11/28/2022]
Abstract
Due to reduced fertility, cryopreserved semen is seldom used for commercial porcine artificial insemination (AI). Predicting the fertility of individual frozen ejaculates for selection of higher quality semen prior to AI would increase overall success. Our objective was to test novel and traditional laboratory analyses to identify characteristics of cryopreserved spermatozoa that are related to boar fertility. Traditional post-thaw analyses of motility, viability, and acrosome integrity were performed on each ejaculate. In vitro fertilization, cleavage, and blastocyst development were also determined. Finally, spermatozoa-oviduct binding and competitive zona-binding assays were applied to assess sperm adhesion to these two matrices. Fertility of the same ejaculates subjected to laboratory assays was determined for each boar by multi-sire AI and defined as (i) the mean percentage of the litter sired and (ii) the mean number of piglets sired in each litter. Means of each laboratory evaluation were calculated for each boar and those values were applied to multiple linear regression analyses to determine which sperm traits could collectively estimate fertility in the simplest model. The regression model to predict the percent of litter sired by each boar was highly effective (p < 0.001, r(2) = 0.87) and included five traits; acrosome-compromised spermatozoa, percent live spermatozoa (0 and 60 min post-thaw), percent total motility, and the number of zona-bound spermatozoa. A second model to predict the number of piglets sired by boar was also effective (p < 0.05, r(2) = 0.57). These models indicate that the fertility of cryopreserved boar spermatozoa can be predicted effectively by including traditional and novel laboratory assays that consider functions of spermatozoa.
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Affiliation(s)
- B W Daigneault
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - K A McNamara
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - P H Purdy
- USDA-ARS-NCGRP-NAGP, Fort Collins, CO, USA
| | - R L Krisher
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA.,National Foundation for Fertility Research, Lone Tree, CO, USA
| | - R V Knox
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - S L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - D J Miller
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
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Yamaguchi M, Yu S, Qiao R, Weissmann F, Miller DJ, VanderLinden R, Brown NG, Frye JJ, Peters JM, Schulman BA. Structure of an APC3-APC16 complex: insights into assembly of the anaphase-promoting complex/cyclosome. J Mol Biol 2014; 427:1748-64. [PMID: 25490258 DOI: 10.1016/j.jmb.2014.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 11/14/2014] [Accepted: 11/15/2014] [Indexed: 01/05/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC/C assembly contains two subcomplexes: the "Platform" centers around a cullin-RING-like E3 ligase catalytic core; the "Arc Lamp" is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) proteins (APC7, APC3, APC6, and APC8) that homodimerize and stack with quasi-2-fold symmetry. Within the APC/C complex, APC3 serves as center for regulation. APC3's TPR motifs recruit substrate-binding coactivators, CDC20 and CDH1, via their C-terminal conserved Ile-Arg (IR) tail sequences. Human APC3 also binds APC16 and APC7 and contains a >200-residue loop that is heavily phosphorylated during mitosis, although the basis for APC3 interactions and whether loop phosphorylation is required for ubiquitination are unclear. Here, we map the basis for human APC3 assembly with APC16 and APC7, report crystal structures of APC3Δloop alone and in complex with the C-terminal domain of APC16, and test roles of APC3's loop and IR tail binding surfaces in APC/C-catalyzed ubiquitination. The structures show how one APC16 binds asymmetrically to the symmetric APC3 dimer and, together with biochemistry and prior data, explain how APC16 recruits APC7 to APC3, show how APC3's C-terminal domain is rearranged in the full APC/C assembly, and visualize residues in the IR tail binding cleft important for coactivator-dependent ubiquitination. Overall, the results provide insights into assembly, regulation, and interactions of TPR proteins and the APC/C.
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Affiliation(s)
- Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremiah J Frye
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105 USA.
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Vanarotti MS, Miller DJ, Guibao CD, Nourse A, Zheng JJ. Structural and mechanistic insights into the interaction between Pyk2 and paxillin LD motifs. J Mol Biol 2014; 426:3985-4001. [PMID: 25174335 DOI: 10.1016/j.jmb.2014.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/15/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022]
Abstract
Proline-rich tyrosine kinase 2 (Pyk2) is a member of the focal adhesion kinase (FAK) subfamily of cytoplasmic tyrosine kinases. The C-terminal Pyk2-focal adhesion targeting (FAT) domain binds to paxillin, an adhesion molecule. Paxillin has five leucine-aspartate (LD) motifs (LD1-LD5). Here, we show that the second LD motif of paxillin, LD2, interacts with Pyk2-FAT, similar to the known Pyk2-FAT/LD4 interaction. Both LD motifs can target two ligand binding sites on Pyk2-FAT. Interestingly, they also share similar binding affinity for Pyk2-FAT with preferential association to one site relative to the other. Nevertheless, the LD2-LD4 region of paxillin (paxillin(133-290)) binds to Pyk2-FAT as a 1:1 complex. However, our data suggest that the Pyk2-FAT and paxillin complex is dynamic and it appears to be a mixture of two distinct conformations of paxillin that almost equally compete for Pyk2-FAT binding. These studies provide insight into the underlying selectivity of paxillin for Pyk2 and FAK that may influence the differing behavior of these two closely related kinases in focal adhesion sites.
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Affiliation(s)
- Murugendra S Vanarotti
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cristina D Guibao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amanda Nourse
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jie J Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Abstract
Melt-spun NdFeB powders can be formed into a number of different types of permanent magnet for a variety of applications in electronics, automotive and clean technology industries. The melt-spinning process produces flake powder with a fine uniform array of nanoscale Nd2Fe14B grains. These powders can be net-shape formed into isotropic polymer-bonded magnets or hot formed into fully dense magnets. This paper discusses the influence of heavy rare earth elements and microstructure on the magnetic performance, thermal stability and material cost of NdFeB magnets. Evidence indicates that melt-spun nanocrystalline NdFeB magnets are less dependent on heavy rare earth elements for high-temperature performance than the alternative coarser-grained sintered NdFeB magnets. In particular, hot-pressed melt-spun magnets are an attractive low-cost solution for applications that require thermal stability up to 175-200 °C.
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Kamadurai HB, Qiu Y, Deng A, Harrison JS, Macdonald C, Actis M, Rodrigues P, Miller DJ, Souphron J, Lewis SM, Kurinov I, Fujii N, Hammel M, Piper R, Kuhlman B, Schulman BA. Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. eLife 2013; 2:e00828. [PMID: 23936628 PMCID: PMC3738095 DOI: 10.7554/elife.00828] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/20/2013] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT domain orienting the E3∼ubiquitin thioester bond for ligation, and restricting the location of the substrate-binding domain to prioritize target lysines for ubiquitination. The data allow visualization of an E2-to-E3-to-substrate ubiquitin transfer cascade, and show how HECT-specific ubiquitin interactions driving multiple reactions are repurposed by a major E3 conformational change to promote ligation. DOI:http://dx.doi.org/10.7554/eLife.00828.001 Ubiquitin is a small protein that can be covalently linked to other, ‘target’, proteins in a cell to influence their behavior. Ubiquitin can be linked to its targets either as single copies or as polyubiquitin chains in which several ubiquitin molecules are bound end-on-end to each other, with one end of the chain attached to the target protein. A multi-step cascade involving enzymes known as E1, E2, and E3 adds ubiquitin to its targets. These enzymes function in a manner like runners in a relay, with ubiquitin a baton that is passed from E1 to E2 to E3 to the target. The E3 enzyme is a ligase that catalyzes the formation of a new chemical bond between a ubiquitin and its target. There are approximately 600 different E3 enzymes in human cells that regulate a wide variety of target proteins. A major class of E3 enzymes, called HECT E3s, attaches ubiquitin to its targets in a unique two-step mechanism: the E2 enzymes covalently link a ubiquitin to a HECT E3 to form a complex that subsequently transfers the ubiquitin to its target protein. The ubiquitin is typically added to a particular amino acid, lysine, on the target protein, but the details of how HECT E3s execute this transfer are not well understood. To address this issue, Kamadurai et al. investigate how Rsp5, a HECT E3 ligase in yeast, attaches ubiquitin to a target protein called Sna3. All HECT E3s have a domain—the HECT domain—that catalyzes the transfer of ubiquitin to its target protein. This domain consists of two sub-structures: the C-lobe, which can receive ubiquitin from E2 and then itself become linked to ubiquitin, and the N-lobe. These lobes were previously thought to adopt various orientations relative to each other to deliver ubiquitin to sites on different target proteins (including to multiple lysines on a single target protein). Unexpectedly, Kamadurai et al. find that in order to transfer the ubiquitin to Sna3, Rsp5 adopts a discrete HECT domain architecture that creates an active site in which parts of the C-lobe and the N-lobe, which are normally separated, are brought together with a ubiquitin molecule. This architecture also provides a mechanism that dictates which substrate lysines can be ubiquitinated based on how accessible they are to this active site. The same regions of Rsp5 transfer ubiquitin to targets other than Sna3, suggesting that a uniform mechanism—which Kamadurai et al. show is conserved in two related human HECT E3 ligases—might transfer ubiquitin to all its targets. These studies therefore represent a significant step toward understanding how a major class of E3 enzymes modulates the functions of their targets. DOI:http://dx.doi.org/10.7554/eLife.00828.002
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Affiliation(s)
- Hari B Kamadurai
- Department of Structural Biology , St Jude Children's Research Hospital , Memphis , United States
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Richards ZT, Miller DJ, Wallace CC. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol 2013; 69:837-51. [PMID: 23850500 DOI: 10.1016/j.ympev.2013.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 06/18/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.
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Affiliation(s)
- Z T Richards
- Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.
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Duda DM, Olszewski JL, Schuermann JP, Kurinov I, Miller DJ, Nourse A, Alpi AF, Schulman BA. Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 2013; 21:1030-41. [PMID: 23707686 DOI: 10.1016/j.str.2013.04.019] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 12/20/2022]
Abstract
A distinct mechanism for ubiquitin (Ub) ligation has recently been proposed for the RING1-IBR-RING2 (RBR) family of E3s: an N-terminal RING1 domain recruits a thioester-linked intermediate complex between Ub and the E2 UbcH7, and a structurally distinct C-terminal RING2 domain displays a catalytic cysteine required for Ub ligation. To obtain insights into RBR E3s, we determined the crystal structure of the human homolog of Ariadne (HHARI), which reveals the individual RING1, IBR, and RING2 domains embedded in superdomains involving sequences specific to the Ariadne RBR subfamily. The central IBR is flanked on one side by RING1, which is exposed and binds UbcH7. On the other side, a C-terminal autoinhibitory "Ariadne domain" masks the RING2 active site. Insights into RBR E3 mechanisms are provided by structure-based mutations that indicate distinct steps of relief from autoinhibition, Ub transfer from E2 to HHARI, and ligation from the HHARI cysteine to a terminal acceptor.
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Affiliation(s)
- David M Duda
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Monda JK, Scott DC, Miller DJ, Lydeard J, King D, Harper JW, Bennett EJ, Schulman BA. Structural conservation of distinctive N-terminal acetylation-dependent interactions across a family of mammalian NEDD8 ligation enzymes. Structure 2013; 21:42-53. [PMID: 23201271 PMCID: PMC3786212 DOI: 10.1016/j.str.2012.10.013] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/20/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.
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Affiliation(s)
- Julie K. Monda
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Daniel C. Scott
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Darcie J. Miller
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - John Lydeard
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - David King
- HHMI Mass Spectrometry Laboratory, University of California, Berkeley CA 94720
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - Eric J. Bennett
- Department of Cell Biology, Harvard Medical School, Boston MA 02115,Division of Biological Sciences, University of California San Diego, La Jolla CA 92093
| | - Brenda A. Schulman
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
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Fang L, Jia Y, Miller DJ, Latimer ML, Xiao ZL, Welp U, Crabtree GW, Kwok WK. Catalyst-free growth of millimeter-long topological insulator Bi₂Se₃ nanoribbons and the observation of the π-Berry phase. Nano Lett 2012; 12:6164-9. [PMID: 23126261 DOI: 10.1021/nl302989v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We report the growth of single-crystalline Bi(2)Se(3) nanoribbons with lengths up to several millimeters via a catalyst-free physical vapor deposition method. Scanning transmission electron microscopy analysis reveals that the nanoribbons grow along the (112̅0) direction. We obtain a detailed characterization of the electronic structure of the Bi(2)Se(3) nanoribbons from measurements of Shubnikov-de Haas (SdH) quantum oscillations. Angular dependent magneto-transport measurements reveal a dominant two-dimensional contribution originating from surface states. The catalyst-free synthesis yields high-purity nanocrystals enabling the observation of a large number of SdH oscillation periods and allowing for an accurate determination of the π-Berry phase, one of the key features of Dirac fermions in topological insulators. The long-length nanoribbons open the possibility for fabricating multiple nanoelectronic devices on a single nanoribbon.
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Affiliation(s)
- L Fang
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60565, United States.
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Langenfeld JJ, Hawthorne SB, Miller DJ. Quantitative analysis of fuel-related hydrocarbons in surface water and wastewater samples by solid-phase microextraction. Anal Chem 2012; 68:144-55. [PMID: 21619230 DOI: 10.1021/ac950862w] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid-phase microextraction (SPME) parameters were examined on water contaminated with hydrocarbons including benzene and alkylbenzenes, n-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Absorption equilibration times ranged from several minutes for low molecular weight compounds such as benzene to 5 h for high molecular weight compounds such as benzo[a]pyrene. Under equilibrium conditions, SPME analysis with GC/FID was linear over 3-6 orders of magnitude, with linear correlation coefficients (r(2)) greater than 0.96. Experimentally determined FID detection limits ranged from ∼30 ppt (w/w hydrocarbon/sample water) for high molecular weight PAHs (e.g., MW > 202) to ∼1 ppb for low molecular weight aromatic hydrocarbons. Experimental distribution constants (K) were different with 100- and 7-μm poly(dimethylsiloxane) fibers, and poor correlations with previously published values suggest that K depends on the fiber coating thickness and the sorbent preparation method. The sensitivity of SPME analysis is not significantly enhanced by larger sample volumes, since increasing the water volume (e.g., from 1 to 100 mL) has little effect on the number of analyte molecules absorbed by the fiber, especially for compounds with K < 500. Water sample storage should utilize silanized glassware, since hydrocarbon losses up to 70% could be attributed to unsilanized glassware walls when samples were stored for 48 h. Hydrocarbon losses at part-per-billion concentrations also occurred with surface waters due to partitioning onto part-per-thousand concentrations of suspended solids. Quantitative determinations of aromatic and aliphatic hydrocarbons (e.g., in gasoline-contaminated water) can be performed using GC/MS with deuterated internal standard or standard addition calibration as long as the target components or standards had unique ions for quantitation or sufficient chromatographic resolution from interferences. SPME analysis gave good quantitative performance with surface waters having high suspended sediment contents, as well as with coal gasification wastewater which contained matrix organics at 10(6)-fold higher concentrations than the target aromatic hydrocarbons. Good agreement was obtained between a 45-min SPME and methylene chloride extraction for the determination of PAH concentrations in creosote-contaminated water, demonstrating that SPME is a useful technique for the rapid determination of hydrocarbons in complex water matrices.
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Affiliation(s)
- J J Langenfeld
- Energy and Environmental Research Center, P.O. Box 9018, University of North Dakota, Grand Forks, North Dakota 58202
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Miller DJ, Öberg H, Kaya S, Sanchez Casalongue H, Friebel D, Anniyev T, Ogasawara H, Bluhm H, Pettersson LGM, Nilsson A. Oxidation of Pt(111) under near-ambient conditions. Phys Rev Lett 2011; 107:195502. [PMID: 22181624 DOI: 10.1103/physrevlett.107.195502] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Indexed: 05/31/2023]
Abstract
The oxidation of Pt(111) at near-ambient O2 pressures has been followed in situ using x-ray photoelectron spectroscopy (XPS) and ex situ using x-ray absorption spectroscopy (XAS). Polarization-dependent XAS signatures at the O K edge reveal significant temperature- and pressure-dependent changes of the Pt-O interaction. Oxide growth commences via a PtO-like surface oxide that coexists with chemisorbed oxygen, while an ultrathin α-PtO2 trilayer is identified as the precursor to bulk oxidation. These results have important implications for understanding the chemical state of Pt in catalysis.
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Affiliation(s)
- D J Miller
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, California 94025, USA
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Levy O, Kaniewska P, Alon S, Eisenberg E, Karako-Lampert S, Bay LK, Reef R, Rodriguez-Lanetty M, Miller DJ, Hoegh-Guldberg O. Complex diel cycles of gene expression in coral-algal symbiosis. Science 2011; 331:175. [PMID: 21233378 DOI: 10.1126/science.1196419] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Circadian regulation of plant-animal endosymbioses is complicated by a diversity of internal and external cues. Here, we show that stress-related genes in corals are coupled to the circadian clock, anticipating major changes in the intracellular milieu. In this regard, numerous chaperones are "hard-wired" to the clock, effectively preparing the coral for the consequences of oxidative protein damage imposed by symbiont photosynthesis (when O(2) > 250% saturation), including synexpression of antioxidant genes being light-gated. Conversely, central metabolism appears to be regulated by the hypoxia-inducible factor system in coral. These results reveal the complexity of endosymbiosis as well as the plasticity regulation downstream of the circadian clock.
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Affiliation(s)
- O Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Wang J, Taherbhoy AM, Hunt HW, Seyedin SN, Miller DW, Miller DJ, Huang DT, Schulman BA. Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways. PLoS One 2010; 5:e15805. [PMID: 21209884 PMCID: PMC3012696 DOI: 10.1371/journal.pone.0015805] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 11/25/2010] [Indexed: 01/07/2023] Open
Abstract
Canonical ubiquitin-like proteins (UBLs) such as ubiquitin, Sumo, NEDD8, and ISG15 are ligated to targets by E1-E2-E3 multienzyme cascades. The Sumo cascade, conserved among all eukaryotes, regulates numerous biological processes including protein localization, transcription, DNA replication, and mitosis. Sumo conjugation is initiated by the heterodimeric Aos1-Uba2 E1 enzyme (in humans called Sae1-Uba2), which activates Sumo's C-terminus, binds the dedicated E2 enzyme Ubc9, and promotes Sumo C-terminal transfer between the Uba2 and Ubc9 catalytic cysteines. To gain insights into details of E1-E2 interactions in the Sumo pathway, we determined crystal structures of the C-terminal ubiquitin fold domain (ufd) from yeast Uba2 (Uba2(ufd)), alone and in complex with Ubc9. The overall structures of both yeast Uba2(ufd) and Ubc9 superimpose well on their individual human counterparts, suggesting conservation of fundamental features of Sumo conjugation. Docking the Uba2(ufd)-Ubc9 and prior full-length human Uba2 structures allows generation of models for steps in Sumo transfer from Uba2 to Ubc9, and supports the notion that Uba2 undergoes remarkable conformational changes during the reaction. Comparisons to previous structures from the NEDD8 cascade demonstrate that UBL cascades generally utilize some parallel E1-E2 interaction surfaces. In addition, the structure of the Uba2(ufd)-Ubc9 complex reveals interactions unique to Sumo E1 and E2. Comparison with a previous Ubc9-E3 complex structure demonstrates overlap between Uba2 and E3 binding sites on Ubc9, indicating that loading with Sumo and E3-catalyzed transfer to substrates are strictly separate steps. The results suggest mechanisms establishing specificity and order in Sumo conjugation cascades.
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Affiliation(s)
- Jing Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Asad M. Taherbhoy
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Harold W. Hunt
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Steven N. Seyedin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - David W. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Danny T. Huang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Brenda A. Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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Affiliation(s)
- D J Miller
- Department of Animal Sciences, University of Illinois, Urbana-Champaign 61801, USA.
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Nayar S, Collings GJ, Miller DJ, Bryars S, Cheshire AC. Uptake and resource allocation of ammonium and nitrate in temperate seagrasses Posidonia and Amphibolis. Mar Pollut Bull 2010; 60:1502-1511. [PMID: 20739251 DOI: 10.1016/j.marpolbul.2010.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 04/26/2010] [Accepted: 04/29/2010] [Indexed: 05/29/2023]
Abstract
Ecologically relevant estimates of seasonal variability in nitrogen uptake and allocation in two species of temperate seagrasses were obtained using in situ isotope-labelling approach. Significantly higher uptake rates of ammonium by leaves, roots and epiphytes of Amphibolis than Posidonia were observed. Overall, root uptake rates were lower than other components. Effect of season was not significant for leaves, roots or epiphytes of the two species. However, plankton uptake varied seasonally with higher rates in winter (0.98 mg N g(-1)D Wh(-1)). In contrast, nitrate uptake rates for various components were significantly affected by seasons. Uptake rates by plankton were highest ranging from 0.003 mg N g(-1)D Wh(-1) (summer, Amphibolis) to 0.69 mg N g(-1)DWh(-1) (winter, Posidonia). Uptake of nitrate by roots was negligible. Biotic uptake rates for nitrate were an order of magnitude slower than ammonium, demonstrating an affinity for ammonium over nitrate as a preferred inorganic nitrogen source. Adelaide coastal waters have lost over 5000 ha of seagrasses, much of this attributed to nutrient inputs from wastewater, industrial and stormwater. Managing these inputs into future requires better understanding of the fate of nutrients, particularly biological uptake. This study attempts to quantify uptake rates of nitrogen by seagrasses.
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Affiliation(s)
- S Nayar
- South Australian Research and Development Institute - Aquatic Sciences, West Beach, SA 5024, Australia.
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Miller DJ, Zhang YM, Subramanian C, Rock CO, White SW. Structural basis for the transcriptional regulation of membrane lipid homeostasis. Nat Struct Mol Biol 2010; 17:971-5. [PMID: 20639888 PMCID: PMC2935088 DOI: 10.1038/nsmb.1847] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 05/07/2010] [Indexed: 11/21/2022]
Abstract
DesT is a transcriptional repressor that regulates the genes which control the unsaturated:saturated fatty acid ratio available for membrane lipid synthesis. DesT bound to unsaturated acyl-CoA has a high affinity for its cognate palindromic DNA-binding site, whereas DesT bound to saturated acyl-CoA does not bind to this site. Structural analyses of the DesT–oleoyl-CoA–DNA and DesT–palmitoyl-CoA complexes reveal that acyl chain shape directly influences the packing of hydrophobic core residues within the DesT ligand-binding domain. These changes are propagated to the paired DNA-binding domains via conformational changes to modulate DNA binding. These structural interpretations are supported by the in vitro and in vivo characterization of site-directed mutants. The regulation of DesT by the unsaturated:saturated ratio of acyl chains rather than the concentration of a single ligand is a paradigm for understanding transcriptional regulation of membrane lipid homeostasis.
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Affiliation(s)
- Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Kamadurai HB, Souphron J, Scott DC, Duda DM, Miller DJ, Stringer D, Piper RC, Schulman BA. Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol Cell 2010; 36:1095-102. [PMID: 20064473 DOI: 10.1016/j.molcel.2009.11.010] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 09/01/2009] [Accepted: 09/23/2009] [Indexed: 01/25/2023]
Abstract
In E1-E2-E3 ubiquitin (Ub) conjugation cascades, the E2 first forms a transient E2 approximately Ub covalent complex and then interacts with an E3 for Ub transfer. For cascades involving E3s in the HECT class, Ub is transferred from an associated E2 to the acceptor cysteine in the HECT domain C lobe. To gain insights into this process, we determined the crystal structure of a complex between the HECT domain of NEDD4L and the E2 UbcH5B bearing a covalently linked Ub at its active site (UbcH5B approximately Ub). Noncovalent interactions between UbcH5B and the HECT N lobe and between Ub and the HECT domain C lobe lead to an overall compact structure, with the Ub C terminus sandwiched between UbcH5B and HECT domain active sites. The structure suggests a model for E2-to-HECT Ub transfer, in which interactions between a donor Ub and an acceptor domain constrain upstream and downstream enzymes for conjugation.
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Affiliation(s)
- Hari B Kamadurai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Zhuang M, Calabrese MF, Liu J, Waddell MB, Nourse A, Hammel M, Miller DJ, Walden H, Duda DM, Seyedin SN, Hoggard T, Harper JW, White KP, Schulman BA. Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. Mol Cell 2009; 36:39-50. [PMID: 19818708 DOI: 10.1016/j.molcel.2009.09.022] [Citation(s) in RCA: 354] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 07/31/2009] [Accepted: 09/11/2009] [Indexed: 10/20/2022]
Abstract
In the largest E3 ligase subfamily, Cul3 binds a BTB domain, and an associated protein-interaction domain such as MATH recruits substrates for ubiquitination. Here, we present biochemical and structural analyses of the MATH-BTB protein, SPOP. We define a SPOP-binding consensus (SBC) and determine structures revealing recognition of SBCs from the phosphatase Puc, the transcriptional regulator Ci, and the chromatin component MacroH2A. We identify a dimeric SPOP-Cul3 assembly involving a conserved helical structure C-terminal of BTB domains, which we call "3-box" due to its facilitating Cul3 binding and its resemblance to F-/SOCS-boxes in other cullin-based E3s. Structural flexibility between the substrate-binding MATH and Cul3-binding BTB/3-box domains potentially allows a SPOP dimer to engage multiple SBCs found within a single substrate, such as Puc. These studies provide a molecular understanding of how MATH-BTB proteins recruit substrates to Cul3 and how their dimerization and conformational variability may facilitate avid interactions with diverse substrates.
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Affiliation(s)
- Min Zhuang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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