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Gorb L, Voiteshenko I, Hurmach V, Zarudnaya M, Nyporko A, Shyryna T, Platonov M, Roszak S, Rasulev B. From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA. NAR Genom Bioinform 2024; 6:lqae062. [PMID: 38835951 PMCID: PMC11148665 DOI: 10.1093/nargab/lqae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.
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Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Ivan Voiteshenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Vasyl Hurmach
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Margarita Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Tetiana Shyryna
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Maksym Platonov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Szczepan Roszak
- Faculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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