51
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Bottaro S, Gil-Ley A, Bussi G. RNA folding pathways in stop motion. Nucleic Acids Res 2016; 44:5883-91. [PMID: 27091499 PMCID: PMC4937309 DOI: 10.1093/nar/gkw239] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/29/2016] [Accepted: 03/29/2016] [Indexed: 11/19/2022] Open
Abstract
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions.
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Affiliation(s)
- Sandro Bottaro
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy
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52
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Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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53
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Grzybkowska A, Jędrzejczyk D, Rostkowski M, Chworos A, Dybala-Defratyka A. RNA model evaluation based on MD simulation of four tRNA analogs. RSC Adv 2016. [DOI: 10.1039/c6ra14933b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characteristic of 3D structures of tRNA analogs generated from primary sequence, subjected to all-atom MD simulation and assessed using selected RNA model evaluation methods.
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Affiliation(s)
- Anna Grzybkowska
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Dominika Jędrzejczyk
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Arkadiusz Chworos
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
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54
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Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. J Phys Chem B 2015; 119:15176-90. [DOI: 10.1021/acs.jpcb.5b08876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Havrila
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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55
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Pérez-Villa A, Darvas M, Bussi G. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Res 2015; 43:8725-34. [PMID: 26358809 PMCID: PMC4605317 DOI: 10.1093/nar/gkv872] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/18/2015] [Indexed: 01/05/2023] Open
Abstract
Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures.
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Affiliation(s)
- Andrea Pérez-Villa
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
| | - Maria Darvas
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea, I-34136 Trieste, Italy
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56
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Olsson S, Cavalli A. Quantification of Entropy-Loss in Replica-Averaged Modeling. J Chem Theory Comput 2015; 11:3973-7. [DOI: 10.1021/acs.jctc.5b00579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Simon Olsson
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Ticino, Switzerland
- Laboratory
of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Zürich, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Ticino, Switzerland
- Department
of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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