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Tillmanns J, Kicuntod J, Lösing J, Marschall M. 'Getting Better'-Is It a Feasible Strategy of Broad Pan-Antiherpesviral Drug Targeting by Using the Nuclear Egress-Directed Mechanism? Int J Mol Sci 2024; 25:2823. [PMID: 38474070 DOI: 10.3390/ijms25052823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The herpesviral nuclear egress represents an essential step of viral replication efficiency in host cells, as it defines the nucleocytoplasmic release of viral capsids. Due to the size limitation of the nuclear pores, viral nuclear capsids are unable to traverse the nuclear envelope without a destabilization of this natural host-specific barrier. To this end, herpesviruses evolved the regulatory nuclear egress complex (NEC), composed of a heterodimer unit of two conserved viral NEC proteins (core NEC) and a large-size extension of this complex including various viral and cellular NEC-associated proteins (multicomponent NEC). Notably, the NEC harbors the pronounced ability to oligomerize (core NEC hexamers and lattices), to multimerize into higher-order complexes, and, ultimately, to closely interact with the migrating nuclear capsids. Moreover, most, if not all, of these NEC proteins comprise regulatory modifications by phosphorylation, so that the responsible kinases, and additional enzymatic activities, are part of the multicomponent NEC. This sophisticated basis of NEC-specific structural and functional interactions offers a variety of different modes of antiviral interference by pharmacological or nonconventional inhibitors. Since the multifaceted combination of NEC activities represents a highly conserved key regulatory stage of herpesviral replication, it may provide a unique opportunity towards a broad, pan-antiherpesviral mechanism of drug targeting. This review presents an update on chances, challenges, and current achievements in the development of NEC-directed antiherpesviral strategies.
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Affiliation(s)
- Julia Tillmanns
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Josephine Lösing
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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Kicuntod J, Häge S, Lösing J, Kopar S, Muller YA, Marschall M. An antiviral targeting strategy based on the inducible interference with cytomegalovirus nuclear egress complex. Antiviral Res 2023; 212:105557. [PMID: 36796541 DOI: 10.1016/j.antiviral.2023.105557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The nucleocytoplasmic capsid egress of herpesviruses like the human cytomegalovirus (HCMV) is based on a uniquely regulated process. The core nuclear egress complex (NEC) of HCMV, represented by the pUL50-pUL53 heterodimer, is able to oligomerize and thus to build hexameric lattices. Recently, we and others validated the NEC as a novel target for antiviral strategies. So far, the experimental targeting approaches included the development of NEC-directed small molecules, cell-penetrating peptides and NEC-directed mutagenesis. Our postulate states that an interference with the hook-into-groove interaction of pUL50-pUL53 prevents NEC formation and strictly limits viral replication efficiency. Here, we provide an experimental proof-of-concept of the antiviral strategy: the inducible intracellular expression of a NLS-Hook-GFP construct exerted a pronounced level of antiviral activity. The data provide evidence for the following points: (i) generation of a primary fibroblast population with inducible NLS-Hook-GFP expression showed nuclear localization of the construct, (ii) interaction between NLS-Hook-GFP and the viral core NEC was found specific for cytomegaloviruses but not for other herpesviruses, (iii) construct overexpression exerted a strong antiviral activity against three strains of HCMV, (iv) confocal imaging demonstrated the interference with NEC nuclear rim formation in HCMV-infected cells, and (v) quantitative nuclear egress assay confirmed the block of viral nucleocytoplasmic transition and, consequently, an inhibitory effect onto viral cytoplasmic virion assembly complex (cVAC). Combined, data confirmed that the specific interference with protein-protein interaction of the HCMV core NEC represents an efficient antiviral targeting strategy.
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Affiliation(s)
- Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Sigrun Häge
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Josephine Lösing
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Serli Kopar
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, FAU, Erlangen, Germany.
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Semenova MD, Popov SA, Sorokina IV, Meshkova YV, Baev DS, Tolstikova TG, Shults EE. Conjugates of Lupane Triterpenoids with Arylpyrimidines: Synthesis and Anti-inflammatory Activity. Steroids 2022; 184:109042. [PMID: 35580647 DOI: 10.1016/j.steroids.2022.109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/24/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Semisynthetic triterpenoid betulonic acid is of significant interest due to its biological activity and synthetic application. In this study, we report the synthesis of hybrid compounds, containing betulonic acid carboxamide and arylpyrimidine fragments. A total of 15 conjugates were prepared using the cyclocondensation reaction of new terpenoid alkynyl ketones with amidinium salts. The main synthetic approach to betulonic acid amide-derived alkynylketones was based on the cross-coupling reaction of N-(4-ethynylphenyl)- or N-(2-(4-ethynylphenyl)-1-(methoxycarbonyl)ethyl)- substituted betulonic acid carboxamide with aroylchlorides. Cyclocondensation of alkynones with amidine or guanidine hydrochlorides by reflux in MeCN in the presence of K2CO3 led to the formation of terpenoid pyrimidine hybrids in 52-89% isolated yield. Anti-inflammatory properties of new type of triterpenoid-pyrimidine conjugates were studied using the histamine- and concanavalin A- induced mouse paw edema models. In a model of acute inflammation betulonic acid amide-arylpyrimidines containing a 4-fluorophenyl substituent at the C-6 position of pyrimidine ring exhibited significant and selective anti-inflammatory activity. Compounds containing the 4-bromophenyl- substituent in the pyrimidine ring revealed selective anti-inflammatory activity in the model of immunogenic inflammation (concanavalin-A model). It should be noted that the methoxycarbonyl substituted ethane link between pharmacophore ligands (betulonic acid carboxamide and arylpyrimidine) has a significant effect on anti-inflammatory activity in both in vivo models of inflammation. It was shown by molecular docking that the new derivatives are incorporated into the binding site of the protein Keap1 Kelch-domain by their pyrimidine substituent with the formation of more non-covalent bonds.
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Affiliation(s)
- Maria D Semenova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Sergey A Popov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Irina V Sorokina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Yulia V Meshkova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Dmitry S Baev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Tatyana G Tolstikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation
| | - Elvira E Shults
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'ev Ave. 9, 630090 Novosibirsk, Russian Federation.
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Computational Resources for the Interpretation of Variations in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:177-198. [DOI: 10.1007/978-3-030-91836-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mironov ME, Borisov SA, Rybalova TV, Baev DS, Tolstikova TG, Shults EE. Synthesis of Anti-Inflammatory Spirostene-Pyrazole Conjugates by a Consecutive Multicomponent Reaction of Diosgenin with Oxalyl Chloride, Arylalkynes and Hydrazines or Hydrazones. Molecules 2021; 27:molecules27010162. [PMID: 35011399 PMCID: PMC8746855 DOI: 10.3390/molecules27010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Steroid sapogenin diosgenin is of significant interest due to its biological activity and synthetic application. A consecutive one-pot reaction of diosgenin, oxalyl chloride, arylacetylenes, and phenylhydrazine give rise to steroidal 1,3,5-trisubstituted pyrazoles (isolated yield 46–60%) when the Stephens–Castro reaction and heterocyclization steps were carried out by heating in benzene. When the cyclization step of alkyndione with phenylhydrazine was performed in 2-methoxyethanol at room temperature, steroidal α,β-alkynyl (E)- and (Z)-hydrazones were isolated along with 1,3,5-trisubstituted pyrazole and the isomeric 2,3,5-trisubstituted pyrazole. The consecutive reaction of diosgenin, oxalyl chloride, phenylacetylene and benzoic acid hydrazides efficiently forms steroidal 1-benzoyl-5-hydroxy-3-phenylpyrazolines. The structure of new compounds was unambiguously corroborated by comprehensive NMR spectroscopy, mass-spectrometry, and X-ray structure analyses. Performing the heterocyclization step of ynedione with hydrazine monohydrate in 2-methoxyethanol allowed the synthesis of 5-phenyl substituted steroidal pyrazole, which was found to exhibit high anti-inflammatory activity, comparable to that of diclofenac sodium, a commercial pain reliever. It was shown by molecular docking that the new derivatives are incorporated into the binding site of the protein Keap1 Kelch-domain by their alkynylhydrazone or pyrazole substituent with the formation of more non-covalent bonds and have higher affinity than the initial spirostene core.
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Affiliation(s)
- Maksim E. Mironov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
- Department of Natural Sciences, Novosibirsk State University, Piragova Str., 1, 630090 Novosibirsk, Russia
| | - Sergey A. Borisov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
| | - Tatyana V. Rybalova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
| | - Dmitry S. Baev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
| | - Tatyana G. Tolstikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
- Department of Natural Sciences, Novosibirsk State University, Piragova Str., 1, 630090 Novosibirsk, Russia
| | - Elvira E. Shults
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentyev Ave., 9, 630090 Novosibirsk, Russia; (M.E.M.); (S.A.B.); (T.V.R.); (D.S.B.); (T.G.T.)
- Correspondence: ; Tel.: +7-(383)-3308-533
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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7
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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Davies JA. SynPharm and the guide to pharmacology database: A toolset for conferring drug control on engineered proteins. Protein Sci 2021; 30:160-167. [PMID: 33047381 PMCID: PMC7737777 DOI: 10.1002/pro.3971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/09/2023]
Abstract
Optimizing synthetic biological systems, for example novel metabolic pathways, becomes more complicated with more protein components. One method of taming the complexity and allowing more rapid optimization is engineering external control into components. Pharmacology is essentially the science of controlling proteins using (mainly) small molecules, and a great deal of information, spread between different databases, is known about structural interactions between these ligands and their target proteins. In principle, protein engineers can use an inverse pharmacological approach to include drug response in their design, by identifying ligand-binding domains from natural proteins that are amenable to being included in a designed protein. In this context, "amenable" means that the ligand-binding domain is in a relatively self-contained subsequence of the parent protein, structurally independent of the rest of the molecule so that its function should be retained in another context. The SynPharm database is a tool, built on to the Guide to Pharmacology database and connected to various structural databases, to help protein engineers identify ligand-binding domains suitable for transfer. This article describes the tool, and illustrates its use in seeking candidate domains for transfer. It also briefly describes already-published proof-of-concept studies in which the CRISPR effectors Cas9 and Cpf1 were placed separately under the control of tamoxifen and mefipristone, by including ligand-binding domains of the Estrogen Receptor and Progesterone Receptor in modified versions of Cas9 and Cpf1. The advantages of drug control or the rival protein-control technology of optogenetics, for different purposes and in different situations, are also briefly discussed.
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Affiliation(s)
- Jamie A. Davies
- Synthsys Centre for Systems and Synthetic Biology, Deanery of Biomedical ScienceUniversity of EdinburghEdinburghUK
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9
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Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, Fish P, Harsha B, Hathaway C, Jupe SC, Kok CY, Noble K, Ponting L, Ramshaw CC, Rye CE, Speedy HE, Stefancsik R, Thompson SL, Wang S, Ward S, Campbell PJ, Forbes SA. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res 2020; 47:D941-D947. [PMID: 30371878 PMCID: PMC6323903 DOI: 10.1093/nar/gky1015] [Citation(s) in RCA: 2684] [Impact Index Per Article: 671.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/11/2018] [Indexed: 01/17/2023] Open
Abstract
COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC’s deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.
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Affiliation(s)
- John G Tate
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sally Bamford
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Harry C Jubb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - Zbyslaw Sondka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David M Beare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nidhi Bindal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Harry Boutselakis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Charlotte G Cole
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Celestino Creatore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Elisabeth Dawson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peter Fish
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bhavana Harsha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Charlie Hathaway
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Steve C Jupe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Chai Yin Kok
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kate Noble
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Ponting
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Claire E Rye
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helen E Speedy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ray Stefancsik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam L Thompson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Shicai Wang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sari Ward
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peter J Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simon A Forbes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Davies JA, Ireland S, Harding S, Sharman JL, Southan C, Dominguez-Monedero A. Inverse pharmacology: Approaches and tools for introducing druggability into engineered proteins. Biotechnol Adv 2019; 37:107439. [PMID: 31494210 PMCID: PMC6891246 DOI: 10.1016/j.biotechadv.2019.107439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/24/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023]
Abstract
A major feature of twenty-first century medical research is the development of therapeutic strategies that use 'biologics' (large molecules, usually engineered proteins) and living cells instead of, or as well as, the small molecules that were the basis of pharmacology in earlier eras. The high power of these techniques can bring correspondingly high risk, and therefore the need for the potential for external control. One way of exerting control on therapeutic proteins is to make them responsive to small molecules; in a clinical context, these small molecules themselves have to be safe. Conventional pharmacology has resulted in thousands of small molecules licensed for use in humans, and detailed structural data on their binding to their protein targets. In principle, these data can be used to facilitate the engineering of drug-responsive modules, taken from natural proteins, into synthetic proteins. This has been done for some years (for example, Cre-ERT2) but usually in a painstaking manner. Recently, we have developed the bioinformatic tool SynPharm to facilitate the design of drug-responsive proteins. In this review, we outline the history of the field, the design and use of the Synpharm tool, and describe our own experiences in engineering druggability into the Cpf1 effector of CRISPR gene editing.
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Affiliation(s)
- Jamie A Davies
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XB, UK.
| | - Sam Ireland
- Biomolecular Structure & Modelling Unit, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Simon Harding
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XB, UK
| | - Joanna L Sharman
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XB, UK; Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd, Innovation Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | | | - Alazne Dominguez-Monedero
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XB, UK
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Vamathevan J, Apweiler R, Birney E. Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Technological advances have continuously driven the generation of bio-molecular data and the development of bioinformatics infrastructure, which enables data reuse for scientific discovery. Several types of data management resources have arisen, such as data deposition databases, added-value databases or knowledgebases, and biology-driven portals. In this review, we provide a unique overview of the gradual evolution of these resources and discuss the goals and features that must be considered in their development. With the increasing application of genomics in the health care context and with 60 to 500 million whole genomes estimated to be sequenced by 2022, biomedical research infrastructure is transforming, too. Systems for federated access, portable tools, provision of reference data, and interpretation tools will enable researchers to derive maximal benefits from these data. Collaboration, coordination, and sustainability of data resources are key to ensure that biomedical knowledge management can scale with technology shifts and growing data volumes.
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Affiliation(s)
- Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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12
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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13
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Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. A call for public archives for biological image data. Nat Methods 2018; 15:849-854. [PMID: 30377375 PMCID: PMC6884425 DOI: 10.1038/s41592-018-0195-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the first public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery.
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Affiliation(s)
- Jan Ellenberg
- European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Jason R Swedlow
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Charles E Cook
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
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14
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Jubb HC, Saini HK, Verdonk ML, Forbes SA. COSMIC-3D provides structural perspectives on cancer genetics for drug discovery. Nat Genet 2018; 50:1200-1202. [PMID: 30158682 PMCID: PMC6159874 DOI: 10.1038/s41588-018-0214-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
COSMIC-3D is a comprehensive integration of cancer mutations with protein structure across the human genome and structural proteome, seeking to support the identification and characterisation of protein targets for novel drug design in precision oncology. As an interactive system to explore cancer mutations in three-dimensions, COSMIC-3D is designed to enable a greater understanding of the functional impact of mutations, generate new hypotheses on which mutations are cancer drivers, and provide new opportunities for addressing these mutations pharmaceutically. This combination of genetics, structural proteomics, and drug development, can be best described as “mutation-guided drug design”.
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Affiliation(s)
- Harry C Jubb
- COSMIC, Wellcome Sanger Institute, Cambridge, UK.
- Astex Pharmaceuticals, Cambridge, UK.
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15
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Ireland SM, Southan C, Dominguez-Monedero A, Harding SD, Sharman JL, Davies JA. SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. ACS OMEGA 2018; 3:7993-8002. [PMID: 30087931 PMCID: PMC6068591 DOI: 10.1021/acsomega.8b00659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/26/2018] [Indexed: 05/03/2023]
Abstract
A major challenge in synthetic biology, particularly for mammalian systems, is the inclusion of adequate external control for the synthetic system activities. Control at the transcriptional level can be achieved by adaptation of bacterial repressor-operator systems (e.g., TetR), but altering the activity of a protein by controlling transcription is indirect and for longer half-life mRNAs, decreasing activity this way can be inconveniently slow. Where possible, direct modulation of protein activity by soluble ligands has many advantages, including rapid action. Decades of drug discovery and pharmacological research have uncovered detailed information on the interactions between large numbers of small molecules and their primary protein targets (as well as off-target secondary interactions), many of which have been well studied in mammals, including humans. In principle, this accumulated knowledge would be a powerful resource for synthetic biology. Here, we present SynPharm, a tool that draws together information from the pharmacological database GtoPdb and the structural database, PDB, to help synthetic biologists identify ligand-binding domains of natural proteins. Consequently, as sequence cassettes, these may be suitable for building into engineered proteins to confer small-molecule modulation on them. The tool has ancillary utilities which include assessing contact changes among different ligands in the same protein, predicting possible effects of genetic variants on binding residues, and insights into ligand cross-reactivity among species.
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16
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van Haren MJ, Thomas MG, Sartini D, Barlow DJ, Ramsden DB, Emanuelli M, Klamt F, Martin NI, Parsons RB. The kinetic analysis of the N-methylation of 4-phenylpyridine by nicotinamide N-methyltransferase: Evidence for a novel mechanism of substrate inhibition. Int J Biochem Cell Biol 2018; 98:127-136. [PMID: 29549048 DOI: 10.1016/j.biocel.2018.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/23/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
The N-methylation of 4-phenylpyridine produces the neurotoxin 1-methyl-4-phenylpyridinium ion (MPP+). We investigated the kinetics of 4-phenylpyridine N-methylation by nicotinamide N-methyltransferase (NNMT) and its effect upon 4-phenylpyridine toxicity in vitro. Human recombinant NNMT possessed 4-phenylpyridine N-methyltransferase activity, with a specific activity of 1.7 ± 0.03 nmol MPP+ produced/h/mg NNMT. Although the Km for 4-phenylpyridine was similar to that reported for nicotinamide, its kcat of 9.3 × 10-5 ± 2 × 10-5 s-1 and specificity constant, kcat/Km, of 0.8 ± 0.8 s-1 M-1 were less than 0.15% of the respective values for nicotinamide, demonstrating that 4-phenylpyridine is a poor substrate for NNMT. At low (<2.5 mM) substrate concentration, 4-phenylpyridine N-methylation was competitively inhibited by dimethylsulphoxide, with a Ki of 34 ± 8 mM. At high (>2.5 mM) substrate concentration, enzyme activity followed substrate inhibition kinetics, with a Ki of 4 ± 1 mM. In silico molecular docking suggested that 4-phenylpyridine binds to the active site of NNMT in two non-redundant poses, one a substrate binding mode and the other an inhibitory mode. Finally, the expression of NNMT in the SH-SY5Y cell-line had no effect cell death, viability, ATP content or mitochondrial membrane potential. These data demonstrate that 4-phenylpyridine N-methylation by NNMT is unlikely to serve as a source of MPP+. The possibility for competitive inhibition by dimethylsulphoxide should be considered in NNMT-based drug discovery studies. The potential for 4-phenylpyridine to bind to the active site in two binding orientations using the same active site residues is a novel mechanism of substrate inhibition.
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Affiliation(s)
- Matthijs J van Haren
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Martin G Thomas
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - Davide Sartini
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - David J Barlow
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - David B Ramsden
- University of Birmingham, Institute of Metabolism and Systems Research, Edgbaston, Birmingham B15 2TH, UK
| | - Monica Emanuelli
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - Fábio Klamt
- Universidade Federal do Rio Grande do Sul, Departmento de Bioquímica, Instituto de Ciêncas Básicas de Saúde, Rua Ramiro Barcelos, Porto Alegre, RS 90035 003, Brazil
| | - Nathaniel I Martin
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
| | - Richard B Parsons
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK.
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17
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Grimes JM, Hall DR, Ashton AW, Evans G, Owen RL, Wagner A, McAuley KE, von Delft F, Orville AM, Sorensen T, Walsh MA, Ginn HM, Stuart DI. Where is crystallography going? Acta Crystallogr D Struct Biol 2018; 74:152-166. [PMID: 29533241 PMCID: PMC5947779 DOI: 10.1107/s2059798317016709] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022] Open
Abstract
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
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Affiliation(s)
- Jonathan M. Grimes
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David R. Hall
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Alun W. Ashton
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Gwyndaf Evans
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Robin L. Owen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Katherine E. McAuley
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Frank von Delft
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Allen M. Orville
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Thomas Sorensen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Martin A. Walsh
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Helen M. Ginn
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
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18
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Abstract
Background RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs. Results Since its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structural-alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures into one-dimensional (1D) structural sequences and applies BLAST to the resulting structural sequences for searching similar substructures of RNAs. In this study, we have upgraded R3D-BLAST to develop a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept an RNA structure in the mmCIF format as an input. The results of our experiments on a benchmark dataset have demonstrated that R3D-BLAST2 indeed performs very well in comparison to its earlier version R3D-BLAST and other similar tools RNA FRABASE, FASTR3D and RAG-3D by searching a larger number of RNA 3D substructures resembling those of the input RNA. Conclusions R3D-BLAST2 is a valuable BLAST-like search tool that can more accurately scan the PDB database for similar RNA 3D substructures. It is publicly available at http://genome.cs.nthu.edu.tw/R3D-BLAST2/.
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19
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Howard RJ, Carnevale V, Delemotte L, Hellmich UA, Rothberg BS. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:927-942. [PMID: 29258839 DOI: 10.1016/j.bbamem.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022]
Abstract
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden.
| | - Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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20
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Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SCH, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074783. [PMID: 28365730 PMCID: PMC5467563 DOI: 10.1093/database/bax006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. Database URL:http://sfld.rbvi.ucsf.edu/
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Michael A Hicks
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Human Longevity, Inc, San Diego, CA 92121, USA
| | - John H Morris
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Conrad C Huang
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Elaine C Meng
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | | | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
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21
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Kinjo AR, Bekker GJ, Wako H, Endo S, Tsuchiya Y, Sato H, Nishi H, Kinoshita K, Suzuki H, Kawabata T, Yokochi M, Iwata T, Kobayashi N, Fujiwara T, Kurisu G, Nakamura H. New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). Protein Sci 2017; 27:95-102. [PMID: 28815765 PMCID: PMC5734392 DOI: 10.1002/pro.3273] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/14/2017] [Indexed: 11/23/2022]
Abstract
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode‐Elastic server for normal mode analysis, a virtual reality system for the eF‐site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Wako
- School of Social Sciences, Waseda University, 1-6-1 Nishi-Waseda, Shinjuku-ku, Tokyo, 169-8050, Japan
| | - Shigeru Endo
- School of Science, Kitasato University, 1-15-1, Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yuko Tsuchiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiromu Sato
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aoba, Aramaki-aza Aoba-ku, Sendai, 980-8579, Japan
| | - Hafumi Nishi
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aoba, Aramaki-aza Aoba-ku, Sendai, 980-8579, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aoba, Aramaki-aza Aoba-ku, Sendai, 980-8579, Japan
| | - Hirofumi Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masashi Yokochi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Iwata
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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22
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Marschall M, Muller YA, Diewald B, Sticht H, Milbradt J. The human cytomegalovirus nuclear egress complex unites multiple functions: Recruitment of effectors, nuclear envelope rearrangement, and docking to nuclear capsids. Rev Med Virol 2017; 27. [PMID: 28664574 DOI: 10.1002/rmv.1934] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Nuclear replication represents a common hallmark of herpesviruses achieved by a number of sequentially unrolled regulatory processes. A rate-limiting step is provided by nucleo-cytoplasmic capsid export, for which a defined multiregulatory protein complex, namely, the nuclear egress complex (NEC), is assembled comprising both viral and cellular components. The NEC regulates at least 3 aspects of herpesviral nuclear replication: (1) multimeric recruitment of NEC-associated effector proteins, (2) reorganization of the nuclear lamina and membranes, and (3) the docking to nuclear capsids. Here, we review published data and own experimental work that characterizes the NEC of HCMV and other herpesviruses. METHODS A systematic review of information on nuclear egress of HCMV compared to selected alpha-, beta-, and gamma-herpesviruses: proteomics-based approaches, high-resolution imaging techniques, and functional investigations. RESULTS A large number of reports on herpesviral NECs have been published during the last two decades, focusing on protein-protein interactions, nuclear localization, regulatory phosphorylation, and functional validation. The emerging picture provides an illustrated example of well-balanced and sophisticated protein networking in virus-host interaction. CONCLUSIONS Current evidence refined the view about herpesviral NECs. Datasets published for HCMV, murine CMV, herpes simplex virus, and Epstein-Barr virus illustrate the marked functional consistency in the way herpesviruses achieve nuclear egress. However, this compares with only limited sequence conservation of core NEC proteins and a structural conservation restricted to individual domains. The translational use of this information might help to define a novel antiviral strategy on the basis of NEC-directed small molecules.
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Affiliation(s)
- Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, FAU, Erlangen, Germany
| | - Benedikt Diewald
- Division of Bioinformatics, Institute of Biochemistry, FAU, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, FAU, Erlangen, Germany
| | - Jens Milbradt
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
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23
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Abstract
The importance of preserving and making available the original experimental data underlying biological structural models is discussed, both for crystallography, where the raw data images pose particular challenges, and for other structure determination techniques.
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Affiliation(s)
- Edward N. Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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24
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Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40:163-185. [PMID: 27939973 DOI: 10.1016/j.sbi.2016.11.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023]
Abstract
Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
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Affiliation(s)
- Mykola Dimura
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas O Peulen
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian A Hanke
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Aiswaria Prakash
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus Am Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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25
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Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res 2016; 45:D282-D288. [PMID: 27789697 PMCID: PMC5210648 DOI: 10.1093/nar/gkw962] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 11/14/2022] Open
Abstract
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuko Tsuchiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuyo Ikegawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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