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Kunze T, Dreßler C, Lauer C, Paul W, Sebastiani D. Reverse Mapping of Coarse Grained Polyglutamine Conformations from PRIME20 Sampling. Chemphyschem 2024; 25:e202300521. [PMID: 38314956 DOI: 10.1002/cphc.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
An inverse coarse-graining protocol is presented for generating and validating atomistic structures of large (bio-) molecules from conformations obtained via a coarse-grained sampling method. Specifically, the protocol is implemented and tested based on the (coarse-grained) PRIME20 protein model (P20/SAMC), and the resulting all-atom conformations are simulated using conventional biomolecular force fields. The phase space sampling at the coarse-grained level is performed with a stochastical approximation Monte Carlo approach. The method is applied to a series of polypeptides, specifically dimers of polyglutamine with varying chain length in aqueous solution. The majority (>70 %) of the conformations obtained from the coarse-grained peptide model can successfully be mapped back to atomistic structures that remain conformationally stable during 10 ns of molecular dynamics simulations. This work can be seen as the first step towards the overarching goal of improving our understanding of protein aggregation phenomena through simulation methods.
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Affiliation(s)
- Thomas Kunze
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Christian Dreßler
- Institut für Physik, Ilmenau University of Technology, Weimarer Straße 32, 98693, Ilmenau, Germany
| | - Christian Lauer
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Wolfgang Paul
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Daniel Sebastiani
- Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany
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2
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Thiel BC, Poblete S, Hofacker IL. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline. Methods Mol Biol 2024; 2726:377-399. [PMID: 38780739 DOI: 10.1007/978-1-0716-3519-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Aside from the well-known role in protein synthesis, RNA can perform catalytic, regulatory, and other essential biological functions which are determined by its three-dimensional structure. In this regard, a great effort has been made during the past decade to develop computational tools for the prediction of the structure of RNAs from the knowledge of their sequence, incorporating experimental data to refine or guide the modeling process. Nevertheless, this task can become exceptionally challenging when dealing with long noncoding RNAs, constituted by more than 200 nucleotides, due to their large size and the specific interactions involved. In this chapter, we describe a multiscale approach to predict such structures, incorporating SAXS experimental data into a hierarchical procedure which couples two coarse-grained representations: Ernwin, a helix-based approach, which deals with the global arrangement of secondary structure elements, and SPQR, a nucleotide-centered coarse-grained model, which corrects and refines the structures predicted at the coarser level.We describe the methodology through its application on the Braveheart long noncoding RNA, starting from the SAXS and secondary structure data to propose a refined, all-atom structure.
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Affiliation(s)
- Bernhard C Thiel
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia, Chile
- Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad SanSebastián, Santiago, Chile
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.
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NARall: a novel tool for reconstruction of the all-atom structure of nucleic acids from heavily coarse-grained model. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractNucleic acids are one of the most important cellular components. These molecules have been studied both experimentally and theoretically. As all-atom simulations are still limited to short time scales, coarse-grain modeling allows to study of those molecules on a longer time scale. Nucleic-Acid united RESidue (NARES-2P) is a low-resolution coarse-grained model with two centers of interaction per repeating unit. It has been successfully applied to study DNA self-assembly and telomeric properties. This force field enables the study of nucleic acids Behavior on a long time scale but lacks atomistic details. In this article, we present new software to reconstruct atomistic details from the NARES-2P model. It has been applied to RNA pseudoknot, nucleic acid four-way junction, G-quadruplex and DNA duplex converted to NARES-2P model and back. Moreover, it was applied to DNA structure folded and self-assembled with NARES-2P.
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Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021; 13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Affiliation(s)
- Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
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Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. J Am Chem Soc 2021; 143:8333-8343. [PMID: 34039006 PMCID: PMC8188756 DOI: 10.1021/jacs.1c01094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/17/2022]
Abstract
The 5' untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.
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Affiliation(s)
- Sandro Bottaro
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Giovanni Bussi
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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Li M, Teng B, Lu W, Zhang JZ. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J Mol Model 2020; 26:31. [PMID: 31965325 DOI: 10.1007/s00894-020-4298-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/14/2020] [Indexed: 11/29/2022]
Abstract
Coarse-grained (CG) model has been a powerful tool in bridging the gap between theoretical studies and experimental phenomena in biological computing field. The reconstruction from a CG model to an atomic-detail structure is especially important in CG studies of biological systems. In this work, a rigid-fragment- and local-frame-based (RF-LF) backmapping method was proposed to achieve reverse mapping from CG models to atomic-level structures. The initial atomic-level structures were further refined to yield the final backmapping ones. With the popular Martini force field, the performance of the RF-LF method was extensively examined in the CG → AA (CG to AA) backmapping of protein/DNA/RNA systems. Besides, the RF-LF method was also extended to the backmapping of the TMFF model. Numerical results illustrate that the RF-LF backmapping method is generic and parameter-free and can provide a promising way to tackle atomic-level studies in CG models.
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Affiliation(s)
- Min Li
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
| | - Bing Teng
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - WenCai Lu
- College of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - John ZengHui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, People's Republic of China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, People's Republic of China.
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Peng J, Yuan C, Ma R, Zhang Z. Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference. J Chem Theory Comput 2019; 15:3344-3353. [PMID: 30908042 DOI: 10.1021/acs.jctc.9b00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coarse-grained (CG) simulations have allowed access to larger length scales and longer time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) molecular dynamics (MD) simulations. Backmapping from CG models to AA structures has long been studied because it enables us to gain detailed structure insights from CG simulations. Many methods first construct an AA structure from the CG model by fragments, random placement, or geometrical rules and subsequently optimize the solution via energy minimization, simulated annealing or position-restrained simulations. However, such methods may only work well on residue-level CG models and cannot consider the deviations of CG models. In this work, we describe, to the best of our knowledge, a new backmapping method based on Bayesian inference and restrained MD simulations. Restraints with log harmonic energy terms are defined according to the target CG model using the Bayesian inference in which the CG deviations can be estimated. From an initial AA structure obtained from either high-resolution experiments or homology modeling, a MD simulation with the aforementioned restraints is performed to obtain a final AA structure that is a backmapping of the target CG model. The method was validated using multiresolution CG models of the soluble extracellular region of the human epidermal growth factor receptor and was further applied to construct AA structures from CG simulations of the nucleosome core particle. The results demonstrate that our method can generate accurate AA structures of different types of biomolecules from multiple CG models with either residue-level resolution or much lower resolution than one-site-per-residue.
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Affiliation(s)
- Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Chuang Yuan
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
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Sulpizi M, Faller R, Pantano S. Multiscale modeling on biological systems. Biochem Biophys Res Commun 2018; 498:263. [PMID: 29496451 DOI: 10.1016/j.bbrc.2018.02.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marialore Sulpizi
- Department of Physics, Johannes Gutenberg University, Mainz, Germany
| | - Roland Faller
- Department of Chemical Engineering, University of California-Davis, Davis, CA, USA
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