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Valimberti I, Tiberti M, Lambrughi M, Sarcevic B, Papaleo E. E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft. Sci Rep 2015; 5:14849. [PMID: 26463729 PMCID: PMC4604453 DOI: 10.1038/srep14849] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/19/2015] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation is a modification that offers a dynamic and reversible mechanism to regulate the majority of cellular processes. Numerous diseases are associated with aberrant regulation of phosphorylation-induced switches. Phosphorylation is emerging as a mechanism to modulate ubiquitination by regulating key enzymes in this pathway. The molecular mechanisms underpinning how phosphorylation regulates ubiquitinating enzymes, however, are elusive. Here, we show the high conservation of a functional site in E2 ubiquitin-conjugating enzymes. In catalytically active E2s, this site contains aspartate or a phosphorylatable serine and we refer to it as the conserved E2 serine/aspartate (CES/D) site. Molecular simulations of substrate-bound and -unbound forms of wild type, mutant and phosphorylated E2s, provide atomistic insight into the role of the CES/D residue for optimal E2 activity. Both the size and charge of the side group at the site play a central role in aligning the substrate lysine toward E2 catalytic cysteine to control ubiquitination efficiency. The CES/D site contributes to the fingerprint of the E2 superfamily. We propose that E2 enzymes can be divided into constitutively active or regulated families. E2s characterized by an aspartate at the CES/D site signify constitutively active E2s, whereas those containing a serine can be regulated by phosphorylation.
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Affiliation(s)
- Ilaria Valimberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Tiberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Lambrughi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Boris Sarcevic
- Cell Cycle and Cancer Unit, St. Vincent's Institute of Medical Research and The Department of Medicine, St. Vincent's Hospital, The University of Melbourne, Fitzroy, Melbourne, Victoria 3065, Australia
| | - Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
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53
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Ferruz N, Harvey MJ, Mestres J, De Fabritiis G. Insights from Fragment Hit Binding Assays by Molecular Simulations. J Chem Inf Model 2015; 55:2200-5. [DOI: 10.1021/acs.jcim.5b00453] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Noelia Ferruz
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003 Barcelona, Barcelona, Spain
| | - Matthew J. Harvey
- Acellera, Barcelona
Biomedical Research Park (PRBB), Doctor
Aiguader 88, 08003, Barcelona, Barcelona, Spain
| | - Jordi Mestres
- Systems
Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Barcelona, Catalonia, Spain
| | - Gianni De Fabritiis
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003 Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Barcelona, Spain
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54
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Reubold TF, Faelber K, Plattner N, Posor Y, Ketel K, Curth U, Schlegel J, Anand R, Manstein DJ, Noé F, Haucke V, Daumke O, Eschenburg S. Crystal structure of the dynamin tetramer. Nature 2015; 525:404-8. [PMID: 26302298 DOI: 10.1038/nature14880] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 08/03/2015] [Indexed: 12/21/2022]
Abstract
The mechanochemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes. Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane. Previous studies have described the architecture of dynamin dimers, but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here we present the crystal structure of the human dynamin tetramer in the nucleotide-free state. Combining structural data with mutational studies, oligomerization measurements and Markov state models of molecular dynamics simulations, we suggest a mechanism by which oligomerization of dynamin is linked to the release of intramolecular autoinhibitory interactions. We elucidate how mutations that interfere with tetramer formation and autoinhibition can lead to the congenital muscle disorders Charcot-Marie-Tooth neuropathy and centronuclear myopathy, respectively. Notably, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.
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Affiliation(s)
- Thomas F Reubold
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Katja Faelber
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Nuria Plattner
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - York Posor
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Katharina Ketel
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Ute Curth
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Forschungseinrichtung Strukturanalyse, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Jeanette Schlegel
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Roopsee Anand
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Dietmar J Manstein
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Forschungseinrichtung Strukturanalyse, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Frank Noé
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Volker Haucke
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Susanne Eschenburg
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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55
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Ahalawat N, Arora S, Murarka RK. Structural Ensemble of CD4 Cytoplasmic Tail (402–419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution. J Phys Chem B 2015; 119:11229-42. [DOI: 10.1021/acs.jpcb.5b03092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Navjeet Ahalawat
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Simran Arora
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Rajesh K. Murarka
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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56
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Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat Commun 2015; 6:7653. [PMID: 26134632 PMCID: PMC4506540 DOI: 10.1038/ncomms8653] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/28/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the structural mechanisms of protein–ligand binding and their dependence on protein sequence and conformation is of fundamental importance for biomedical research. Here we investigate the interplay of conformational change and ligand-binding kinetics for the serine protease Trypsin and its competitive inhibitor Benzamidine with an extensive set of 150 μs molecular dynamics simulation data, analysed using a Markov state model. Seven metastable conformations with different binding pocket structures are found that interconvert at timescales of tens of microseconds. These conformations differ in their substrate-binding affinities and binding/dissociation rates. For each metastable state, corresponding solved structures of Trypsin mutants or similar serine proteases are contained in the protein data bank. Thus, our wild-type simulations explore a space of conformations that can be individually stabilized by adding ligands or making suitable changes in protein sequence. These findings provide direct evidence of conformational plasticity in receptors. Conformational plasticity influences several aspects of protein function. Here the authors combine extensive MD simulations with Markov state models—using trypsin as model—to reveal new mechanistic details of how conformational plasticity influence ligand-receptors interactions.
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57
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Stanley N, De Fabritiis G. High throughput molecular dynamics for drug discovery. In Silico Pharmacol 2015; 3:3. [PMID: 25717426 PMCID: PMC4339319 DOI: 10.1186/s40203-015-0007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/04/2015] [Indexed: 02/01/2023] Open
Abstract
Molecular dynamics simulations hold the promise to be an important tool for biological research and drug discovery. Historically, however, there were several obstacles for it to become a practical research tool. Limitations in computer hardware had previously made it difficult to simulate for long enough to see interesting biological processes. Recent improvements in hardware and algorithms have largely removed this issue, leaving data analysis as the main obstacle. Advances in Markov state modeling appear to be on the way to remove this obstacle. We outline these advances here and discuss numerous recent studies that demonstrate that molecular dynamics simulations will start to be an important tool for pharmaceutical research.
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Affiliation(s)
- Nathaniel Stanley
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, Barcelona, 08003 Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, Barcelona, 08010 Spain
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