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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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2
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Wang F, Xia R, Su Y, Cai P, Xu X. Quantifying RNA structures and interactions with a unified reduced chain representation model. Int J Biol Macromol 2023; 253:127181. [PMID: 37793523 DOI: 10.1016/j.ijbiomac.2023.127181] [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] [Received: 06/07/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
RNA is a pivotal molecule that plays critical roles in various cellular processes. Quantifying RNA structures and interactions is essential to understanding RNA function and developing RNA-based therapeutics. Using a unified five-bead model and a non-redundant database, this paper investigates the structural features and interactions of five commonly occurring RNA motifs, i.e., double-stranded helices, hairpin loops, internal/bulge loops, multi-branched junctions, and single-stranded terminal tails. Analyzing detailed distributions of RNA local structural features and base-base interactions reveals a preference for helical structures in both local backbone structures and base orientations. The interactions between adjacent bases exhibit motif-specific and sequence-dependent characteristics, reflecting the distinct topological constraints imposed by different loop-helix connection modes and the varying pairing and stacking interactions among different sequences. These findings shed light on the stability of RNA helices, emphasizing their significance in providing dominant base pairing and stacking interactions for RNA structures and stability. The four non-helix motifs encompass unpaired nucleotide loops and exhibit diverse base-base interactions, contributing to the structural diversity observed in RNA. Overall, the complexity of RNA structure arises from the intricate interplay of base-base interactions.
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Affiliation(s)
- Fengfei Wang
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Renjie Xia
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Yangyang Su
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Pinggen Cai
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China.
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3
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Mu ZC, Tan YL, Liu J, Zhang BG, Shi YZ. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding. Molecules 2023; 28:4833. [PMID: 37375388 DOI: 10.3390/molecules28124833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
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4
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Li T, Hendrix E, He Y. Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server. J Phys Chem B 2023; 127:2177-2186. [PMID: 36827446 DOI: 10.1021/acs.jpcb.2c08945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded proteins, resulting in a lack of hydrophobic core(s) and a tendency to adopt rapidly interconverting structures rather than well-defined structures. The structural heterogeneity of IDPs, encoded by the amino acid sequence, is closely related to their unique roles in biological pathways, which require them to interact with different binding partners. Recently, Robustelli and co-workers have demonstrated that a balanced all-atom force field can be used to sample heterogeneous structures of disordered proteins ( Proc. Natl. Acad. Sci. U.S.A. 2018, 115, E4758-E4766). However, such a solution requires extensive computational resources, such as Anton supercomputers. Here, we propose a simple and effective solution to sample the conformational space of IDPs using a publicly available web server, namely, the UNited-RESidue (UNRES) web server. Our proposed solution requires no investment in computational resources and no prior knowledge of UNRES. UNRES Replica Exchange Molecular Dynamics (REMD) simulations were carried out on a set of eight disordered proteins at temperatures spanning from 270 to 430 K. Utilizing the latest UNRES force field designed for structured proteins, with proper selections of temperatures, we were able to produce comparable results to all-atom force fields as reported in work done by Robustelli and co-workers. In addition, NMR observables and the radius of gyration calculated from UNRES ensembles were directly compared with the experimental data to further evaluate the accuracy of the UNRES model at all temperatures. Our results suggest that carrying out the UNRES simulations at optimal temperatures using the UNRES web server can be a good alternative to sample heterogeneous structures of IDPs.
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Affiliation(s)
- Tongtong Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, United States
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5
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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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6
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Mu ZC, Tan YL, Zhang BG, Liu J, Shi YZ. Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. PLoS Comput Biol 2022; 18:e1010501. [PMID: 36260618 PMCID: PMC9621594 DOI: 10.1371/journal.pcbi.1010501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/31/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs. To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na+ and Mg2+) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- * E-mail:
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7
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Hendrix E, Motta S, Gahl RF, He Y. Insight into the Initial Stages of the Folding Process in Onconase Revealed by UNRES. J Phys Chem B 2022; 126:7934-7942. [PMID: 36179061 DOI: 10.1021/acs.jpcb.2c04770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unfolded state of proteins presents many challenges to elucidate the structural basis for biological function. This state is characterized by a large degree of structural heterogeneity which makes it difficult to generate structural models. However, recent experiments into the initial folding events of the 104-residue ribonuclease homologue onconase (ONC) were able to identify the regions in the protein that participate in the initial folding of this protein. Therefore, to gain additional structural insight into the unfolded state of proteins, this study utilized molecular dynamics simulations using the UNited-RESidue (UNRES) force field to evaluate whether there is a good agreement between the experimentally determined initial structures and the structures identified by computer simulations along a folding pathway. Indeed, these UNRES simulations accurately identified the two regions experimentally observed to form the initial native structure along the folding pathway of ONC. In addition, these regions are determined to be chain folding initiation sites (CFIS) according to methods developed previously. Subsequent self-organization maps (SOM) analysis has revealed key structural states involved in these early folding events.
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Affiliation(s)
- Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan20126, Italy
| | - Robert F Gahl
- Division of Extramural Activities, National Cancer Institute, National Institutes of Health, Bethesda, Maryland20850, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico87131, United States
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8
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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9
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Feng C, Tan YL, Cheng YX, Shi YZ, Tan ZJ. Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement. Front Mol Biosci 2021; 8:666369. [PMID: 33928126 PMCID: PMC8078894 DOI: 10.3389/fmolb.2021.666369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.
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Affiliation(s)
- Chenjie Feng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yu-Xuan Cheng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Zhi-Jie Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
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10
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Zerze GH, Stillinger FH, Debenedetti PG. Thermodynamics of DNA Hybridization from Atomistic Simulations. J Phys Chem B 2021; 125:771-779. [PMID: 33434025 DOI: 10.1021/acs.jpcb.0c09237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- and l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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11
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Liwo A, Czaplewski C, Sieradzan AK, Lubecka EA, Lipska AG, Golon Ł, Karczyńska A, Krupa P, Mozolewska MA, Makowski M, Ganzynkowicz R, Giełdoń A, Maciejczyk M. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:73-122. [PMID: 32145953 DOI: 10.1016/bs.pmbts.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and β-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
| | | | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland
| | | | - Łukasz Golon
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maciej Maciejczyk
- Department of Physics and Biophysics, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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12
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Liwo A, Czaplewski C. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins. J Chem Phys 2020; 152:054902. [DOI: 10.1063/1.5138991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
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13
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Liwo A, Sieradzan AK, Lipska AG, Czaplewski C, Joung I, Żmudzińska W, Hałabis A, Ołdziej S. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. J Chem Phys 2019; 150:155104. [PMID: 31005069 DOI: 10.1063/1.5093015] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were calculated from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, and the respective analytical expressions, derived by using the scale-consistent formalism, were fitted to them. The parameters of all these potentials depend on single-residue types, thus reducing their number and preventing over-fitting. The UNRES force field with the revised backbone-local and backbone-correlation terms was calibrated with a set of four small proteins with basic folds: tryptophan cage variant (TRP1; α), Full Sequence Design (FSD; α + β), villin headpiece (villin; α), and a truncated FBP-28 WW-domain variant (2MWD; β) (the NEWCT-4P force field) and, subsequently, with an enhanced set of 9 proteins composed of TRP1, FSD, villin, 1BDC (α), 2I18 (α), 1QHK (α + β), 2N9L (α + β), 1E0L (β), and 2LX7 (β) (the NEWCT-9P force field). The NEWCT-9P force field performed better than NEWCT-4P in a blind-prediction-like test with a set of 26 proteins not used in calibration and outperformed, in a test with 76 proteins, the most advanced OPT-WTFSA-2 version of UNRES with former backbone-local and backbone-correlation terms that contained more energy terms and more optimizable parameters. The NEWCT-9P force field reproduced the bimodal distribution of backbone-virtual-bond angles in the simulated structures, as observed in experimental protein structures.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - InSuk Joung
- School of Computational Sciences, Korea Institute for Advanced Study, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
| | - Wioletta Żmudzińska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Anna Hałabis
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307 Gdańsk, Poland
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14
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Samsonov SA, Lubecka EA, Bojarski KK, Ganzynkowicz R, Liwo A. Local and long range potentials for heparin‐protein systems for coarse‐grained simulations. Biopolymers 2019; 110:e23269. [DOI: 10.1002/bip.23269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/31/2022]
Affiliation(s)
| | - Emilia A. Lubecka
- Faculty of ChemistryUniversity of Gdańsk Gdańsk Poland
- Faculty of Mathematics, Physics and Informatics, Institute of InformaticsUniversity of Gdańsk Gdańsk Poland
| | | | | | - Adam Liwo
- Faculty of ChemistryUniversity of Gdańsk Gdańsk Poland
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15
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Dans PD, Gallego D, Balaceanu A, Darré L, Gómez H, Orozco M. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. Chem 2019. [DOI: 10.1016/j.chempr.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Sieradzan AK, Giełdoń A, Yin Y, He Y, Scheraga HA, Liwo A. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J Comput Chem 2018; 39:2360-2370. [PMID: 30306573 PMCID: PMC6487257 DOI: 10.1002/jcc.25571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/29/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein-nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al., J. Chem Theory Comput. 2015, 11, 1792). The Debye-Hückel screening has been applied to the electrostatic-interaction energy between the phosphate groups and charged amino-acid side chains. The model has been integrated into the UNRES package for coarse-grained molecular dynamics simulations of proteins and the implementation has been tested for energy conservation in microcanonical molecular dynamics runs and for temperature conservation in canonical molecular dynamics runs. Two case studies were performed: (i) the dynamics of the Ku protein heterodimer bound to DNA, for which it was found that the Ku70/Ku80 protein complex plays an active role in DNA repairing and (ii) conformational changes of the multiple antibiotic resistance (MarA) protein occurring during DNA binding, for which the functionally important motions occurring during this process were identified. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Yanping Yin
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
| | - Yi He
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
- School of Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA 95343, U.S.A
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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17
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Jin L, Shi YZ, Feng CJ, Tan YL, Tan ZJ. Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions. Biophys J 2018; 115:1403-1416. [PMID: 30236782 DOI: 10.1016/j.bpj.2018.08.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/10/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
Double-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability, and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions for 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions for thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that the thermally unfolding pathway of dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix, and the calculated salt-dependent persistence lengths are in good accordance with experiments.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Chen-Jie Feng
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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18
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Krupa P, Wales DJ, Sieradzan AK. Computational Studies of the Mechanical Stability for Single-Strand Break DNA. J Phys Chem B 2018; 122:8166-8173. [DOI: 10.1021/acs.jpcb.8b05417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - David J. Wales
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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19
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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20
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Lubecka EA, Liwo A. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains. J Chem Phys 2017; 147:115101. [DOI: 10.1063/1.4994130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Emilia A. Lubecka
- Institute of Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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