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Balasco N, Esposito L, Smaldone G, Salvatore M, Vitagliano L. A Comprehensive Analysis of the Structural Recognition between KCTD Proteins and Cullin 3. Int J Mol Sci 2024; 25:1881. [PMID: 38339159 PMCID: PMC10856315 DOI: 10.3390/ijms25031881] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
KCTD ((K)potassium Channel Tetramerization Domain-containing) proteins constitute an emerging class of proteins involved in fundamental physio-pathological processes. In these proteins, the BTB domain, which represents the defining element of the family, may have the dual role of promoting oligomerization and favoring functionally important partnerships with different interactors. Here, by exploiting the potential of recently developed methodologies for protein structure prediction, we report a comprehensive analysis of the interactions of all KCTD proteins with their most common partner Cullin 3 (Cul3). The data here presented demonstrate the impressive ability of this approach to discriminate between KCTDs that interact with Cul3 and those that do not. Indeed, reliable and stable models of the complexes were only obtained for the 15 members of the family that are known to interact with Cul3. The generation of three-dimensional models for all KCTD-Cul3 complexes provides interesting clues on the determinants of the structural basis of this partnership as clear structural differences emerged between KCTDs that bind or do not bind Cul3. Finally, the availability of accurate three-dimensional models for KCTD-Cul3 interactions may be valuable for the ad hoc design and development of compounds targeting specific KCTDs that are involved in several common diseases.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Luciana Esposito
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | | | | | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
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2
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Knecht W, Fisher SZ, Lou J, Sele C, Ma S, Rasmussen AA, Pinotsis N, Kozielski F. Oligomeric State of β-Coronavirus Non-Structural Protein 10 Stimulators Studied by Small Angle X-ray Scattering. Int J Mol Sci 2023; 24:13649. [PMID: 37686452 PMCID: PMC10563069 DOI: 10.3390/ijms241713649] [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: 06/29/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The β-coronavirus family, encompassing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Severe Acute Respiratory Syndrome Coronavirus (SARS), and Middle East Respiratory Syndrome Coronavirus (MERS), has triggered pandemics within the last two decades. With the possibility of future pandemics, studying the coronavirus family members is necessary to improve knowledge and treatment. These viruses possess 16 non-structural proteins, many of which play crucial roles in viral replication and in other vital functions. One such vital protein is non-structural protein 10 (nsp10), acting as a pivotal stimulator of nsp14 and nsp16, thereby influencing RNA proofreading and viral RNA cap formation. Studying nsp10 of pathogenic coronaviruses is central to unraveling its multifunctional roles. Our study involves the biochemical and biophysical characterisation of full-length nsp10 from MERS, SARS and SARS-CoV-2. To elucidate their oligomeric state, we employed a combination of Multi-detection Size exclusion chromatography (Multi-detection SEC) with multi-angle static light scattering (MALS) and small angle X-ray scattering (SAXS) techniques. Our findings reveal that full-length nsp10s primarily exist as monomers in solution, while truncated versions tend to oligomerise. SAXS experiments reveal a globular shape for nsp10, a trait conserved in all three coronaviruses, although MERS nsp10, diverges most from SARS and SARS-CoV-2 nsp10s. In summary, unbound nsp10 proteins from SARS, MERS, and SARS-CoV-2 exhibit a globular and predominantly monomeric state in solution.
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Affiliation(s)
- Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - S. Zoë Fisher
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
- European Spallation Source ERIC, P.O. Box 176, 22100 Lund, Sweden
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
| | - Céleste Sele
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
| | - Anna Andersson Rasmussen
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
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Wang Z, Ding W, Ruan M, Liu Y, Yang J, Zhang H, Shen B, Wang J, Li Y. NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes. Biomolecules 2023; 13:biom13050719. [PMID: 37238591 DOI: 10.3390/biom13050719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
The mitochondrial pyruvate carrier (Mpc) plays an indispensable role in the transport of pyruvates across the mitochondrial inner membrane. Despite the two distinct homologous proteins, Mpc1 and Mpc2, were identified in 2012, there are still controversies on the basic functional units and oligomeric state of Mpc complexes. In this study, yeast Mpc1 and Mpc2 proteins were expressed in a prokaryotic heterologous system. Both homo- and hetero-dimers were successfully reconstituted in mixed detergents. Interactions among Mpc monomers were recorded utilizing paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) methods. By single-channel patch-clamp assays, we discovered that both the Mpc1-Mpc2 hetero-dimer and Mpc1 homo-dimer are able to transport K+ ions. Furthermore, the Mpc1-Mpc2 hetero-dimer demonstrated the ability to transport pyruvates, at a rate significantly higher than that of the Mpc1 homo-dimer, indicating that it could be the basic functional unit of Mpc complexes. Our findings provide valuable insights for further structural determination and the study of the transport mechanism of Mpc complexes.
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Affiliation(s)
- Zhen Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
| | - Wen Ding
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Maosen Ruan
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yong Liu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
| | - Jing Yang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Huiqin Zhang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yunyan Li
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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4
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Žerovnik E. Human stefin B: from its structure, folding, and aggregation to its function in health and disease. Front Mol Neurosci 2022; 15:1009976. [PMID: 36340691 PMCID: PMC9634419 DOI: 10.3389/fnmol.2022.1009976] [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: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2024] Open
Abstract
Mutations in the gene for human stefin B (cystatin B) cause progressive myoclonic epilepsy type 1 (EPM1), a neurodegenerative disorder. The most common change is dodecamer repeats in the promoter region of the gene, though missense and frameshift mutations also appear. Human stefin B primarily acts as a cysteine cathepsin inhibitor, and it also exhibits alternative functions. It plays a protective role against oxidative stress, likely via reducing mitochondrial damage and thus generating fewer mitochondrial reactive oxygen species (ROS). Accordingly, lack of stefin B results in increased inflammation and NLRP3 inflammasome activation, producing more ROS. The protein is cytosolic but also has an important role in the nucleus, where it prevents cleavage of the N terminal part of histone 3 by inhibiting cathepsins L and B and thus regulates transcription and cell cycle. Furthermore, it has been shown that stefin B is oligomeric in cells and that it has a specific role in the physiology of the synapse and in vesicular transport. On the basis of my research team's data on the structure, folding, and aggregation of stefin B, we have proposed that it might regulate proteostasis, possessing a chaperone-like function. In this review, I synthesize these observations and derive some conclusions on possible sources of EPM1 pathology. The interaction partners of stefin B and other gene mutations leading to EPM1-like pathology are discussed and common pathways are pinpointed.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
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5
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Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 2021; 89:1800-1823. [PMID: 34453465 PMCID: PMC8616814 DOI: 10.1002/prot.26222] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 05/20/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
Abstract
We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.
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Affiliation(s)
- Marc F Lensink
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
| | - Guillaume Brysbaert
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
| | - Théo Mauri
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
| | - Nurul Nadzirin
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | - Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Bin Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Guangbo Yang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Ming Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Hang Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xufeng Lu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Raj S Roy
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Farhan Quadir
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Jian Liu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Anna Antoniak
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Artur Giełdoń
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Mateusz Kogut
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland
| | | | | | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Patryk A Wesołowski
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Karolina Zięba
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Eiichiro Ichiishi
- International University of Health and Welfare Hospital (IUHW Hospital), Nasushiobara City, Japan
| | - Ameya Harmalkar
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey J Gray
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Francesco Ambrosetti
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Rodrigo Vargas Honorato
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Zuzana Jandova
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Brian Jiménez-García
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Panagiotis I Koukos
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Siri Van Keulen
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Charlotte W Van Noort
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Manon Réau
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Jorge Roel-Touris
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
- Innopolis University, Russia
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Andrey Alekseenko
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
- Institute of Computer-Aided Design of the Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Israel Desta
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Ryota Ashizawa
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Zhuyezi Sun
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Usman Ghani
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Nasser Hashemi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Mireia Rosell
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Luis A Rodríguez-Lumbreras
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Juan Fernandez-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Sergei Grudinin
- Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
| | - Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Peicong Lin
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Tunde Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Tsukasa Nakamura
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yuya Hanazono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, Japan
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
| | - Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
| | - Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
| | - Ghazaleh Taherzadeh
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA
| | | | - Zhen Cao
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Romina Oliva
- University of Naples "Parthenope", Napoli, Italy
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
| | - Shaowen Zhu
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
| | - Taeyong Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyeonuk Woo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jinsol Yang
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Sohee Kwon
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jonghun Won
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Yasuomi Kiyota
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
| | | | - Yoshiki Harada
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
| | | | - Petras J Kundrotas
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Amar Singh
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Ilya A Vakser
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Justas Dapkūnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rui Duan
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Shuang Zhang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Xiaoqin Zou
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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6
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Tam C, Zhang KYJ. FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins. Proteins 2021; 90:732-746. [PMID: 34676905 DOI: 10.1002/prot.26270] [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: 05/13/2021] [Revised: 09/19/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Fluorescent protein (FP) design is among the challenging protein design problems due to the tradeoffs among multiple properties to be optimized. Despite the accumulated efforts in design and characterization, progress has been slow in gaining a full understanding of sequence-property relationships to tackle the multiobjective design problem in FPs. In this study, we approach this problem by developing FPredX, a collection of gradient-boosted decision tree models, which mapped FP sequences to four major design targets of FPs, including excitation maximum, emission maximum, brightness, and oligomeric state. By training using one-hot encoded multiple aligned sequences with hyperparameters optimization in each model, FPredX models showed excellent prediction performance for all target properties compared with existing methods. We further interpreted the FPredX models by comparing the importance of positions along the aligned FP sequence to the predictive performance and suggested positions, which showed differential importance deemed by FPredX models to the prediction of each target property.
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Affiliation(s)
- Chunlai Tam
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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7
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Harding SE. Analytical Ultracentrifugation as a Matrix-Free Probe for the Study of Kinase Related Cellular and Bacterial Membrane Proteins and Glycans. Molecules 2021; 26:molecules26196080. [PMID: 34641622 PMCID: PMC8512968 DOI: 10.3390/molecules26196080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and association/dissociation constants for self-association, and assay of ligand binding of kinase related membrane proteins and glycans. It has the great property of being matrix free-providing separation and analysis of macromolecular species without the need of a separation matrix or membrane or immobilisation onto a surface. This short review-designed for the non-hydrodynamic expert-examines the potential of modern sedimentation velocity and sedimentation equilibrium and the challenges posed for these molecules particularly those which have significant cytoplasmic or extracellular domains in addition to the transmembrane region. These different regions can generate different optimal requirements in terms of choice of the appropriate solvent (aqueous/detergent). We compare how analytical ultracentrifugation has contributed to our understanding of two kinase related cellular or bacterial protein/glycan systems (i) the membrane erythrocyte band 3 protein system-studied in aqueous and detergent based solvent systems-and (ii) what it has contributed so far to our understanding of the enterococcal VanS, the glycan ligand vancomycin and interactions of vancomycin with mucins from the gastrointestinal tract.
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Affiliation(s)
- Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK;
- Science for Cultural History (SciCult) Laboratory, Kulturhistorisk Museum, University of Oslo, St. Olavs Plass, 0130 Oslo, Norway
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8
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Renard K, Byrne B. Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins. Int J Mol Sci 2021; 22:9026. [PMID: 34445730 DOI: 10.3390/ijms22169026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
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9
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Espinoza-Corral R, Schwenkert S, Lundquist PK. Molecular changes of Arabidopsis thaliana plastoglobules facilitate thylakoid membrane remodeling under high light stress. Plant J 2021; 106:1571-1587. [PMID: 33783866 DOI: 10.1111/tpj.15253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 11/02/2020] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 05/21/2023]
Abstract
Plants require rapid responses to adapt to environmental stresses. This includes dramatic changes in the size and number of plastoglobule lipid droplets within chloroplasts. Although the morphological changes of plastoglobules are well documented, little is known about the corresponding molecular changes. To address this gap, we have compared the quantitative proteome, oligomeric state, prenyl-lipid content and kinase activities of Arabidopsis thaliana plastoglobules under unstressed and 5-day light-stressed conditions. Our results show a specific recruitment of proteins related to leaf senescence and jasmonic acid biosynthesis under light stress, and identify nearly half of the plastoglobule proteins in high native molecular weight masses. Additionally, a specific increase in plastoglobule carotenoid abundance under the light stress was consistent with enhanced thylakoid disassembly and leaf senescence, supporting a specific role for plastoglobules in senescence and thylakoid remodeling as an intermediate storage site for photosynthetic pigments. In vitro kinase assays of isolated plastoglobules demonstrated kinase activity towards multiple target proteins, which was more pronounced in the plastoglobules of unstressed than light-stressed leaf tissue, and which was diminished in plastoglobules of the abc1k1/abc1k3 double-mutant. These results strongly suggest that plastoglobule-localized ABC1 kinases hold endogenous kinase activity, as these were the only known or putative kinases identified in the isolated plastoglobules by deep bottom-up proteomics. Collectively, our study reveals targeted changes to the protein and prenyl-lipid composition of plastoglobules under light stress that present strategies by which plastoglobules appear to facilitate stress adaptation within chloroplasts.
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Affiliation(s)
- Roberto Espinoza-Corral
- Department of Biochemistry and Molecular Biology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Serena Schwenkert
- Department I, Plant Biochemistry, Ludwig Maximilians University Munich, Großhadernerstr. 2-4, Planegg-Martinsried, 82152, Germany
| | - Peter K Lundquist
- Department of Biochemistry and Molecular Biology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
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10
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Kunji ERS, Ruprecht JJ. The mitochondrial ADP/ATP carrier exists and functions as a monomer. Biochem Soc Trans 2020; 48:1419-32. [PMID: 32725219 DOI: 10.1042/BST20190933] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
For more than 40 years, the oligomeric state of members of the mitochondrial carrier family (SLC25) has been the subject of debate. Initially, the consensus was that they were dimeric, based on the application of a large number of different techniques. However, the structures of the mitochondrial ADP/ATP carrier, a member of the family, clearly demonstrated that its structural fold is monomeric, lacking a conserved dimerisation interface. A re-evaluation of previously published data, with the advantage of hindsight, concluded that technical errors were at the basis of the earlier dimer claims. Here, we revisit this topic, as new claims for the existence of dimers of the bovine ADP/ATP carrier have emerged using native mass spectrometry of mitochondrial membrane vesicles. However, the measured mass does not agree with previously published values, and a large number of post-translational modifications are proposed to account for the difference. Contrarily, these modifications are not observed in electron density maps of the bovine carrier. If they were present, they would interfere with the structure and function of the carrier, including inhibitor and substrate binding. Furthermore, the reported mass does not account for three tightly bound cardiolipin molecules, which are consistently observed in other studies and are important stabilising factors for the transport mechanism. The monomeric carrier has all of the required properties for a functional transporter and undergoes large conformational changes that are incompatible with a stable dimerisation interface. Thus, our view that the native mitochondrial ADP/ATP carrier exists and functions as a monomer remains unaltered.
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11
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Nguyen GTT, Sutinen A, Raasakka A, Muruganandam G, Loris R, Kursula P. Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights into Ligand Binding and Clustering of Disease Mutations. Front Mol Biosci 2021; 7:631232. [PMID: 33585569 PMCID: PMC7873046 DOI: 10.3389/fmolb.2020.631232] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neurological disorders. Despite the common involvement of ganglioside-induced differentiation-associated protein 1 (GDAP1) in CMT, the protein structure and function, as well as the pathogenic mechanisms, remain unclear. We determined the crystal structure of the complete human GDAP1 core domain, which shows a novel mode of dimerization within the glutathione S-transferase (GST) family. The long GDAP1-specific insertion forms an extended helix and a flexible loop. GDAP1 is catalytically inactive toward classical GST substrates. Through metabolite screening, we identified a ligand for GDAP1, the fatty acid hexadecanedioic acid, which is relevant for mitochondrial membrane permeability and Ca2+ homeostasis. The fatty acid binds to a pocket next to a CMT-linked residue cluster, increases protein stability, and induces changes in protein conformation and oligomerization. The closest homologue of GDAP1, GDAP1L1, is monomeric in its full-length form. Our results highlight the uniqueness of GDAP1 within the GST family and point toward allosteric mechanisms in regulating GDAP1 oligomeric state and function.
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Affiliation(s)
- Giang Thi Tuyet Nguyen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Arne Raasakka
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Biomedicine, University of Bergen, Bergen, Norway
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12
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Georgescauld F, Song Y, Dautant A. Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Int J Mol Sci 2020; 21:E6779. [PMID: 32947863 DOI: 10.3390/ijms21186779] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/29/2022] Open
Abstract
Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Monomers are functionally independent from each other inside NDPK complexes and the nucleoside kinase catalytic mechanism involves transient phosphorylation of the conserved catalytic histidine. To be active, monomers must assemble into conserved head to tail dimers, which further assemble into hexamers or tetramers. The interfaces between these oligomeric states are very different but, surprisingly, the assembly structure barely affects the catalytic efficiency of the enzyme. While it has been shown that assembly into hexamers induces full formation of the catalytic site and stabilizes the complex, it is unclear why assembly into tetramers is required for function. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. However, we still lack the high resolution structural data of NDPK in complex with different partners, which is necessary for deciphering the mechanism of these diverse functions. In this review we discuss advances in the structure, folding and stability of NDPKs.
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13
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Lourenço RF, Saurabh S, Herrmann J, Wakatsuki S, Shapiro L. The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA. mBio 2020; 11:e00448-20. [PMID: 32518183 DOI: 10.1128/mBio.00448-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacteria organize their genetic material in a structure called the nucleoid, which needs to be compact to fit inside the cell and, at the same time, dynamic to allow high rates of replication and transcription. Nucleoid-associated proteins (NAPs) play a pivotal role in this process, so their detailed characterization is crucial for our understanding of DNA organization into bacterial cells. Even though NAPs affect DNA-related processes differently, all of them have to oligomerize and bind DNA for their function. The significance of this study is the identification of structural elements involved in the oligomerization and DNA binding of a newly discovered NAP in C. crescentus and the demonstration that structural elements are conserved in evolutionarily distant and functionally distinct NAPs. Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA.
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14
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Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Subraman SRMV, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, de Beauchêne IC, Maigret B, Devignes MD, Echartea MER, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Merideth BR, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 2019; 87:1200-1221. [PMID: 31612567 PMCID: PMC7274794 DOI: 10.1002/prot.25838] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
Abstract
We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
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Affiliation(s)
- Marc F. Lensink
- University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Guillaume Brysbaert
- University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nurul Nadzirin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Tereza Gerguri
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Elodie Laine
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France
| | - Alessandra Carbone
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France
- Institut Universitaire de France (IUF), Paris, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Ran-Ran Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xi-Ming Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Hang Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Miriam Eisenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Emilia Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland
| | | | - Paweł Krupa
- Polish Academy of Sciences, Institute of Physics, Warsaw, Poland
| | | | - Łukasz Golon
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea
| | | | - Guillaume Pagès
- Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France
| | | | - Maria Kadukova
- Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mireia Rosell
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain
| | - Luis A. Rodríguez-Lumbreras
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain
| | | | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | | | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Woong-Hee Shin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Tunde Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | | | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | - Dima Kozakov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - Kathryn Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Dzmitry Padhorny
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Israel Desta
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Mikhail Ignatov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Sergey Kotelnikov
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Iain H. Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | | | | | | | | | - Didier Barradas-Bautista
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Zhen Cao
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University of Naples “Parthenope”, Napoli, Italy
| | - Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas
| | - Minkyung Baek
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Taeyong Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyeonuk Woo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Merav Braitbard
- Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lirane Bitton
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Scheidman-Duhovny
- Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Justas Dapkūnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Petras J. Kundrotas
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Saveliy Belkin
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Devlina Chakravarty
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Varsha D. Badal
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Ilya A. Vakser
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Thom Vreven
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sweta Vangaveti
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Tyler Borrman
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Zhiping Weng
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Johnathan D. Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Rui Duan
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Jie Hou
- Department of Computer Science, University of Missouri, Columbia, Missouri
| | - Benjamin Ryan Merideth
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
- Informatics Institute, University of Missouri, Columbia, Missouri
| | - Zhiwei Ma
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, Columbia, Missouri
- Informatics Institute, University of Missouri, Columbia, Missouri
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
- Informatics Institute, University of Missouri, Columbia, Missouri
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Panagiotis I. Koukos
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Jorge Roel-Touris
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Francesco Ambrosetti
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Cunliang Geng
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Jörg Schaarschmidt
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mikael E. Trellet
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Adrien S. J. Melquiond
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Li Xue
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Brian Jiménez-García
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Charlotte W. van Noort
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Rodrigo V. Honorato
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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15
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Tavoulari S, Thangaratnarajah C, Mavridou V, Harbour ME, Martinou JC, Kunji ER. The yeast mitochondrial pyruvate carrier is a hetero-dimer in its functional state. EMBO J 2019; 38:e100785. [PMID: 30979775 PMCID: PMC6517818 DOI: 10.15252/embj.2018100785] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 09/25/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 02/02/2023] Open
Abstract
The mitochondrial pyruvate carrier (MPC) is critical for cellular homeostasis, as it is required in central metabolism for transporting pyruvate from the cytosol into the mitochondrial matrix. MPC has been implicated in many diseases and is being investigated as a drug target. A few years ago, small membrane proteins, called MPC1 and MPC2 in mammals and Mpc1, Mpc2 and Mpc3 in yeast, were proposed to form large protein complexes responsible for this function. However, the MPC complexes have never been isolated and their composition, oligomeric state and functional properties have not been defined. Here, we identify the functional unit of MPC from Saccharomyces cerevisiae In contrast to earlier hypotheses, we demonstrate that MPC is a hetero-dimer, not a multimeric complex. When not engaged in hetero-dimers, the yeast Mpc proteins can also form homo-dimers that are, however, inactive. We show that the earlier described substrate transport properties and inhibitor profiles are embodied by the hetero-dimer. This work provides a foundation for elucidating the structure of the functional complex and the mechanism of substrate transport and inhibition.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Vasiliki Mavridou
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Edmund Rs Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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16
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Batista FA, Bosch SS, Butzloff S, Lunev S, Meissner KA, Linzke M, Romero AR, Wang C, Müller IB, Dömling ASS, Groves MR, Wrenger C. Oligomeric protein interference validates druggability of aspartate interconversion in Plasmodium falciparum. Microbiologyopen 2019; 8:e00779. [PMID: 30821109 PMCID: PMC6612543 DOI: 10.1002/mbo3.779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
The appearance of multi-drug resistant strains of malaria poses a major challenge to human health and validated drug targets are urgently required. To define a protein's function in vivo and thereby validate it as a drug target, highly specific tools are required that modify protein function with minimal cross-reactivity. While modern genetic approaches often offer the desired level of target specificity, applying these techniques is frequently challenging-particularly in the most dangerous malaria parasite, Plasmodium falciparum. Our hypothesis is that such challenges can be addressed by incorporating mutant proteins within oligomeric protein complexes of the target organism in vivo. In this manuscript, we provide data to support our hypothesis by demonstrating that recombinant expression of mutant proteins within P. falciparum leverages the native protein oligomeric state to influence protein function in vivo, thereby providing a rapid validation of potential drug targets. Our data show that interference with aspartate metabolism in vivo leads to a significant hindrance in parasite survival and strongly suggest that enzymes integral to aspartate metabolism are promising targets for the discovery of novel antimalarials.
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Affiliation(s)
- Fernando A. Batista
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Sabine Butzloff
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Sergey Lunev
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Kamila A. Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Atilio R. Romero
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Chao Wang
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Ingrid B. Müller
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Alexander S. S. Dömling
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Matthew R. Groves
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
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17
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Bubić A, Mrnjavac N, Stuparević I, Łyczek M, Wielgus-Kutrowska B, Bzowska A, Luić M, Leščić Ašler I. In the quest for new targets for pathogen eradication: the adenylosuccinate synthetase from the bacterium Helicobacter pylori. J Enzyme Inhib Med Chem 2018; 33:1405-1414. [PMID: 30191734 PMCID: PMC6136348 DOI: 10.1080/14756366.2018.1506773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adenylosuccinate synthetase (AdSS) is an enzyme at regulatory point of purine metabolism. In pathogenic organisms which utilise only the purine salvage pathway, AdSS asserts itself as a promising drug target. One of these organisms is Helicobacter pylori, a wide-spread human pathogen involved in the development of many diseases. The rate of H. pylori antibiotic resistance is on the increase, making the quest for new drugs against this pathogen more important than ever. In this context, we describe here the properties of H. pylori AdSS. This enzyme exists in a dimeric active form independently of the presence of its ligands. Its narrow stability range and pH-neutral optimal working conditions reflect the bacterium’s high level of adaptation to its living environment. Efficient inhibition of H. pylori AdSS with hadacidin and adenylosuccinate gives hope of finding novel drugs that aim at eradicating this dangerous pathogen.
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Affiliation(s)
- Ante Bubić
- a Division of Physical Chemistry , Ruđer Bošković Institute , Zagreb , Croatia
| | - Natalia Mrnjavac
- a Division of Physical Chemistry , Ruđer Bošković Institute , Zagreb , Croatia
| | - Igor Stuparević
- b Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology , University of Zagreb , Zagreb , Croatia
| | - Marta Łyczek
- c Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Warsaw , Poland.,d Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology , University of Warsaw , Warsaw , Poland
| | - Beata Wielgus-Kutrowska
- c Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Warsaw , Poland
| | - Agnieszka Bzowska
- c Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Warsaw , Poland
| | - Marija Luić
- a Division of Physical Chemistry , Ruđer Bošković Institute , Zagreb , Croatia
| | - Ivana Leščić Ašler
- a Division of Physical Chemistry , Ruđer Bošković Institute , Zagreb , Croatia
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18
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Chen W, Dev J, Mezhyrova J, Pan L, Piai A, Chou JJ. The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure 2018; 26:627-634.e4. [PMID: 29551287 PMCID: PMC5884736 DOI: 10.1016/j.str.2018.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 12/07/2017] [Revised: 01/24/2018] [Accepted: 02/09/2018] [Indexed: 01/14/2023]
Abstract
The p7 protein of the hepatitis C virus (HCV) can oligomerize in membrane to form cation channels. Previous studies showed that the channel assembly in detergent micelles adopts a unique flower-shaped oligomer, but the unusual architecture also presented problems for understanding how this viroporin resides in the membrane. Moreover, the oligomeric state of p7 remains controversial, as both hexamer and heptamer have been proposed. Here we address the above issues using p7 reconstituted in bicelles that mimic a lipid bilayer. We found, using a recently developed oligomer-labeling method, that p7 forms hexamers in the bicelles. Solvent paramagnetic relaxation enhancement analyses showed that the bilayer thickness around the HCV ion channel is substantially smaller than expected, and thus a significant portion of the previously assigned membrane-embedded region is solvent exposed. Our study provides an effective approach for characterizing the transmembrane partition of small ion channels in near lipid bilayer environment.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jyoti Dev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Liqiang Pan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, China.
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19
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Charoenwattanasatien R, Tanaka H, Zinzius K, Hochmal AK, Mutoh R, Yamamoto D, Hippler M, Kurisu G. X-ray crystallographic and high-speed AFM studies of peroxiredoxin 1 from Chlamydomonas reinhardtii. Acta Crystallogr F Struct Biol Commun 2018; 74:86-91. [PMID: 29400317 PMCID: PMC5947678 DOI: 10.1107/s2053230x17018507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 11/10/2022] Open
Abstract
Peroxiredoxins (PRXs) are a group of antioxidant enzymes that are found in all organisms, including plants and green algae. The 2-Cys PRX from Chlamydomonas reinhardtii (CrPRX1) is a chloroplast-localized protein that is critical for clearing reactive oxygen species in chloroplasts. CrPRX1 is reduced by thioredoxins or calredoxin (CrCRX), a recently identified calcium-dependent redox protein. The molecular interaction between PRXs and thioredoxin/CrCRX is functionally important, but discussion has been limited owing to a lack of structural information on CrPRX1, especially regarding its oligomeric state. In this study, high-speed atomic force microscopy (HS-AFM) images of CrPRX1 and an X-ray crystallographic analysis have enabled examination of the oligomeric state of CrPRX1. Diffraction data from a crystal of the Cys174Ser mutant of CrPRX1 indicate the existence of noncrystallographic fivefold symmetry. HS-AFM images of CrPRX1 further show that CrPRX1 particles form rings with pentagonal rotational symmetry. On the basis of these findings, the oligomeric state of CrPRX1 is discussed and it is concluded that this PRX exists in a ring-shaped decameric form comprising a pentamer of dimers.
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Affiliation(s)
- Ratana Charoenwattanasatien
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Karen Zinzius
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Ana K. Hochmal
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Risa Mutoh
- Faculty of Science, Fukuoka University, Nanakuma, Jyonan-ku, Fukuoka 814-0180, Japan
| | - Daisuke Yamamoto
- Faculty of Science, Fukuoka University, Nanakuma, Jyonan-ku, Fukuoka 814-0180, Japan
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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20
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Blackburn MR, Hubbard C, Kiessling V, Bi Y, Kloss B, Tamm LK, Zimmer J. Distinct reaction mechanisms for hyaluronan biosynthesis in different kingdoms of life. Glycobiology 2018; 28:108-121. [PMID: 29190396 PMCID: PMC6192386 DOI: 10.1093/glycob/cwx096] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/17/2017] [Accepted: 11/22/2017] [Indexed: 12/19/2022] Open
Abstract
Hyaluronan (HA) is an acidic high molecular weight cell surface polysaccharide ubiquitously expressed by vertebrates, some pathogenic bacteria and even viruses. HA modulates many essential physiological processes and is implicated in numerous pathological conditions ranging from autoimmune diseases to cancer. In various pathogens, HA functions as a non-immunogenic surface polymer that reduces host immune responses. It is a linear polymer of strictly alternating glucuronic acid and N-acetylglucosamine units synthesized by HA synthase (HAS), a membrane-embedded family-2 glycosyltransferase. The enzyme synthesizes HA and secretes the polymer through a channel formed by its own membrane-integrated domain. To reveal how HAS achieves these tasks, we determined the biologically functional units of bacterial and viral HAS in a lipid bilayer environment by co-immunoprecipitation, single molecule fluorescence photobleaching, and site-specific cross-linking analyses. Our results demonstrate that bacterial HAS functions as an obligate homo-dimer with two functional HAS copies required for catalytic activity. In contrast, the viral enzyme, closely related to vertebrate HAS, functions as a monomer. Using site-specific cross-linking, we identify the dimer interface of bacterial HAS and show that the enzyme uses a reaction mechanism distinct from viral HAS that necessitates a dimeric assembly.
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Affiliation(s)
- Matthew R Blackburn
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Caitlin Hubbard
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Yunchen Bi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis (COMPPÅ), New York Structural Biology Center (NYSBC), 89 Convent Avenue, New York, NY 10027, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
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21
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Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. The challenge of modeling protein assemblies: the CASP12-CAPRI experiment. Proteins 2017; 86 Suppl 1:257-273. [PMID: 29127686 DOI: 10.1002/prot.25419] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [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: 07/18/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 12/18/2022]
Abstract
We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP-CAPRI protein assembly prediction experiment. These targets comprised 12 homo-oligomers and 3 hetero-complexes. The bulk of the analysis focuses on 10 targets (of CAPRI Round 37), which included all 3 hetero-complexes, and whose protein chains or the full assembly could be readily modeled from structural templates in the PDB. On average, 28 CAPRI groups and 10 CASP groups (including automatic servers), submitted models for each of these 10 targets. Additionally, about 16 groups participated in the CAPRI scoring experiments. A range of acceptable to high quality models were obtained for 6 of the 10 Round 37 targets, for which templates were available for the full assembly. Poorer results were achieved for the remaining targets due to the lower quality of the templates available for the full complex or the individual protein chains, highlighting the unmet challenge of modeling the structural adjustments of the protein components that occur upon binding or which must be accounted for in template-based modeling. On the other hand, our analysis indicated that residues in binding interfaces were correctly predicted in a sizable fraction of otherwise poorly modeled assemblies and this with higher accuracy than published methods that do not use information on the binding partner. Lastly, the strengths and weaknesses of the assessment methods are evaluated and improvements suggested.
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Affiliation(s)
- Marc F Lensink
- University Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minkyung Baek
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Lim Heo
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Shoshana J Wodak
- VIB Structural Biology Research Center, VUB, Pleinlaan 2, Brussels, Belgium
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22
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Cukier CD, Tourdes A, El-Mazouni D, Guillet V, Nomme J, Mourey L, Milon A, Merdes A, Gervais V. NMR secondary structure and interactions of recombinant human MOZART1 protein, a component of the gamma-tubulin complex. Protein Sci 2017; 26:2240-2248. [PMID: 28851027 PMCID: PMC5654863 DOI: 10.1002/pro.3282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022]
Abstract
Mitotic‐spindle organizing protein associated with a ring of γ‐tubulin 1 (MOZART1) is an 8.5 kDa protein linked to regulation of γ‐tubulin ring complexes (γTuRCs), which are involved in nucleation of microtubules. Despite its small size, MOZART1 represents a challenging target for detailed characterization in vitro. We described herein a protocol for efficient production of recombinant human MOZART1 in Escherichia coli and assessed the properties of the purified protein using a combination of size exclusion chromatography coupled with multiangle light scattering (SEC‐MALS), dynamic light scattering (DLS), and nuclear magnetic resonance (NMR) experiments. MOZART1 forms heterogeneous oligomers in solution. We identified optimal detergent and buffer conditions for recording well resolved NMR experiments allowing nearly full protein assignment and identification of three distinct alpha‐helical structured regions. Finally, using NMR, we showed that MOZART1 interacts with the N‐terminus (residues 1–250) of GCP3 (γ‐tubulin complex protein 3). Our data illustrate the capacity of MOZART1 to form oligomers, promoting multiple contacts with a subset of protein partners in the context of microtubule nucleation.
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Affiliation(s)
- Cyprian D Cukier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Audrey Tourdes
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dounia El-Mazouni
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Valérie Guillet
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julian Nomme
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alain Milon
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Andreas Merdes
- Centre de Biologie du Développement, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Virginie Gervais
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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23
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Henrich E, Peetz O, Hein C, Laguerre A, Hoffmann B, Hoffmann J, Dötsch V, Bernhard F, Morgner N. Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology. eLife 2017; 6. [PMID: 28067619 PMCID: PMC5291076 DOI: 10.7554/elife.20954] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 08/25/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps, such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane-integrated enzymes assembling up to hexameric complexes. We further indicate a lipid-dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent-free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provide a versatile platform for the analysis of membrane proteins in a native environment.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Beate Hoffmann
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
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24
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Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber APM. Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts. Mol Plant 2017; 10:197-211. [PMID: 27794502 DOI: 10.1016/j.molp.2016.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 08/03/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
Blue native-PAGE (BN-PAGE) resolves protein complexes in their native state. When combined with immunoblotting, it can be used to identify the presence of high molecular weight complexes at high resolution for any protein, given a suitable antibody. To identify proteins in high molecular weight complexes on a large scale and to bypass the requirement for specific antibodies, we applied a tandem mass spectrometry (MS/MS) approach to BN-PAGE-resolved chloroplasts. Fractionation of the gel into six bands allowed identification and label-free quantification of 1000 chloroplast proteins with native molecular weight separation. Significantly, this approach achieves a depth of identification comparable with traditional shotgun proteomic analyses of chloroplasts, indicating much of the known chloroplast proteome is amenable to MS/MS identification under our fractionation scheme. By limiting the number of fractionation bands to six, we facilitate scaled-up comparative analyses, as we demonstrate with the reticulata chloroplast mutant displaying a reticulated leaf phenotype. Our comparative proteomics approach identified a candidate interacting protein of RETICULATA as well as effects on lipid remodeling proteins, amino acid metabolic enzymes, and plastid division machinery. We additionally highlight selected proteins from each sub-compartment of the chloroplast that provide novel insight on known or hypothesized protein complexes to further illustrate the utility of this approach. Our results demonstrate the high sensitivity and reproducibility of this technique, which is anticipated to be widely adaptable to other sub-cellular compartments.
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Affiliation(s)
- Peter K Lundquist
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Otho Mantegazza
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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25
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Khadria AS, Senes A. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET. Biopolymers 2016; 104:247-64. [PMID: 25968159 DOI: 10.1002/bip.22667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 02/10/2015] [Revised: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
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26
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Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. eLife 2016; 5. [PMID: 27288545 PMCID: PMC4946880 DOI: 10.7554/elife.14770] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [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: 01/27/2016] [Accepted: 06/10/2016] [Indexed: 01/17/2023] Open
Abstract
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Biomathematics Graduate Program, North Carolina State University, Raleigh, United States
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Cara M Winter
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Giuseppe Crosti
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen, Netherlands
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
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27
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Li C, Ching Han Chang C, Nagel J, Porebski BT, Hayashida M, Akutsu T, Song J, Buckle AM. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform 2016; 17:270-82. [PMID: 26177815 PMCID: PMC6078162 DOI: 10.1093/bib/bbv047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a fundamental role in subcellular infrastructure and controlling trafficking of eukaryotic cells. Given the importance of coiled-coils, multiple bioinformatics tools have been developed to facilitate the systematic and high-throughput prediction of CCDs in proteins. In this article, we review and compare 12 sequence-based bioinformatics approaches and tools for coiled-coil prediction. These approaches can be categorized into two classes: coiled-coil detection and coiled-coil oligomeric state prediction. We evaluated and compared these methods in terms of their input/output, algorithm, prediction performance, validation methods and software utility. All the independent testing data sets are available at http://lightning.med.monash.edu/coiledcoil/. In addition, we conducted a case study of nine human polyglutamine (PolyQ) disease-related proteins and predicted CCDs and oligomeric states using various predictors. Prediction results for CCDs were highly variable among different predictors. Only two peptides from two proteins were confirmed to be CCDs by majority voting. Both domains were predicted to form dimeric coiled-coils using oligomeric state prediction. We anticipate that this comprehensive analysis will be an insightful resource for structural biologists with limited prior experience in bioinformatics tools, and for bioinformaticians who are interested in designing novel approaches for coiled-coil and its oligomeric state prediction.
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28
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Lee Y, Willers C, Kunji ER, Crichton PG. Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin. Proc Natl Acad Sci U S A 2015; 112:6973-8. [PMID: 26038550 DOI: 10.1073/pnas.1503833112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uncoupling protein 1 (UCP1) catalyzes fatty acid-activated, purine nucleotide-sensitive proton leak across the mitochondrial inner membrane of brown adipose tissue to produce heat, and could help combat obesity and metabolic disease in humans. Studies over the last 30 years conclude that the protein is a dimer, binding one nucleotide molecule per two proteins, and unlike the related mitochondrial ADP/ATP carrier, does not bind cardiolipin. Here, we have developed novel methods to purify milligram amounts of UCP1 from native sources by using covalent chromatography that, unlike past methods, allows the protein to be prepared in defined conditions, free of excess detergent and lipid. Assessment of purified preparations by TLC reveal that UCP1 retains tightly bound cardiolipin, with a lipid phosphorus content equating to three molecules per protein, like the ADP/ATP carrier. Cardiolipin stabilizes UCP1, as demonstrated by reconstitution experiments and thermostability assays, indicating that the lipid has an integral role in the functioning of the protein, similar to other mitochondrial carriers. Furthermore, we find that UCP1 is not dimeric but monomeric, as indicated by size exclusion analysis, and has a ligand titration profile in isothermal calorimetric measurements that clearly shows that one nucleotide binds per monomer. These findings reveal the fundamental composition of UCP1, which is essential for understanding the mechanism of the protein. Our assessment of the properties of UCP1 indicate that it is not unique among mitochondrial carriers and so is likely to use a common exchange mechanism in its primary function in brown adipose tissue mitochondria.
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Chakravarty D, Chakraborti S, Chakrabarti P. Flexibility in the N-terminal actin-binding domain: clues from in silico mutations and molecular dynamics. Proteins 2015; 83:696-710. [PMID: 25620004 DOI: 10.1002/prot.24767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 07/16/2014] [Revised: 12/31/2014] [Accepted: 01/10/2015] [Indexed: 01/01/2023]
Abstract
Dystrophin is a long, rod-shaped cytoskeleton protein implicated in muscular dystrophy (MDys). Utrophin is the closest autosomal homolog of dystrophin. Both proteins have N-terminal actin-binding domain (N-ABD), a central rod domain and C-terminal region. N-ABD, composed of two calponin homology (CH) subdomains joined by a helical linker, harbors a few disease causing missense mutations. Although the two proteins share considerable homology (>72%) in N-ABD, recent structural and biochemical studies have shown that there are significant differences (including stability, mode of actin-binding) and their functions are not completely interchangeable. In this investigation, we have used extensive molecular dynamics simulations to understand the differences and the similarities of these two proteins, along with another actin-binding protein, fimbrin. In silico mutations were performed to identify two key residues that might be responsible for the dynamical difference between the molecules. Simulation points to the inherent flexibility of the linker region, which adapts different conformations in the wild type dystrophin. Mutations T220V and G130D in dystrophin constrain the flexibility of the central helical region, while in the two known disease-causing mutants, K18N and L54R, the helicity of the region is compromised. Phylogenetic tree and sequence analysis revealed that dystrophin and utrophin genes have probably originated from the same ancestor. The investigation would provide insight into the functional diversity of two closely related proteins and fimbrin, and contribute to our understanding of the mechanism of MDys.
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Affiliation(s)
- Devlina Chakravarty
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, 700054, India
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30
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Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D. Isolation of Plant Photosystem II Complexes by Fractional Solubilization. Front Plant Sci 2015. [PMID: 26697050 DOI: 10.3389/fols.2015.01100] [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] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Photosystem II (PSII) occurs in different forms and supercomplexes in thylakoid membranes. Using a transplastomic strain of Nicotiana tabacum histidine tagged on the subunit PsbE, we have previously shown that a mild extraction protocol with β-dodecylmaltoside enriches PSII characteristic of lamellae and grana margins. Here, we characterize residual granal PSII that is not extracted by this first solubilization step. Using affinity purification, we demonstrate that this PSII fraction consists of PSII-LHCII mega- and supercomplexes, PSII dimers, and PSII monomers, which were separated by gel filtration and functionally characterized. Our findings represent an alternative demonstration of different PSII populations in thylakoid membranes, and they make it possible to prepare PSII-LHCII supercomplexes in high yield.
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Affiliation(s)
- Patrycja Haniewicz
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Davide Floris
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Domenica Farci
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Joanna Kirkpatrick
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Germany
| | - Maria C Loi
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Claudia Büchel
- Laboratory of Plant Cell Physiology, Institute of Molecular Biosciences, Goethe-University Frankfurt Frankfurt am Main, Germany
| | - Matthias Bochtler
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell Biology Warsaw, Poland ; Department of Bioinformatics, Institute of Biochemistry and Biophysics Warsaw, Poland
| | - Dario Piano
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell Biology Warsaw, Poland ; Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
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Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D. Isolation of Plant Photosystem II Complexes by Fractional Solubilization. Front Plant Sci 2015; 6:1100. [PMID: 26697050 PMCID: PMC4674563 DOI: 10.3389/fpls.2015.01100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/22/2015] [Indexed: 05/19/2023]
Abstract
Photosystem II (PSII) occurs in different forms and supercomplexes in thylakoid membranes. Using a transplastomic strain of Nicotiana tabacum histidine tagged on the subunit PsbE, we have previously shown that a mild extraction protocol with β-dodecylmaltoside enriches PSII characteristic of lamellae and grana margins. Here, we characterize residual granal PSII that is not extracted by this first solubilization step. Using affinity purification, we demonstrate that this PSII fraction consists of PSII-LHCII mega- and supercomplexes, PSII dimers, and PSII monomers, which were separated by gel filtration and functionally characterized. Our findings represent an alternative demonstration of different PSII populations in thylakoid membranes, and they make it possible to prepare PSII-LHCII supercomplexes in high yield.
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Affiliation(s)
- Patrycja Haniewicz
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell BiologyWarsaw, Poland
| | - Davide Floris
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of CagliariCagliari, Italy
| | - Domenica Farci
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of CagliariCagliari, Italy
| | - Joanna Kirkpatrick
- Proteomics Core Facility, European Molecular Biology LaboratoryHeidelberg, Germany
| | - Maria C. Loi
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of CagliariCagliari, Italy
| | - Claudia Büchel
- Laboratory of Plant Cell Physiology, Institute of Molecular Biosciences, Goethe-University FrankfurtFrankfurt am Main, Germany
| | - Matthias Bochtler
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell BiologyWarsaw, Poland
- Department of Bioinformatics, Institute of Biochemistry and BiophysicsWarsaw, Poland
| | - Dario Piano
- Laboratory of Structural Biology, Department of Molecular Biology, International Institute of Molecular and Cell BiologyWarsaw, Poland
- Laboratory of Photosynthesis and Photobiology, Department of Life and Environmental Sciences, University of CagliariCagliari, Italy
- *Correspondence: Dario Piano,
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Kalynych S, Cherney M, Bostina M, Rouiller I, Cygler M. Quaternary structure of WzzB and WzzE polysaccharide copolymerases. Protein Sci 2014; 24:58-69. [PMID: 25307743 DOI: 10.1002/pro.2586] [Citation(s) in RCA: 17] [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: 09/17/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023]
Abstract
Bacteria have evolved cellular control mechanisms to ensure proper length specification for surface-bound polysaccharides. Members of the Polysaccharide Copolymerase (PCP) family are central to this process. PCP-1 family members are anchored to the inner membrane through two transmembrane helices and contain a large periplasm-exposed domain. PCPs are known to form homooligomers but their exact stoichiometry is controversial in view of conflicting structural and biochemical data. Several prior investigations addressing this question indicated a nonameric, hexameric, or tetrameric organization of several PCP-1 family members. In this work, we gathered additional evidence that E.coli WzzB and WzzE PCPs form octameric homo-oligomeric complexes. Detergent-solubilized PCPs were purified to homogeneity and subjected to blue native gel analysis, which indicated the presence of a predominant high-molecular product of over 500 kDa in mass. Molecular mass of WzzE and WzzB-detergent oligomers was estimated to be 550 kDA by size-exclusion coupled to multiangle laser light scattering (SEC-MALLS). Oligomeric organization of purified WzzB and WzzE was further investigated by negative stain electron microscopy and by X-ray crystallography, respectively. Analysis of EM-derived molecular envelope of WzzB indicated that the full-length protein is composed of eight protomers. Crystal structure of LDAO-solubilized WzzE was solved to 6 Å resolutions and revealed its octameric subunit stoichiometry. In summary, we identified a possible biological unit utilized for the glycan chain length determination by two PCP-1 family members. This provides an important step toward further unraveling of the mechanistic basis of chain length control of the O-antigen and the enterobacterial common antigen.
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Affiliation(s)
- Sergei Kalynych
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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Haniewicz P, De Sanctis D, Büchel C, Schröder WP, Loi MC, Kieselbach T, Bochtler M, Piano D. Isolation of monomeric photosystem II that retains the subunit PsbS. Photosynth Res 2013; 118:199-207. [PMID: 23975205 PMCID: PMC3825537 DOI: 10.1007/s11120-013-9914-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 12/22/2012] [Accepted: 08/07/2013] [Indexed: 05/03/2023]
Abstract
Photosystem II has been purified from a transplastomic strain of Nicotiana tabacum according to two different protocols. Using the procedure described in Piano et al. (Photosynth Res 106:221-226, 2010) it was possible to isolate highly active PSII composed of monomers and dimers but depleted in their PsbS protein content. A "milder" procedure than the protocol reported by Fey et al. (Biochim Biophys Acta 1777:1501-1509, 2008) led to almost exclusively monomeric PSII complexes which in part still bind the PsbS protein. This finding might support a role for PSII monomers in higher plants.
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Affiliation(s)
- Patrycja Haniewicz
- International Institute of Molecular and Cell Biology, Ul. Ks. Trojdena 4, 02109 Warsaw, Poland
| | - Daniele De Sanctis
- European Synchrotron Radiation Facility, Rue Jules Horowitz 6, 38000 Grenoble, France
| | - Claudia Büchel
- Institute of Molecular Biosciences, University of Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Wolfgang P. Schröder
- Umeå Plant Science Center and Institute of Chemistry, Linnaeus väg 10, 90187 Umeå, Sweden
| | - Maria Cecilia Loi
- Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy
| | - Thomas Kieselbach
- Umeå Plant Science Center and Institute of Chemistry, Linnaeus väg 10, 90187 Umeå, Sweden
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Ul. Ks. Trojdena 4, 02109 Warsaw, Poland
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dario Piano
- International Institute of Molecular and Cell Biology, Ul. Ks. Trojdena 4, 02109 Warsaw, Poland
- European Synchrotron Radiation Facility, Rue Jules Horowitz 6, 38000 Grenoble, France
- Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy
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Luan W, Fesseler J, Chechik M, Buttner CR, Antson AA, Smits C. Recombinant portal protein from Staphylococcus epidermidis bacteriophage CNPH82 is a 13-subunit oligomer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1267-70. [PMID: 23027764 PMCID: PMC3490468 DOI: 10.1107/s1744309112037645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 07/24/2012] [Accepted: 08/31/2012] [Indexed: 11/13/2022]
Abstract
The portal protein cn3 of bacteriophage CNPH82 is predicted to serve as a gateway for translocation of viral genome into preformed pro-capsid, like portal proteins from other double-stranded DNA tailed bacteriophages. The host of bacteriophage CNPH82 is the opportunistic human pathogenic bacterium Staphylococcus epidermidis, a major cause of nosocomial infections. The portal protein of this phage has been cloned, overexpressed and purified. Size-exclusion chromatography-multi-angle laser light scattering analysis has indicated that the portal protein contains ∼13 subunits. Crystals of the portal protein, diffracting to 4.2 Å, have been obtained. These crystals belong to the space group C222(1) with the unit-cell parameters of a = 252.4, b = 367.0, c = 175.5 Å. The self-rotation function revealed the presence of a single 13-subunit oligomer in the asymmetric unit.
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Affiliation(s)
- Weisha Luan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Jochen Fesseler
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Carina R. Buttner
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
| | - Callum Smits
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, England
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von Stetten D, Noirclerc-Savoye M, Goedhart J, Gadella TWJ, Royant A. Structure of a fluorescent protein from Aequorea victoria bearing the obligate-monomer mutation A206K. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:878-82. [PMID: 22869113 PMCID: PMC3412764 DOI: 10.1107/s1744309112028667] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 06/24/2012] [Indexed: 11/10/2022]
Abstract
The green fluorescent protein (GFP) from the jellyfish Aequoria victoria has been shown to dimerize at high concentrations, which could lead to artefacts in imaging experiments. To ensure a truly monomeric state, an A206K mutation has been introduced into most of its widely used variants, with minimal effect on the spectroscopic properties. Here, the first structure of one of these variants, the cyan fluorescent protein mTurquoise, is presented and compared with that of its dimeric version mTurquoise-K206A. No significant structural change is detected in the chromophore cavity, reinforcing the notion that this mutation is spectroscopically silent and validating that the structural analysis performed on dimeric mutants also applies to monomeric versions. Finally, it is explained why cyan versions of GFP containing the Y66W and N146I mutations do not require the A206K mutation to prevent dimerization at high concentrations.
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Affiliation(s)
- David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
- Université Joseph Fourier, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, The Netherlands
| | - Theodorus W. J. Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
- CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
- Université Joseph Fourier, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, 38027 Grenoble, France
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36
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Raunser S, Mathai JC, Abeyrathne PD, Rice AJ, Zeidel ML, Walz T. Oligomeric structure and functional characterization of the urea transporter from Actinobacillus pleuropneumoniae. J Mol Biol 2009; 387:619-27. [PMID: 19361419 PMCID: PMC2682783 DOI: 10.1016/j.jmb.2009.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/28/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
Urea transporters (UTs) facilitate urea permeation across cell membranes in prokaryotes and eukaryotes. Bacteria use urea as a means to survive in acidic environments and/or as a nitrogen source. The UT from Actinobacillus pleuropneumoniae, ApUT, the pathogen that causes porcine pleurisy and pneumonia, was expressed in Escherichia coli and purified. Analysis of the recombinant protein using cross-linking and blue-native gel electrophoresis established that ApUT is a dimer in detergent solution. Purified protein was reconstituted into proteoliposomes and urea efflux was measured by stopped-flow fluorometry to determine the urea transport kinetics of ApUT. The measured urea flux was saturable, could be inhibited by phloretin, and was not affected by pH. Two-dimensional crystals of the biologically active ApUT show that it is also dimeric in a lipid membrane and provide the first structural information on a member of the UT family.
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Affiliation(s)
- Stefan Raunser
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - John C. Mathai
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115
| | | | - Amanda J. Rice
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Mark L. Zeidel
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute
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Bamber L, Harding M, Monné M, Slotboom DJ, Kunji ERS. The yeast mitochondrial ADP/ATP carrier functions as a monomer in mitochondrial membranes. Proc Natl Acad Sci U S A 2007; 104:10830-4. [PMID: 17566106 PMCID: PMC1891095 DOI: 10.1073/pnas.0703969104] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial carriers are believed widely to be dimers both in structure and function. However, the structural fold is a barrel of six transmembrane alpha-helices without an obvious dimerisation interface. Here, we show by negative dominance studies that the yeast mitochondrial ADP/ATP carrier 2 from Saccharomyces cerevisiae (AAC2) is functional as a monomer in the mitochondrial membrane. Adenine nucleotide transport by wild-type AAC2 is inhibited by the sulfhydryl reagent 2-sulfonatoethyl-methanethiosulfonate (MTSES), whereas the activity of a mutant AAC2, devoid of cysteines, is unaffected. Wild-type and cysteine-less AAC2 were coexpressed in different molar ratios in yeast mitochondrial membranes. After addition of MTSES the residual transport activity correlated linearly with the fraction of cysteine-less carrier present in the membranes, and so the two versions functioned independently of each other. Also, the cysteine-less and wild-type carriers were purified separately, mixed in defined ratios and reconstituted into liposomes. Again, the residual transport activity in the presence of MTSES depended linearly on the amount of cysteine-less carrier. Thus, the entire transport cycle for ADP/ATP exchange is carried out by the monomer.
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Affiliation(s)
- Lisa Bamber
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Marilyn Harding
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Magnus Monné
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Dirk-Jan Slotboom
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Edmund R. S. Kunji
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom
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Abstract
Mitochondrial carriers are believed widely to be homodimers both in the inner membrane of the organelle and in detergents. The dimensions and molecular masses of the detergent and protein-detergent micelles were measured for yeast ADP/ATP carriers in a range of different detergents. The radius of the carrier at the midpoint of the membrane, its average radius, its Stokes' radius, its molecular mass, and its excluded volume were determined. These parameters are consistent with the known structural model of the bovine ADP/ATP carrier and they demonstrate that the yeast mitochondrial ADP/ATP carriers are monomeric in detergents. Therefore, models of substrate transport have to be considered in which the carrier operates as a monomer rather than as a dimer.
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Affiliation(s)
| | | | - P. Jonathan G. Butler
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, CB2 2XY Cambridge, United Kingdom
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Abstract
Previous experiments using intermolecular thiol cross-linking to determine surface-exposed positions in the transmembrane helices of the lactose permease suggest that only positions accessible from the aqueous phase are susceptible to cross-linking. This approach is now extended to most of the remaining positions in the molecule. Of an additional 143 single-Cys mutants studied, homodimer formation is observed with both a 5-A- and a 21-A-long crosslinking agent containing bis-methane thiosulfonate reactive groups in 33 mutants and exclusively with the 21-A-long reagent in 43 mutants. Furthermore, intermolecular cross-linking has little or no effect on transport activity, thereby providing further support for the argument that lactose permease is functionally, as well as structurally, a monomer in the membrane. In addition, evidence is presented indicating that reentrance loops are unlikely in this polytopic membrane transport protein.
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Affiliation(s)
- Natalia Ermolova
- Howard Hughes Medical Institute, Department of Physiology and Microbiology, University of California, Los Angeles, CA 90095-1662, USA
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