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Flores-Solis D, Lushpinskaia IP, Polyansky AA, Changiarath A, Boehning M, Mirkovic M, Walshe J, Pietrek LM, Cramer P, Stelzl LS, Zagrovic B, Zweckstetter M. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nat Commun 2023; 14:5979. [PMID: 37749095 PMCID: PMC10519987 DOI: 10.1038/s41467-023-41633-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 01/09/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023] Open
Abstract
Eukaryotic gene regulation and pre-mRNA transcription depend on the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. Due to its highly repetitive, intrinsically disordered sequence, the CTD enables clustering and phase separation of Pol II. The molecular interactions that drive CTD phase separation and Pol II clustering are unclear. Here, we show that multivalent interactions involving tyrosine impart temperature- and concentration-dependent self-coacervation of the CTD. NMR spectroscopy, molecular ensemble calculations and all-atom molecular dynamics simulations demonstrate the presence of diverse tyrosine-engaging interactions, including tyrosine-proline contacts, in condensed states of human CTD and other low-complexity proteins. We further show that the network of multivalent interactions involving tyrosine is responsible for the co-recruitment of the human Mediator complex and CTD during phase separation. Our work advances the understanding of the driving forces of CTD phase separation and thus provides the basis to better understand CTD-mediated Pol II clustering in eukaryotic gene transcription.
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Affiliation(s)
- David Flores-Solis
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Irina P Lushpinskaia
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Arya Changiarath
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Milana Mirkovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - James Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lisa M Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Strasße 3, 60438, Frankfurt am Main, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany.
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany.
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2
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Polyansky AA, Gallego LD, Efremov RG, Köhler A, Zagrovic B. Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales. eLife 2023; 12:e80038. [PMID: 37470705 PMCID: PMC10406433 DOI: 10.7554/elife.80038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/18/2023] [Indexed: 07/21/2023] Open
Abstract
Non-membrane-bound biomolecular condensates have been proposed to represent an important mode of subcellular organization in diverse biological settings. However, the fundamental principles governing the spatial organization and dynamics of condensates at the atomistic level remain unclear. The Saccharomyces cerevisiae Lge1 protein is required for histone H2B ubiquitination and its N-terminal intrinsically disordered fragment (Lge11-80) undergoes robust phase separation. This study connects single- and multi-chain all-atom molecular dynamics simulations of Lge11-80 with the in vitro behavior of Lge11-80 condensates. Analysis of modeled protein-protein interactions elucidates the key determinants of Lge11-80 condensate formation and links configurational entropy, valency, and compactness of proteins inside the condensates. A newly derived analytical formalism, related to colloid fractal cluster formation, describes condensate architecture across length scales as a function of protein valency and compactness. In particular, the formalism provides an atomistically resolved model of Lge11-80 condensates on the scale of hundreds of nanometers starting from individual protein conformers captured in simulations. The simulation-derived fractal dimensions of condensates of Lge11-80 and its mutants agree with their in vitro morphologies. The presented framework enables a multiscale description of biomolecular condensates and embeds their study in a wider context of colloid self-organization.
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Affiliation(s)
- Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
| | - Laura D Gallego
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Roman G Efremov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
| | - Alwin Köhler
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Biochemistry and Cell BiologyViennaAustria
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
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3
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Polyansky AA, Efremov RG. On a mechanistic impact of transmembrane tetramerization in the pathological activation of RTKs. Comput Struct Biotechnol J 2023; 21:2837-2844. [PMID: 37216019 PMCID: PMC10192832 DOI: 10.1016/j.csbj.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Constitutive activation of receptor tyrosine kinases (RTKs) via different mutations has a strong impact on the development of severe human disorders, including cancer. Here we propose a putative activation scenario of RTKs, whereby transmembrane (TM) mutations can also promote higher-order oligomerization of the receptors that leads to the subsequent ligand-free activation. We illustrate this scenario using a computational modelling framework comprising sequence-based structure prediction and all-atom 1 µs molecular dynamics (MD) simulations in a lipid membrane for a previously characterised oncogenic TM mutation V536E in platelet-derived growth factor receptor alpha (PDGFRA). We show that in the course of MD simulations the mutant TM tetramer retains stable and compact configuration strengthened by tight protein-protein interactions, while the wild type TM tetramer demonstrates looser packing and a tendency to dissociate. Moreover, the mutation affects the characteristic motions of mutated TM helical segments by introducing additional non-covalent crosslinks in the middle of the TM tetramer, which operate as mechanical hinges. This leads to dynamic decoupling of the C-termini from the rigidified N-terminal parts and facilitates more pronounced possible displacement between the C-termini of the mutant TM helical regions that can provide more freedom for mutual rearrangement of the kinase domains located downstream. Our results for the V536E mutation in the context of PDGFRA TM tetramer allow for the possibility that the effect of oncogenic TM mutations can go beyond alternating the structure and dynamics of TM dimeric states and might also promote the formation of higher-order oligomers directly contributing to ligand-independent signalling effectuated by PDGFRA and other RTKs.
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Affiliation(s)
- Anton A. Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 20 Myasnitskaya St., Moscow 101000, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141701, Russia
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Fell CW, Hagelkruys A, Cicvaric A, Horrer M, Liu L, Li JSS, Stadlmann J, Polyansky AA, Mereiter S, Tejada MA, Kokotović T, Achuta VS, Scaramuzza A, Twyman KA, Morrow MM, Juusola J, Yan H, Wang J, Burmeister M, Choudhury B, Andersen TL, Wirnsberger G, Holmskov U, Perrimon N, Žagrović B, Monje FJ, Moeller JB, Penninger JM, Nagy V. FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder. EMBO Mol Med 2022; 14:e15829. [PMID: 35916241 PMCID: PMC9449597 DOI: 10.15252/emmm.202215829] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Whole-exome sequencing of two patients with idiopathic complex neurodevelopmental disorder (NDD) identified biallelic variants of unknown significance within FIBCD1, encoding an endocytic acetyl group-binding transmembrane receptor with no known function in the central nervous system. We found that FIBCD1 preferentially binds and endocytoses glycosaminoglycan (GAG) chondroitin sulphate-4S (CS-4S) and regulates GAG content of the brain extracellular matrix (ECM). In silico molecular simulation studies and GAG binding analyses of patient variants determined that such variants are loss-of-function by disrupting FIBCD1-CS-4S association. Gene knockdown in flies resulted in morphological disruption of the neuromuscular junction and motor-related behavioural deficits. In humans and mice, FIBCD1 is expressed in discrete brain regions, including the hippocampus. Fibcd1 KO mice exhibited normal hippocampal neuronal morphology but impaired hippocampal-dependent learning. Further, hippocampal synaptic remodelling in acute slices from Fibcd1 KO mice was deficient but restored upon enzymatically modulating the ECM. Together, we identified FIBCD1 as an endocytic receptor for GAGs in the brain ECM and a novel gene associated with an NDD, revealing a critical role in nervous system structure, function and plasticity.
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Affiliation(s)
- Christopher W Fell
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Astrid Hagelkruys
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Ana Cicvaric
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
- Department of Psychiatry and Behavioral Sciences, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Marion Horrer
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Lucy Liu
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Joshua Shing Shun Li
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Johannes Stadlmann
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Institute of BiochemistryUniversity of Natural Resource and Life SciencesViennaAustria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | - Stefan Mereiter
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Miguel Angel Tejada
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Research Unit on Women's Health‐Institute of Health Research INCLIVAValenciaSpain
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Venkat Swaroop Achuta
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Angelica Scaramuzza
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | | | | | | | - Huifang Yan
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Jingmin Wang
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Margit Burmeister
- Michigan Neuroscience InstituteUniversity of MichiganAnn ArborMIUSA
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Biswa Choudhury
- Department of Cellular and Molecular MedicineUCSDLa JollaCAUSA
| | - Thomas Levin Andersen
- Clinical Cell Biology, Department of PathologyOdense University HospitalOdenseDenmark
- Pathology Research Unit, Department of Clinical Research and Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Gerald Wirnsberger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Apeiron Biologics AG, Vienna BioCenter CampusViennaAustria
| | - Uffe Holmskov
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Bojan Žagrović
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Francisco J Monje
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Jesper Bonnet Moeller
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Danish Institute for Advanced StudyUniversity of Southern DenmarkOdenseDenmark
| | - Josef M Penninger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Department of Medical Genetics, Life Science InstituteUniversity of British ColumbiaVancouverBCCanada
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
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5
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Aliper ET, Krylov NA, Nolde DE, Polyansky AA, Efremov RG. A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain. Int J Mol Sci 2022; 23:ijms23169221. [PMID: 36012488 PMCID: PMC9409440 DOI: 10.3390/ijms23169221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting “dynamic MHP portraits” and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Dmitry E. Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Anton A. Polyansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Correspondence:
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Aliper ET, Krylov NA, Polyansky AA, Efremov RG. Intricacies of the SARS-CoV-2 spike transmembrane trimer organization. Biophys J 2022. [PMCID: PMC8833073 DOI: 10.1016/j.bpj.2021.11.1040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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7
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Sponga A, Arolas JL, Schwarz TC, Jeffries CM, Kostan J, Polyansky AA, Zagrovic B, Svergun D, Warscheid B, Konrat R, Gautel M, Djinovic-Carugo K. Sarcomeric Protein Fatz Forms a Tight Fuzzy Complex with α-Actinin and Phase-Separates in Vitro. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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8
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Polyansky AA, Kreuter M, Sutherland JD, Zagrovic B. Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides. Nucleic Acids Res 2020; 47:11077-11089. [PMID: 31612955 PMCID: PMC6868383 DOI: 10.1093/nar/gkz902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/23/2019] [Accepted: 10/04/2019] [Indexed: 02/04/2023] Open
Abstract
To address the structural and dynamical consequences of amino-acid attachment at 2'- or 3'-hydroxyls of the terminal ribose in oligoribonucleotides, we have performed an extensive set of molecular dynamics simulations of model aminoacylated RNA trinucleotides. Our simulations suggest that 3'-modified trinucleotides exhibit higher solvent exposure of the aminoacylester bond and may be more susceptible to hydrolysis than their 2' counterparts. Moreover, we observe an invariant adoption of well-defined collapsed and extended conformations for both stereoisomers. We show that the average conformational preferences of aminoacylated trinucleotides are determined by their nucleotide composition and are fine-tuned by amino-acid attachment. Conversely, solvent exposure of the aminoacylester bond depends on the attachment site, the nature of attached amino acid and the strength of its interactions with the bases. Importantly, aminoacylated CCA trinucleotides display a systematically higher solvent exposure of the aminoacylester bond and a weaker dependence of such exposure on sidechain interactions than other trinucleotides. These features could facilitate hydrolytic release of the amino acid, especially for 3' attachment, and may have contributed to CCA becoming the universal acceptor triplet in tRNAs. Our results provide novel atomistic details about fundamental aspects of biological translation and furnish clues about its primordial origins.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria.,National Research University Higher School of Economics, Moscow 101000, Russia
| | - Mathias Kreuter
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria
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9
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Efremov RG, Polyansky AA, Chugunov A, Krylov NA, Nolde D, Volynsky PE, Kuznetsov A, Maurice P. Dynamic “Molecular Portraits” of Proteins and Cell Membranes: A Computational View. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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Polyansky AA, Bocharov EV, Velghe AI, Kuznetsov AS, Bocharova OV, Urban AS, Arseniev AS, Zagrovic B, Demoulin JB, Efremov RG. Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain. Biochim Biophys Acta Gen Subj 2018; 1863:82-95. [PMID: 30253204 DOI: 10.1016/j.bbagen.2018.09.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/12/2018] [Accepted: 09/16/2018] [Indexed: 12/14/2022]
Abstract
Single-point mutations in the transmembrane (TM) region of receptor tyrosine kinases (RTKs) can lead to abnormal ligand-independent activation. We use a combination of computational modeling, NMR spectroscopy and cell experiments to analyze in detail the mechanism of how TM domains contribute to the activation of wild-type (WT) PDGFRA and its oncogenic V536E mutant. Using a computational framework, we scan all positions in PDGFRA TM helix for identification of potential functional mutations for the WT and the mutant and reveal the relationship between the receptor activity and TM dimerization via different interfaces. This strategy also allows us design a novel activating mutation in the WT (I537D) and a compensatory mutation in the V536E background eliminating its constitutive activity (S541G). We show both computationally and experimentally that single-point mutations in the TM region reshape the TM dimer ensemble and delineate the structural and dynamic determinants of spontaneous activation of PDGFRA via its TM domain. Our atomistic picture of the coupling between TM dimerization and PDGFRA activation corroborates the data obtained for other RTKs and provides a foundation for developing novel modulators of the pathological activity of PDGFRA.
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Affiliation(s)
- Anton A Polyansky
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
| | - Eduard V Bocharov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow 123182, Russia
| | - Amélie I Velghe
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Andrey S Kuznetsov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Olga V Bocharova
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Anatoly S Urban
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Alexander S Arseniev
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Jean-Baptiste Demoulin
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Roman G Efremov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
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11
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Zagrovic B, Bartonek L, Polyansky AA. RNA-protein interactions in an unstructured context. FEBS Lett 2018; 592:2901-2916. [PMID: 29851074 PMCID: PMC6175095 DOI: 10.1002/1873-3468.13116] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/12/2018] [Accepted: 05/13/2018] [Indexed: 02/02/2023]
Abstract
Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA-protein interactions in general.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Lukas Bartonek
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Anton A. Polyansky
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria,MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
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12
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Fleck M, Polyansky AA, Zagrovic B. Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy. J Chem Theory Comput 2018; 14:3796-3810. [PMID: 29799751 PMCID: PMC9245193 DOI: 10.1021/acs.jctc.8b00100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The
recently developed NMR techniques enable estimation of protein
configurational entropy change from the change in the average methyl
order parameters. This experimental observable, however, does not
directly measure the contribution of intramolecular couplings, protein
main-chain motions, or angular dynamics. Here, we carry out a self-consistent
computational analysis of the impact of these missing contributions
on an extensive set of molecular dynamics simulations of different
proteins undergoing binding. Specifically, we compare the configurational
entropy change in protein complex formation as obtained by the maximum
information spanning tree approximation (MIST), which treats the above
entropy contributions directly, and the change in the average NMR
methyl and NH order parameters. Our parallel implementation of MIST
allows us to treat hard angular degrees of freedom as well as couplings
up to full pairwise order explicitly, while still involving a high
degree of sampling and tackling molecules of biologically relevant
sizes. First, we demonstrate a remarkably strong linear relationship
between the total configurational entropy change and the average change
in both methyl and backbone-NH order parameters. Second, in contrast
to canonical assumptions, we show that the main-chain and angular
terms contribute significantly to the overall configurational entropy
change and also scale linearly with it. Consequently, linear models
starting from the average methyl order parameters are able to capture
the contribution of main-chain and angular terms well. After applying
the quantum-mechanical harmonic oscillator entropy formalism, we establish
a similarly strong linear relationship for X-ray crystallographic
B-factors. Finally, we demonstrate that the observed linear relationships
remain robust against drastic undersampling and argue that they reflect
an intrinsic property of compact proteins. Despite their remarkable
strength, however, the above linear relationships yield estimates
of configurational entropy change whose accuracy appears to be sufficient
for qualitative applications only.
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Affiliation(s)
- Markus Fleck
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
| | - Anton A. Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
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13
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Kaufmann T, Grishkovskaya I, Polyansky AA, Kostrhon S, Kukolj E, Olek KM, Herbert S, Beltzung E, Mechtler K, Peterbauer T, Gotzmann J, Zhang L, Hartl M, Zagrovic B, Elsayad K, Djinovic-Carugo K, Slade D. A novel non-canonical PIP-box mediates PARG interaction with PCNA. Nucleic Acids Res 2017; 45:9741-9759. [PMID: 28934471 PMCID: PMC5766153 DOI: 10.1093/nar/gkx604] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 02/07/2023] Open
Abstract
Poly(ADP-ribose) glycohydrolase (PARG) regulates cellular poly(ADP-ribose) (PAR) levels by rapidly cleaving glycosidic bonds between ADP-ribose units. PARG interacts with proliferating cell nuclear antigen (PCNA) and is strongly recruited to DNA damage sites in a PAR- and PCNA-dependent fashion. Here we identified PARG acetylation site K409 that is essential for its interaction with PCNA, its localization within replication foci and its recruitment to DNA damage sites. We found K409 to be part of a non-canonical PIP-box within the PARG disordered regulatory region. The previously identified putative N-terminal PIP-box does not bind PCNA directly but contributes to PARG localization within replication foci. X-ray structure and MD simulations reveal that the PARG non-canonical PIP-box binds PCNA in a manner similar to other canonical PIP-boxes and may represent a new type of PIP-box. While the binding of previously described PIP-boxes is based on hydrophobic interactions, PARG PIP-box binds PCNA via both stabilizing hydrophobic and fine-tuning electrostatic interactions. Our data explain the mechanism of PARG–PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding.
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Affiliation(s)
- Tanja Kaufmann
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Eva Kukolj
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Karin M Olek
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sebastien Herbert
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Etienne Beltzung
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology, Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Thomas Peterbauer
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Josef Gotzmann
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Lijuan Zhang
- VBCF-Advanced Microscopy, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max F. Perutz Laboratories, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Kareem Elsayad
- VBCF-Advanced Microscopy, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Campus Vienna Biocenter 5, 1030 Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecčna pot 113, 1000 Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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14
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de Ruiter A, Polyansky AA, Zagrovic B. Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties. J Chem Theory Comput 2017; 13:4504-4513. [DOI: 10.1021/acs.jctc.6b01202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Anita de Ruiter
- Department of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - Anton A. Polyansky
- Department of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - Bojan Zagrovic
- Department of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna A-1030, Austria
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15
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Weichselbaum D, Zagrovic B, Polyansky AA. Fuento: functional enrichment for bioinformatics. Bioinformatics 2017; 33:2604-2606. [PMID: 28379299 PMCID: PMC5870553 DOI: 10.1093/bioinformatics/btx179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 03/03/2017] [Accepted: 03/29/2017] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The currently available functional enrichment software focuses mostly on gene expression analysis, whereby server- and graphical-user-interface-based tools with specific scope dominate the field. Here we present an efficient, user-friendly, multifunctional command-line-based functional enrichment tool (fu-en-to), tailored for the bioinformatics researcher. AVAILABILITY AND IMPLEMENTATION Source code and binaries freely available for download at github.com/DavidWeichselbaum/fuento, implemented in C ++ and supported on Linux and OS X. CONTACT newant@gmail.com or bojan.zagrovic@univie.ac.at.
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Affiliation(s)
- David Weichselbaum
- Department of Structural and Computational Biology, Max F. Perutz Laboratories & University of Vienna, Campus Vienna Biocenter 5, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories & University of Vienna, Campus Vienna Biocenter 5, Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories & University of Vienna, Campus Vienna Biocenter 5, Vienna, Austria
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16
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Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, Arseniev AS. The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment. Biochemistry 2017; 56:1697-1705. [DOI: 10.1021/acs.biochem.6b01085] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduard V. Bocharov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Pavel E. Bragin
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin V. Pavlov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Olga V. Bocharova
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin S. Mineev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Anton A. Polyansky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Department of Structural and Computational
Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna
Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Roman G. Efremov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russian Federation
| | - Alexander S. Arseniev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
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17
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Abstract
A central intermediate in purine catabolism, the inosine nucleobase hypoxanthine is also one of the most abundant modified nucleobases in RNA and plays key roles in the regulation of gene expression and determination of cell fate. It is known that hypoxanthine acts as guanine when interacting with other nucleobases and base pairs most favorably with cytosine. However, its preferences when it comes to interactions with amino acids remain unknown. Here we present for the first time the absolute binding free energies and the associated interaction modes between hypoxanthine and all standard, non-glycyl/non-prolyl amino acid side chain analogs as derived from molecular dynamics simulations and umbrella sampling in high- and low-dielectric environments. We illustrate the biological relevance of the derived affinities by providing a quantitative explanation for the specificity of hypoxanthine-guanine phosphoribosyltransferase, a key enzyme in the purine salvage pathway. Our results demonstrate that in its affinities for protein side chains, hypoxanthine closely matches guanine, much more so than its precursor adenine.
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Affiliation(s)
- Matea Hajnic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - Anita de Ruiter
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna A-1030, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna A-1030, Austria
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18
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Nagy V, Cole T, Van Campenhout C, Khoung TM, Leung C, Vermeiren S, Novatchkova M, Wenzel D, Cikes D, Polyansky AA, Kozieradzki I, Meixner A, Bellefroid EJ, Neely GG, Penninger JM. The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception. Cell Cycle 2016; 14:1799-808. [PMID: 25891934 DOI: 10.1080/15384101.2015.1036209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
PR homology domain-containing member 12 (PRDM12) belongs to a family of conserved transcription factors implicated in cell fate decisions. Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution. Expression of wild-type human PRDM12 in Xenopus induced the expression of sensory neuronal markers, which was reduced using various human PRDM12 mutants. In Drosophila, we identified Hamlet as the functional PRDM12 homolog that controls nociceptive behavior in sensory neurons. Furthermore, expression analysis of human patient fibroblasts with PRDM12 mutations uncovered possible downstream target genes. Knockdown of several of these target genes including thyrotropin-releasing hormone degrading enzyme (TRHDE) in Drosophila sensory neurons resulted in altered cellular morphology and impaired nociception. These data show that PRDM12 and its functional fly homolog Hamlet are evolutionary conserved master regulators of sensory neuronal specification and play a critical role in pain perception. Our data also uncover novel pathways in multiple species that regulate evolutionary conserved nociception.
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Key Words
- BSA, bovine serum albumin
- Brn3d, brain 3d
- CGNL1, cyclin L1
- ChIP, chromatin immunoprecipitation
- DAPI, 4′,6-diamidino-2-phenylindole
- DDK, DYKDDDDK epitope
- Drgx, dorsal root ganglia homeobox
- ECL, enhanced chemiluminescence
- En1, engrailed-1
- FDR, false discovery rate
- FPKM, fragments per kilobase exon
- GAPDH, glyceraldehyde 3-phospate dehydrogenase
- GEO, gene expression omnibus
- GFP, green fluorescent protein
- HEK293, human embryonic kidney cell 293
- HRP, horseraddish peroxidase
- HSAN, hereditary and sensory autonomic neuropathy
- Hamlet
- Hmx3, H6 family homeobox 3
- IL1R1, interleukin 1 receptor type 1
- MO, morpholino oligonucleotide
- NBT/BCIP, nitro blue tetrazolium / 5-bromo-4-chloro-3-indolyl-phosphate
- PBS, phosphate buffered saline
- PDB, protein data base
- PMID, pubmed identification.
- PRDM12
- PRDM12, PR homology domain-containing member 12
- RA, retinoic acid
- RT-qPCR, real-time quantitative polymerase chain reaction
- S1PR1, Sphi8ngosine-1-phosphate receptor 1
- SET, Su(var)3–9 and ‘Enhancer of zeste’
- Sncg, Synuclein Gamma (Breast Cancer-Specific Protein 1)
- TRH(DE), tryrotropin-releasing hormone degrading enzyme
- TRHDE
- TRHDE, tyrotropin-releasing hormone degrading enzyme
- Tlx3, T-cell leukemia homeobox 3
- nociception
- pCMV6, plasmid cytomegalovirus
- sensory neurons
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Affiliation(s)
- Vanja Nagy
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria; UNSW Medicine, Sydney, Australia
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Fleck M, Polyansky AA, Zagrovic B. PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems. J Chem Theory Comput 2016; 12:2055-65. [DOI: 10.1021/acs.jctc.5b01217] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Markus Fleck
- Department
of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, 1030, Austria
| | - Anton A. Polyansky
- Department
of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, 1030, Austria
| | - Bojan Zagrovic
- Department
of Structural
and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, 1030, Austria
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20
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Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG. Adaptable Lipid Matrix Promotes Protein–Protein Association in Membranes. J Chem Theory Comput 2015; 11:4415-26. [DOI: 10.1021/acs.jctc.5b00206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrey S. Kuznetsov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Anton A. Polyansky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Markus Fleck
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Roman G. Efremov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Higher School of Economics, Myasnitskaya Str., 20, Moscow 101000, Russia
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21
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Efremov RG, Pyrkova DV, Krylov NA, Volynsky PE, Polyansky AA. Dynamic Structural/Amphiphilic “Portrait” of Biomembranes as their Fundamental Property Relevant to Function: Results of Atomistic Simulations. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Ribeiro EDA, Pinotsis N, Ghisleni A, Salmazo A, Konarev PV, Kostan J, Sjöblom B, Schreiner C, Polyansky AA, Gkougkoulia EA, Holt MR, Aachmann FL, Zagrović B, Bordignon E, Pirker KF, Svergun DI, Gautel M, Djinović-Carugo K. The structure and regulation of human muscle α-actinin. Cell 2014; 159:1447-60. [PMID: 25433700 PMCID: PMC4259493 DOI: 10.1016/j.cell.2014.10.056] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022]
Abstract
The spectrin superfamily of proteins plays key roles in assembling the actin cytoskeleton in various cell types, crosslinks actin filaments, and acts as scaffolds for the assembly of large protein complexes involved in structural integrity and mechanosensation, as well as cell signaling. α-actinins in particular are the major actin crosslinkers in muscle Z-disks, focal adhesions, and actin stress fibers. We report a complete high-resolution structure of the 200 kDa α-actinin-2 dimer from striated muscle and explore its functional implications on the biochemical and cellular level. The structure provides insight into the phosphoinositide-based mechanism controlling its interaction with sarcomeric proteins such as titin, lays a foundation for studying the impact of pathogenic mutations at molecular resolution, and is likely to be broadly relevant for the regulation of spectrin-like proteins. Structure of human α-actinin-2 in an autoinhibited closed conformation Facilitation of PIP2-induced allosteric modulation for opening and titin binding Essentiality of structural flexibility for crosslinking antiparallel F-actin Relevance for the intramolecular pseudoligand regulation mechanism of the spectrin family
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Nikos Pinotsis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Andrea Ghisleni
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Anita Salmazo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Petr V Konarev
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Julius Kostan
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Björn Sjöblom
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eirini A Gkougkoulia
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Mark R Holt
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Finn L Aachmann
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491 Trondheim, Norway
| | - Bojan Zagrović
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Enrica Bordignon
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland; Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Katharina F Pirker
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Mathias Gautel
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK.
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia.
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Polyansky AA, Hlevnjak M, Zagrovic B. Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs. Nat Commun 2014; 4:2784. [PMID: 24253588 PMCID: PMC3868254 DOI: 10.1038/ncomms3784] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/16/2013] [Indexed: 12/21/2022] Open
Abstract
Being related by the genetic code, mRNAs and their cognate proteins exhibit mutually interdependent compositions, which implies the possibility of a direct connection between their general physicochemical properties. Here we probe the general potential of the cell to encode information about proteins in the average characteristics of their cognate mRNAs and decode it in a ribosome-independent manner. We show that average protein hydrophobicity, calculated from either sequences or 3D structures, can be encoded in an analogue fashion by many different average mRNA sequence properties with the only constraint being that pyrimidine and purine bases be clearly distinguishable on average. Moreover, average characteristics of mRNA sequences enable discrimination between cytosolic and membrane proteins even in the absence of topogenic signal-based mechanisms. Our results suggest that protein and mRNA localization may be partly determined by basic physicochemical rationales and interdependencies between the two biomolecules. mRNA transport contributes to the proper localization of its cognate proteins. Here the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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24
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Peter B, Polyansky AA, Fanucchi S, Dirr HW. A Lys-Trp cation-π interaction mediates the dimerization and function of the chloride intracellular channel protein 1 transmembrane domain. Biochemistry 2013; 53:57-67. [PMID: 24328417 DOI: 10.1021/bi401433f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chloride intracellular channel protein 1 (CLIC1) is a dual-state protein that can exist either as a soluble monomer or in an integral membrane form. The oligomerization of the transmembrane domain (TMD) remains speculative despite it being implicated in pore formation. The extent to which electrostatic and van der Waals interactions drive folding and association of the dimorphic TMD is unknown and is complicated by the requirement of interactions favorable in both aqueous and membrane environments. Here we report a putative Lys37-Trp35 cation-π interaction and show that it stabilizes the dimeric form of the CLIC1 TMD in membranes. A synthetic 30-mer peptide comprising a K37M TMD mutant was examined in 2,2,2-trifluoroethanol, sodium dodecyl sulfate micelles, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes using far-ultraviolet (UV) circular dichroism, fluorescence, and UV absorbance spectroscopy. Our data suggest that Lys37 is not implicated in the folding, stability, or membrane insertion of the TMD peptide. However, removal of this residue impairs the formation of dimers and higher-order oligomers. This is accompanied by a 30-fold loss of chloride influx activity, suggesting that dimerization modulates the rate of chloride conductance. We propose that, within membranes, individual TMD helices associate via a Lys37-mediated cation-π interaction to form active dimers. The latter findings are also supported by results of modeling a putative TMD dimer conformation in which Lys37 and Trp35 form cation-π pairs at the dimer interface. Dimeric helix bundles may then associate to form fully active ion channels. Thus, within a membrane-like environment, aromatic interactions involving a polar lysine side chain provide a thermodynamic driving force for helix-helix association.
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Affiliation(s)
- Bradley Peter
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand , Johannesburg 2050, South Africa
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25
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Polyansky AA, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG. PREDDIMER: a web server for prediction of transmembrane helical dimers. Bioinformatics 2013; 30:889-90. [DOI: 10.1093/bioinformatics/btt645] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Polyansky AA, Hlevnjak M, Zagrovic B. Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code. RNA Biol 2013; 10:1248-54. [PMID: 23945356 PMCID: PMC3817144 DOI: 10.4161/rna.25977] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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] [Indexed: 02/07/2023] Open
Abstract
Despite more than 50 years of effort, the origin of the genetic code remains enigmatic. Among different theories, the stereochemical hypothesis suggests that the code evolved as a consequence of direct interactions between amino acids and appropriate bases. If indeed true, such physicochemical foundation of the mRNA/protein relationship could also potentially lead to novel principles of protein-mRNA interactions in general. Inspired by this promise, we have recently explored the connection between the physicochemical properties of mRNAs and their cognate proteins at the proteome level. Using experimentally and computationally derived measures of solubility of amino acids in aqueous solutions of pyrimidine analogs together with knowledge-based interaction preferences of amino acids for different nucleobases, we have revealed a statistically significant matching between the composition of mRNA coding sequences and the base-binding preferences of their cognate protein sequences. Our findings provide strong support for the stereochemical hypothesis of genetic code's origin and suggest the possibility of direct complementary interactions between mRNAs and cognate proteins even in present-day cells.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology; Max F. Perutz Laboratories; University of Vienna; Vienna, Austria
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27
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Abstract
Recently, the ability to interact with messenger RNA (mRNA) has been reported for a number of known RNA-binding proteins, but surprisingly also for different proteins without recognizable RNA binding domains including several transcription factors and metabolic enzymes. Moreover, direct binding to cognate mRNAs has been detected for multiple proteins, thus creating a strong impetus to search for functional significance and basic physico-chemical principles behind such interactions. Here, we derive interaction preferences between amino acids and RNA bases by analyzing binding interfaces in the known 3D structures of protein-RNA complexes. By applying this tool to human proteome, we reveal statistically significant matching between the composition of mRNA sequences and base-binding preferences of protein sequences they code for. For example, purine density profiles of mRNA sequences mirror guanine affinity profiles of cognate protein sequences with quantitative accuracy (median Pearson correlation coefficient R = -0.80 across the entire human proteome). Notably, statistically significant anti-matching is seen only in the case of adenine. Our results provide strong evidence for the stereo-chemical foundation of the genetic code and suggest that mRNAs and cognate proteins may in general be directly complementary to each other and associate, especially if unstructured.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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28
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Polyansky AA, Chugunov AO, Vassilevski AA, Grishin EV, Efremov RG. Recent advances in computational modeling of α-helical membrane-active peptides. Curr Protein Pept Sci 2013; 13:644-57. [PMID: 23363529 DOI: 10.2174/138920312804142147] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 04/28/2011] [Accepted: 09/19/2011] [Indexed: 11/22/2022]
Abstract
Membrane-active peptides (MAPs) represent a broad variety of molecules, and biological functions of most are directly associated with their ability to interact with membranes. Taking into account the effect of MAPs on living cells they can be nominally divided into three major groups - fusion (FPs), antimicrobial/cytolytic (AMPs/CPs) and cell-penetrating (CPPs) peptides. Although spatial structure of different MAPs varies to a great extent, linear α-helical peptides represent the most studied class. These peptides possess relatively simple structural organization and share a set of similar molecular features, which make them very attractive to both experimental and computational studies. Here, we review different molecular modeling methods in prospective of their applications to study of α-helical MAPs. The most sophisticated of them, such as molecular dynamics simulations, give atomistic information about molecular interactions driving peptide binding to the water-lipid interface, cooperative mechanisms of membrane destabilization and thermodynamics of these processes. Significant progress has been achieved in this field during the last few years, resulting in a possibility to observe computationally MAPs action in realistic peptide-to-lipid ratios and over the microsecond timescale. Other relatively simple but powerful approaches allow assessment of important characteristics of MAPs such as α-helical propensity, amphiphilicity, total hydrophobicity, and spatial distribution of charge and hydrophobic/hydrophilic properties, etc. Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities.
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Affiliation(s)
- Anton A Polyansky
- M M Shemyakin and Yu A OvchinnikovInstitute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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29
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Volynsky PE, Polyansky AA, Fakhrutdinova GN, Bocharov EV, Efremov RG. Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3. J Am Chem Soc 2013; 135:8105-8. [PMID: 23679838 DOI: 10.1021/ja4011942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G380R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative "non-active") symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric ("intermediate") and alternative symmetric (putative "active") models. Results of our simulations provide novel atomistic prospective of the role of G380 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.
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Affiliation(s)
- Pavel E Volynsky
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow, 117997, Russia
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30
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Chugunov AO, Koromyslova AD, Berkut AA, Peigneur S, Tytgat J, Polyansky AA, Pentkovsky VM, Vassilevski AA, Grishin EV, Efremov RG. Modular organization of α-toxins from scorpion venom mirrors domain structure of their targets, sodium channels. J Biol Chem 2013; 288:19014-27. [PMID: 23637230 DOI: 10.1074/jbc.m112.431650] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To gain success in the evolutionary "arms race," venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Na(v)s) and thereby modify the excitability of muscle and nerve cells. Although more than 100 α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Na(v)s is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that despite the small size and relatively rigid structure, these toxins possess modular organization from structural, functional, and evolutionary perspectives. The more conserved and rigid "core module" is supplemented with the "specificity module" (SM) that is comparatively flexible and variable and determines the taxon (mammal versus insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of the extracellular loops of Na(v)s suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain IV, whereas the more versatile SM interacts with the pore domain in repeat I of Na(v)s. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Na(v)s.
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Affiliation(s)
- Anton O Chugunov
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
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31
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Polyansky AA, Volynsky PE, Efremov RG. Multistate Organization of Transmembrane Helical Protein Dimers Governed by the Host Membrane. J Am Chem Soc 2012; 134:14390-400. [DOI: 10.1021/ja303483k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anton A. Polyansky
- Department of Structural and
Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, AT-1030,
Austria
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Pavel E. Volynsky
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Roman G. Efremov
- M.M. Shemyakin
and Yu.A. Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny,
Moscow Region, 141700, Russia
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Hlevnjak M, Polyansky AA, Zagrovic B. Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels. Nucleic Acids Res 2012; 40:8874-82. [PMID: 22844092 PMCID: PMC3467073 DOI: 10.1093/nar/gks679] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A potential connection between physico-chemical properties of mRNAs and cognate proteins, with implications concerning both the origin of the genetic code and mRNA–protein interactions, is unexplored. We compare pyrimidine content of naturally occurring mRNA coding sequences with the propensity of cognate protein sequences to interact with pyrimidines. The latter is captured by polar requirement, a measure of solubility of amino acids in aqueous solutions of pyridines, heterocycles closely related to pyrimidines. We find that the higher the pyrimidine content of an mRNA, the stronger the average propensity of its cognate protein’s amino acids to interact with pyridines. Moreover, window-averaged pyrimidine profiles of individual mRNAs strongly mirror polar-requirement profiles of cognate protein sequences. For example, 4953 human proteins exhibit a correlation between the two with |R| > 0.8. In other words, pyrimidine-rich mRNA regions quantitatively correspond to regions in cognate proteins containing residues soluble in pyrimidine mimetics and vice versa. Finally, by studying randomized genetic code variants we show that the universal genetic code is highly optimized to preserve these correlations. Overall, our findings redefine the stereo-chemical hypothesis concerning code’s origin and provide evidence of direct complementary interactions between mRNAs and cognate proteins before development of ribosomal decoding, but also presently, especially if both are unstructured.
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Affiliation(s)
- Mario Hlevnjak
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
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33
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Polyansky AA, Kuzmanic A, Hlevnjak M, Zagrovic B. On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins. J Chem Theory Comput 2012; 8:3820-9. [PMID: 26593023 DOI: 10.1021/ct300082q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the contribution of linear, pairwise atom-positional correlations (covariances) to absolute and relative conformational entropy as calculated by quasi-harmonic analysis of molecular dynamics (MD) trajectories (SQH and ΔSQH). By analyzing a total of 25 μs of MD simulations of ubiquitin and six of its binding partners in bound and unbound states, and 2.4 μs of simulations of eight different proteins in phosphorylated and unphosphorylated states, we show that ΔSQH represents a remarkably constant fraction of a quasi-harmonic entropy change obtained if one ignores the contribution of covariance terms and uses mass-weighted atom-positional variances only (ΔSVAR). In other words, the relative contribution of linear correlations to conformational entropy change for different proteins and in different biomolecular processes appears to be largely constant. Based on this, we establish an empirical relationship between relative quasi-harmonic conformational entropy and changes in crystallographic B-factors induced by different processes, and we use it to estimate conformational-entropic contribution to the free energy of binding for a large set of protein complexes based on their X-ray structures. Our results suggest a simple way for relating other types of dynamical observables with conformational entropy in the absence of information on correlated motions, such as in the case of NMR order parameters.
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Affiliation(s)
- Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna, AT-1030, Austria
| | - Antonija Kuzmanic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna, AT-1030, Austria
| | - Mario Hlevnjak
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna, AT-1030, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna , Campus Vienna Biocenter 5, Vienna, AT-1030, Austria
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34
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Muhle-Goll C, Hoffmann S, Afonin S, Grage SL, Polyansky AA, Windisch D, Zeitler M, Bürck J, Ulrich AS. Hydrophobic matching controls the tilt and stability of the dimeric platelet-derived growth factor receptor (PDGFR) β transmembrane segment. J Biol Chem 2012; 287:26178-86. [PMID: 22619173 DOI: 10.1074/jbc.m111.325555] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The platelet-derived growth factor receptor β is a member of the cell surface receptor tyrosine kinase family and dimerizes upon activation. We determined the structure of the transmembrane segment in dodecylphosphocholine micelles by liquid-state NMR and found that it forms a stable left-handed helical dimer. Solid-state NMR and oriented circular dichroism were used to measure the tilt angle of the helical segments in macroscopically aligned model membranes with different acyl chain lengths. Both methods showed that decreasing bilayer thickness (DEPC-POPC-DMPC) led to an increase in the helix tilt angle from 10° to 30° with respect to the bilayer normal. At the same time, reconstitution of the comparatively long hydrophobic segment became less effective, eventually resulting in complete protein aggregation in the short-chain lipid DLPC. Unrestrained molecular dynamics simulations of the dimer were carried out in explicit lipid bilayers (DEPC, POPC, DMPC, sphingomyelin), confirming the observed dependence of the helix tilt angle on bilayer thickness. Notably, molecular dynamics revealed that the left-handed dimer gets tilted en bloc, whereas conformational transitions to alternative (e.g. right-handed dimeric) states were not supported. The experimental data along with the simulation results demonstrate a pronounced interplay between the platelet-directed growth factor receptor β transmembrane segment and the bilayer thickness. The effect of hydrophobic mismatch might play a key role in the redistribution and activation of the receptor within different lipid microdomains of the plasma membrane in vivo.
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Affiliation(s)
- Claudia Muhle-Goll
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
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Polyansky AA, Volynsky PE, Efremov RG. Structural, dynamic, and functional aspects of helix association in membranes: a computational view. Adv Protein Chem Struct Biol 2012; 83:129-61. [PMID: 21570667 DOI: 10.1016/b978-0-12-381262-9.00004-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review surveys recent achievements of molecular computer modeling in understanding spatial structure, dynamics, and mechanisms of functioning of transmembrane α-helical dimers in membranes. The factors driving self-association of hydrophobic helices in the membrane milieu are considered with examples of their applications to biologically relevant problems. The emphasis is made on the recent results, which help to understand important aspects of structure-function relations for these systems and their biological activity. Limitations and shortcomings of the methods, along with their perspectives in design of new membrane active agents, are discussed.
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Affiliation(s)
- Anton A Polyansky
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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36
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Abstract
Conformational entropy is an important component of the change in free energy upon binding of a ligand to its target protein. As a consequence, development of computational techniques for reliable estimation of conformational entropies is currently receiving an increased level of attention in the context of computational drug design. Here, we review the most commonly used techniques for conformational entropy estimation from classical molecular dynamics simulations. Although by-and-large still not directly used in practical drug design, these techniques provide a golden standard for developing other, computationally less-demanding methods for such applications, in addition to furthering our understanding of protein-ligand interactions in general. In particular, we focus on the quasi-harmonic approximation and discuss different approaches that can be used to go beyond it, most notably, when it comes to treating anharmonic and/or correlated motions. In addition to reviewing basic theoretical formalisms, we provide a concrete set of steps required to successfully calculate conformational entropy from molecular dynamics simulations, as well as discuss a number of practical issues that may arise in such calculations.
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Affiliation(s)
- Anton A Polyansky
- Laboratory of Computational Biophysics, Department of Structural and Computational Biology, Max Perutz Laboratories, Vienna, Austria
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37
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Polyansky AA, Volynsky PE, Efremov RG. COMPUTER SIMULATIONS OF MEMBRANE-LYTIC PEPTIDES: PERSPECTIVES IN DRUG DESIGN. J Bioinform Comput Biol 2011; 5:611-26. [PMID: 17636865 DOI: 10.1142/s0219720007002783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 02/05/2007] [Accepted: 02/05/2007] [Indexed: 11/18/2022]
Abstract
Structure activity relationships were investigated for membrane-lytic peptides (MLP) Ltc1 and Ltc2a from the latarcin family. The peptides were studied via long-term molecular dynamics (MD) simulations in different membrane environments (detergent micelles, mixed lipid bilayers mimiking eukaryotic and bacterial membranes). The calculated structure of Ltc2a in sodium dodecyl sulfate micelle agrees well with the data obtained by 1H-NMR spectroscopy. This validates the applied modeling approach. The binding mode of MLPs is governed by several factors: (i) the membrane surface curvature; (ii) the conformational plasticity and hydrophobic organization of the peptide, which depend on the arrangement of charged, non-polar and helix-breaking residues in the amino acid sequence. In contrast to Ltc1, insertion of Ltc2a into model membranes induces significant changes in dynamic behavior of lipids in the contact region. Such a prominent membrane destabilization correlates with high membrane-lytic activity of Ltc2a. In all cases the "membrane response" has a local character and is caused by formation of specific peptide-lipid contacts. Results of MD simulations of Ltc2a in model membranes were used to develop a number of its analogs with predefined activity.
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Affiliation(s)
- Anton A Polyansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 16/10 Miklukho Maklaya str., Moscow, 117997, Russia.
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38
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Kordyukova LV, Serebryakova MV, Polyansky AA, Kropotkina EA, Alexeevski AV, Veit M, Efremov RG, Filippova IY, Baratova LA. Linker and/or transmembrane regions of influenza A/Group-1, A/Group-2, and type B virus hemagglutinins are packed differently within trimers. Biochim Biophys Acta 2011; 1808:1843-54. [PMID: 21420932 DOI: 10.1016/j.bbamem.2011.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Revised: 03/11/2011] [Accepted: 03/15/2011] [Indexed: 11/19/2022]
Abstract
Influenza virus hemagglutinin is a homotrimeric spike glycoprotein crucial for virions' attachment, membrane fusion, and assembly reactions. X-ray crystallography data are available for hemagglutinin ectodomains of various types/subtypes but not for anchoring segments. To get structural information for the linker and transmembrane regions of hemagglutinin, influenza A (H1-H16 subtypes except H8 and H15) and B viruses were digested with bromelain or subtilisin Carlsberg, either within virions or in non-ionic detergent micelles. Proteolytical fragments were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Within virions, hemagglutinins of most influenza A/Group-1 and type B virus strains were more susceptible to digestion with bromelain and/or subtilisin compared to A/Group-2 hemagglutinins. The cleavage sites were always located in the hemagglutinin linker sequence. In detergent, 1) bromelain cleaved hemagglutinin of every influenza A subtype in the linker region; 2) subtilisin cleaved Group-2 hemagglutinins in the linker region; 3) subtilisin cleaved Group-1 hemagglutinins in the transmembrane region; 4) both enzymes cleaved influenza B virus hemagglutinin in the transmembrane region. We propose that the A/Group-2 hemagglutinin linker and/or transmembrane regions are more tightly associated within trimers than type A/Group-1 and particularly type B ones. This hypothesis is underpinned by spatial trimeric structure modeling performed for transmembrane regions of both Group-1 and Group-2 hemagglutinin representatives. Differential S-acylation of the hemagglutinin C-terminal anchoring segment with palmitate/stearate residues possibly contributes to fine tuning of transmembrane trimer packing and stabilization since decreased stearate amount correlated with deeper digestion of influenza B and some A/Group-1 hemagglutinins.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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39
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Polyansky AA, Vassilevski AA, Volynsky PE, Vorontsova OV, Samsonova OV, Egorova NS, Krylov NA, Feofanov AV, Arseniev AS, Grishin EV, Efremov RG. N-terminal amphipathic helix as a trigger of hemolytic activity in antimicrobial peptides: A case study in latarcins. FEBS Lett 2009; 583:2425-8. [DOI: 10.1016/j.febslet.2009.06.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/27/2009] [Accepted: 06/24/2009] [Indexed: 01/29/2023]
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40
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Polyansky AA, Volynsky PE, Arseniev AS, Efremov RG. Adaptation of a membrane-active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface. J Phys Chem B 2009; 113:1120-6. [PMID: 19125636 DOI: 10.1021/jp803641x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the first article of this series we demonstrated the importance of specific intrapeptide interactions and peptide-lipid contacts for the membrane binding of penetratin (pAntp). Here in focus was detailed characterization of spatial hydrophobic/hydrophilic properties of the bilayer surface and their influence on the binding mode of pAntp. From the hydrophobicity point of view, the solvent-accessible surfaces of lipid bilayers possess a distinctly "mosaic" character. This correlates well with the occurrence of dynamic clusters of hydrophobic surface area formed by hydrocarbon tails of phospholipids exposed on the interface. Such mosaic patterns are specific for lipid bilayers of particular composition. In an anionic membrane, they determine initial stages of pAntp adsorption, which strongly depends on the "complementarity" between polarity properties of the peptide and its local interfacial environment. If high complementarity is established, then pAntp penetrates deeply into the membrane without significant destabilization of its initial secondary structure. Alternatively, partial unfolding of pAntp takes place in order to compensate unfavorable peptide-membrane interactions upon embedding. Such effects explain complicated behavior of membrane-active peptides, especially if the target membrane surface is of distinctly mosaic nature, depending on the microscopic properties of the water-lipid interface, pAntp is capable of adopting different pathways to exercise its biological activity.
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Polyansky AA, Volynsky PE, Arseniev AS, Efremov RG. Adaptation of a Membrane-active Peptide to Heterogeneous Environment. I. Structural Plasticity of the Peptide. J Phys Chem B 2009; 113:1107-19. [DOI: 10.1021/jp803640e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton A. Polyansky
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Pavel E. Volynsky
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander S. Arseniev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Dubovskii PV, Volynsky PE, Polyansky AA, Karpunin DV, Chupin VV, Efremov RG, Arseniev AS. Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity. Biochemistry 2008; 47:3525-33. [PMID: 18293934 DOI: 10.1021/bi702203w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Latarcins, linear peptides from the Lachesana tarabaevi spider venom, exhibit a broad-spectrum antimicrobial activity, likely acting on the bacterial cytoplasmic membrane. We study their spatial structures and interaction with model membranes by a combination of experimental and theoretical methods to reveal the structure-activity relationship. In this work, a 26 amino acid peptide, Ltc1, was investigated. Its spatial structure in detergent micelles was determined by (1)H nuclear magnetic resonance (NMR) and refined by Monte Carlo simulations in an implicit water-octanol slab. The Ltc1 molecule was found to form a straight uninterrupted amphiphilic helix comprising 8-23 residues. A dye-leakage fluorescent assay and (31)P NMR spectroscopy established that the peptide does not induce the release of fluorescent marker nor deteriorate the bilayer structure of the membranes. The voltage-clamp technique showed that Ltc1 induces the current fluctuations through planar membranes when the sign of the applied potential coincides with the one across the bacterial inner membrane. This implies that Ltc1 acts on the membranes via a specific mechanism, which is different from the carpet mode demonstrated by another latarcin, Ltc2a, featuring a helix-hinge-helix structure with a hydrophobicity gradient along the peptide chain. In contrast, the hydrophobic surface of the Ltc1 helix is narrow-shaped and extends with no gradient along the axis. We have also disclosed a number of peptides, structurally homologous to Ltc1 and exhibiting similar membrane activity. This indicates that the hydrophobic pattern of the Ltc1 helix and related antimicrobial peptides specifies their activity mechanism. The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane.
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Affiliation(s)
- Peter V Dubovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia.
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Polyansky AA, Volynsky PE, Nolde DE, Arseniev AS, Efremov RG. Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations. J Phys Chem B 2007; 109:15052-9. [PMID: 16852905 DOI: 10.1021/jp0510185] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Anionic unsaturated lipid bilayers represent suitable model systems that mimic real cell membranes: they are fluid and possess a negative surface charge. Understanding of detailed molecular organization of water-lipid interfaces in such systems may provide an important insight into the mechanisms of proteins' binding to membranes. Molecular dynamics (MD) of full-atom hydrated lipid bilayers is one of the most powerful tools to address this problem in silico. Unfortunately, wide application of computational methods for such systems is limited by serious technical problems. They are mainly related to correct treatment of long-range electrostatic effects. In this study a physically reliable model of an anionic unsaturated bilayer of 1,2-dioleoyl-sn-glycero-3-phosphoserine (DOPS) was elaborated and subjected to long-term MD simulations. Electrostatic interactions were treated with two different algorithms: spherical cutoff function and particle-mesh Ewald summation (PME). To understand the role of lipid charge in the system behavior, similar calculations were also carried out for zwitterionic bilayer composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). It was shown that, for the charged DOPS bilayer, the PME protocol performs much better than the cutoff scheme. In the last case a number of artifacts in the structural organization of the bilayer were observed. All of them were attributed to inadequate treatment of electrostatic interactions of lipid headgroups with counterions. Electrostatic properties, along with structural and dynamic parameters, of both lipid bilayers were investigated. Comparative analysis of the MD data reveals that the water-lipid interface of the DOPC bilayer is looser than that for DOPS. This makes possible deeper penetration of water molecules inside the zwitterionic (DOPC) bilayer, where they strongly interact with carbonyls of lipids. This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers.
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Affiliation(s)
- Anton A Polyansky
- Department of Bioengineering, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow 119992, Russia.
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Dubovskii PV, Volynsky PE, Polyansky AA, Chupin VV, Efremov RG, Arseniev AS. Spatial Structure and Activity Mechanism of a Novel Spider Antimicrobial Peptide,. Biochemistry 2006; 45:10759-67. [PMID: 16939228 DOI: 10.1021/bi060635w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Latarcins (Ltc), linear peptides (ca. 25 amino acid long) isolated from the venom of the Lachesana tarabaevi spider, exhibit a broad-spectrum antibacterial activity, most likely acting on the bacterial plasmatic membrane. We study the structure-activity relationships in the series of these compounds. At the first stage, we investigated the spatial structure of one of the peptides, Ltc2a, and its mode of membrane perturbation. This was done by a combination of experimental and theoretical methods. The approach includes (i) structural study of the peptide by CD spectroscopy in phospholipid liposomes and by (1)H NMR in detergent micelles, (ii) determination of the effect on the liposomes by a dye leakage fluorescent assay and (31)P NMR spectroscopy, (iii) refinement of the NMR-derived spatial structure via Monte Carlo simulations in an implicit water-octanol slab, and (iv) calculation of the molecular hydrophobicity potential. The molecule of Ltc2a was found to consist of two helical regions (residues 3-9 and 13-21) connected via a poorly ordered fragment. The effect of the peptide on the liposomes suggests the carpet mechanism of the membrane deterioration. This is also supported by the analysis of hydrophobic/hydrophilic characteristics of Ltc2a and homologous antimicrobial peptides. These peptides exhibiting a helix-hinge-helix structural motif are characterized by a distinct and feebly marked amphiphilicity of their N- and C-terminal helices, respectively, and by a hydrophobicity gradient along the peptide chain. The approach we suggested may be useful in studying not only other latarcins but also a wider class of membrane-active peptides.
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Affiliation(s)
- Peter V Dubovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho Maklaya str., Moscow, 117997 Russia
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Volynsky PE, Polyansky AA, Simakov NA, Arseniev AS, Efremov RG. Effect of Lipid Composition on the “Membrane Response” Induced by a Fusion Peptide. Biochemistry 2005; 44:14626-37. [PMID: 16262262 DOI: 10.1021/bi0514562] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To understand the initial stages of membrane destabilization induced by viral proteins, the factors important for binding of fusion peptides to cell membranes must be identified. In this study, effects of lipid composition on the mode of peptides' binding to membranes are explored via molecular dynamics (MD) simulations of the peptide E5, a water-soluble analogue of influenza hemagglutinin fusion peptide, in two full-atom hydrated lipid bilayers composed of dimyristoyl- and dipalmitoylphosphatidylcholine (DMPC and DPPC, respectively). The results show that, although the peptide has a common folding motif in both systems, it possesses different modes of binding. The peptide inserts obliquely into the DMPC membrane mainly with its N-terminal alpha helix, while in DPPC, the helix lies on the lipid/water interface, almost parallel to the membrane surface. The peptide seriously affects structural and dynamical parameters of surrounding lipids. Thus, it induces local thinning of both bilayers and disordering of acyl chains of lipids in close proximity to the binding site. The "membrane response" significantly depends upon lipid composition: distortions of DMPC bilayer are more pronounced than those in DPPC. Implications of the observed effects to molecular events on initial stages of membrane destabilization induced by fusion peptides are discussed.
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Affiliation(s)
- Pavel E Volynsky
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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