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Rao YF, Sun LZ, Luo MB. Na +-Mg 2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition. Int J Biol Macromol 2024; 267:131273. [PMID: 38569994 DOI: 10.1016/j.ijbiomac.2024.131273] [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: 02/04/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.
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Affiliation(s)
- Yi-Fan Rao
- School of Physics, Zhejiang University, Hangzhou 310027, China; Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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2
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Sarkar R, Mainan A, Roy S. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chem Commun (Camb) 2024. [PMID: 38501190 DOI: 10.1039/d3cc06105a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
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3
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Coste A, Slejko E, Zavadlav J, Praprotnik M. Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media. J Chem Theory Comput 2024; 20:411-420. [PMID: 38118122 PMCID: PMC10782447 DOI: 10.1021/acs.jctc.3c00984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Molecular dynamics (MD) simulations of biophysical systems require accurate modeling of their native environment, i.e., aqueous ionic solution, as it critically impacts the structure and function of biomolecules. On the other hand, the models should be computationally efficient to enable simulations of large spatiotemporal scales. Here, we present the deep implicit solvation model for sodium chloride solutions that satisfies both requirements. Owing to the use of the neural network potential, the model can capture the many-body potential of mean force, while the implicit water treatment renders the model inexpensive. We demonstrate our approach first for pure ionic solutions with concentrations ranging from physiological to 2 M. We then extend the model to capture the effective ion interactions in the vicinity and far away from a DNA molecule. In both cases, the structural properties are in good agreement with all-atom MD, showcasing a general methodology for the efficient and accurate modeling of ionic media.
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Affiliation(s)
- Amaury Coste
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Ema Slejko
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Julija Zavadlav
- Professorship
of Multiscale Modeling of Fluid Materials, TUM School of Engineering
and Design, Technical University of Munich, Garching Near Munich DE-85748, Germany
| | - Matej Praprotnik
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana SI-1000, Slovenia
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4
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [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: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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Rossi E, Ferrarini A, Sulpizi M. Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly. Phys Chem Chem Phys 2023; 25:6102-6111. [PMID: 36752043 DOI: 10.1039/d2cp05516c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Following nature's example, there is currently strong interest in using adenosine 5'-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC16 TACN]2+) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn2+ and with methyl-1,4,7-triazacyclononane ([ZnCH3 TACN]2+), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn2+ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH3 TACN which, however, may be important for the build-up of supramolecular assemblies.
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Affiliation(s)
- Emma Rossi
- Department of Chemical Sciences, University of Padova, Via Francesco Marzolo, 1, 35131, Padova, Italy.
| | - Alberta Ferrarini
- Department of Chemical Sciences, University of Padova, Via Francesco Marzolo, 1, 35131, Padova, Italy.
| | - Marialore Sulpizi
- Department of Physics, Ruhr Universität Bochum, NB6, 65, 44780, Bochum, Germany.
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Zhdanov VP. Ionizable lipids in bio-inspired nanocarriers. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:121-127. [PMID: 36810604 PMCID: PMC10039821 DOI: 10.1007/s00249-023-01633-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023]
Abstract
In applications of bio-inspired nanoparticles (NPs), their composition is often optimised by including ionizable lipids. I use a generic statistical model to describe the charge and potential distributions in lipid nanoparticles (LNPs) containing such lipids. The LNP structure is considered to contain the biophase regions separated by narrow interphase boundaries with water. Ionizable lipids are uniformly distributed at the biophase-water boundaries. The potential is there described at the mean-filed level combining the Langmuir-Stern equation for ionizable lipids and the Poisson-Boltzmann equation for other charges in water. The latter equation is used outside a LNP as well. With physiologically reasonable parameters, the model predicts the scale of the potential in a LNP to be rather low, smaller or about [Formula: see text], and to change primarily near the LNP-solution interface or, more precisely, inside an NP near this interface because the charge of ionizable lipids becomes rapidly neutralized along the coordinate towards the center of a LNP. The extent of dissociation-mediated neutralization of ionizable lipids along this coordinate increases but only slightly. Thus, the neutralization is primarily due to the negative and positive ions related to the ionic strength in solution and located inside a LNP.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden.
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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Ali Z, Goyal A, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural and Energetic Features of Base-Base Stacking Contacts in RNA. J Chem Inf Model 2023; 63:655-669. [PMID: 36635230 DOI: 10.1021/acs.jcim.2c01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ambika Goyal
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
- Binary Star Research Services, LaSalle, OntarioN9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
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