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Shi R, Cooper AJ, Tanaka H. Impact of hierarchical water dipole orderings on the dynamics of aqueous salt solutions. Nat Commun 2023; 14:4616. [PMID: 37550299 PMCID: PMC10406952 DOI: 10.1038/s41467-023-40278-x] [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: 03/17/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023] Open
Abstract
Ions exhibit highly ion-specific complex behaviours when solvated in water, which remains a mystery despite the fundamental importance of ion solvation in nature, science, and technology. Here we explain these ion-specific properties by the ion-induced hierarchical dipolar, translational, and bond-orientational orderings of ion hydration shell under the competition between ion-water electrostatic interactions and inter-water hydrogen bonding. We first characterise this competition by a new length λHB(q), explaining the ion-specific effects on solution dynamics. Then, by continuously tuning ion size and charge, we find that the bond-orientational order of the ion hydration shell highly develops for specific ion size and charge combinations. This ordering drastically stabilises the hydration shell; its degree changes the water residence time around ions by 11 orders of magnitude for main-group ions. These findings are fundamental to ionic processes in aqueous solutions, providing a physical principle for electrolyte design and application.
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Affiliation(s)
- Rui Shi
- Zhejiang Province Key Laboratory of Quantum Technology and Device, School of Physics, Zhejiang University, Hangzhou, 310027, China.
- Department of Fundamental Engineering, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Anthony J Cooper
- Department of Fundamental Engineering, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Physics, University of California, Santa Barbara, CA, 93106-9530, USA
| | - Hajime Tanaka
- Department of Fundamental Engineering, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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2
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Ion-pairing equilibria and kinetics of dimethyl phosphate: A model for counter-ion binding to the phosphate backbone of nucleic acids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Henning-Knechtel A, Thirumalai D, Kirmizialtin S. Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts. SCIENCE ADVANCES 2022; 8:eabo1190. [PMID: 35857829 PMCID: PMC9299541 DOI: 10.1126/sciadv.abo1190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The stability of RNA increases as the charge density of the alkali metal cations increases. The molecular mechanism for this phenomenon remains elusive. To fill this gap, we performed all-atom molecular dynamics pulling simulations of HIV-1 trans-activation response RNA. We first established that the free energy landscape obtained in the simulations is in excellent agreement with the single-molecule optical tweezer experiments. The origin of the stronger stability in sodium compared to potassium is found to be due to the differences in the charge density-related binding modes. The smaller hydrated sodium ion preferentially binds to the highly charged phosphates that have high surface area. In contrast, the larger potassium ions interact with the major grooves. As a result, more cations condense around phosphate groups in the case of sodium ions, leading to the reduction of electrostatic repulsion. Because the proposed mechanism is generic, we predict that the same conclusions are valid for divalent alkaline earth metal cations.
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Affiliation(s)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
- Corresponding author. (D.T.); (S.K.)
| | - Serdal Kirmizialtin
- Chemistry Program, Math and Sciences, New York University Abu Dhabi, Abu Dhabi, UAE
- Corresponding author. (D.T.); (S.K.)
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He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022; 2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg2+ cations stabilizes the compact state. The absence of Mg2+ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, United States
| | - Anja Henning-Knechtel
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Correspondence: Serdal Kirmizialtin,
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Neumann J, Schwierz N. Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA. J Chem Theory Comput 2022; 18:1202-1212. [PMID: 35084846 PMCID: PMC8830046 DOI: 10.1021/acs.jctc.1c00752] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Magnesium is an indispensable cofactor in countless vital processes. In order to understand its functional role, the characterization of the binding pathways to biomolecules such as RNA is crucial. Despite the importance, a molecular description is still lacking since the transition from the water-mediated outer-sphere to the direct inner-sphere coordination is on the millisecond time scale and therefore out of reach for conventional simulation techniques. To fill this gap, we use transition path sampling to resolve the binding pathways and to elucidate the role of the solvent in the binding process. The results reveal that the molecular void provoked by the leaving phosphate oxygen of the RNA is immediately filled by an entering water molecule. In addition, water molecules from the first and second hydration shell couple to the concerted exchange. To capture the intimate solute-solvent coupling, we perform a committor analysis as the basis for a machine learning algorithm that derives the optimal deep learning model from thousands of scanned architectures using hyperparameter tuning. The results reveal that the properly optimized deep network architecture recognizes the important solvent structures, extracts the relevant information, and predicts the commitment probability with high accuracy. Our results provide detailed insights into the solute-solvent coupling which is ubiquitous for kosmotropic ions and governs a large variety of biochemical reactions in aqueous solutions.
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Affiliation(s)
- Jan Neumann
- Allianz Global Investors GmbH, Bockenheimer Landstrasse 42, 60323 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, 60438 Frankfurt am Main, Germany
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6
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Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proc Natl Acad Sci U S A 2021; 118:2020837118. [PMID: 33658370 DOI: 10.1073/pnas.2020837118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.
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Sivasubramanian R, Chen GH, Mackey HR. The effectiveness of divalent cation addition for highly saline activated sludge cultures: Influence of monovalent/divalent ratio and specific cations. CHEMOSPHERE 2021; 274:129864. [PMID: 33979942 DOI: 10.1016/j.chemosphere.2021.129864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Saline wastewaters are prevalent in various industries and pose challenges to stable biological treatment. Increasing monovalent cation concentrations are commonly reported to deteriorate treatment and settling performance, while divalent cations can enhance flocculation and settling. However, many previous studies were performed at relatively low salinities and reports conflict on whether concentrations of monovalent cations, divalent cations, or their ratio (M/D) are most critical. This study investigates whether addition of divalent cations shows the same benefits at high salinity (∼40 g NaCl.L-1) and whether divalent ion concentration or M/D is a better predictor of enhancement. Nine sequencing batch reactors were operated at 0.8 M NaCl or KCl monovalent salt concentration, and the concentration of divalent cations (Ca2+ and Mg2+) was varied. M/D was found to be the critical factor that consistently influenced sludge characteristics. It was particularly important in describing hydrophobicity, sludge volume index (SVI) and specific oxygen uptake rate (SOUR), with rpartial of -0.879, 0.971 and 0.966 respectively in models that had an r2adj greater than 0.93. Lower M/D also increased biomass concentrations and reduced extracellular polysaccharides, the latter which in turn correlated strongly with many shape and surface charge measures. The specific monovalent salt (Na+ or K+) influenced treatment performance, biomass concentrations, hydrophobicity, SOUR, extracellular protein and SVI. The specific divalent cation was only important in describing SVI, where Mg2+ was beneficial. Overall, this study shows that addition of divalent cations can greatly benefit high salinity activated sludge systems by improving the sludge structure, settling and organic removal.
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Affiliation(s)
- Raghavendran Sivasubramanian
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hamish Robert Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
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8
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Sarkar R, Jaiswar A, Hennelly SP, Onuchic JN, Sanbonmatsu KY, Roy S. Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. J Phys Chem B 2021; 125:6479-6490. [PMID: 34106719 DOI: 10.1021/acs.jpcb.1c02467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions. A mechanism is proposed for the role of experimentally discovered site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers in bacteria. This mechanism is observed with atomistic simulations performed in a physiological mixed salt environment at a high temperature. The simulations were validated with phosphorothioate interference mapping experiments that help to identify crucial inner-sphere Mg2+ sites prescribing an appropriate initial distribution of inner- and outer-sphere magnesium ions to maintain a physiological ion concentration of monovalent and divalent salts. A concerted role of two chelated magnesium ions is newly discovered since the presence of both supports the formation of the pseudoknot. This constitutes a logical AND gate. The absence of any of these magnesium ions instigates the dissociation of long-range pseudoknot interaction exposing the inner core of the RNA. A base triple is the epicenter of the magnesium chelation effect. It allosterically controls RNA pseudoknot by bolstering the direct effect of magnesium chelation in protecting the functional fold of RNA to control ON and OFF transcription switching.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,New Mexico Consortium, Los Alamos, New Mexico 87544, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas 77005, United States
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,New Mexico Consortium, Los Alamos, New Mexico 87544, United States
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
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9
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Abstract
Quantum-mechanically driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically driven structural transformations. Molecular dynamics (MD) simulations of these processes require quantum mechanical (QM) information in order to accurately describe their reactive dynamics. However, current techniques-empirical force fields, subsystem approaches, ab initio MD, and machine learning-vary in their ability to achieve a consistent chemical description across multiple atom types, and at scale. Here we present a physics-based, atomistic force field, the ensemble DFT charge-transfer embedded-atom method, in which QM forces are described at a uniform level of theory across all atoms, avoiding the need for explicit solution of the Schrödinger equation or large, precomputed training data sets. Coupling between the electronic and atomistic length scales is effected through an ensemble density functional theory formulation of the embedded-atom method originally developed for elemental materials. Charge transfer is expressed in terms of ensembles of ionic state basis densities of individual atoms, and charge polarization, in terms of atomic excited-state basis densities. This provides a highly compact yet general representation of the force field, encompassing both local and system-wide effects. Charge rearrangement is realized through the evolution of ensemble weights, adjusted at each dynamical time step via chemical potential equalization.
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Affiliation(s)
- Susan R Atlas
- Department of Chemistry and Chemical Biology, Department of Physics and Astronomy, and Center for Quantum Information and Control, University of New Mexico, Albuquerque, New Mexico 87131, United States
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10
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Halder A, Kumar S, Valsson O, Reddy G. Mg 2+ Sensing by an RNA Fragment: Role of Mg 2+-Coordinated Water Molecules. J Chem Theory Comput 2020; 16:6702-6715. [PMID: 32941038 DOI: 10.1021/acs.jctc.0c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules selectively bind to specific metal ions to populate their functional active states, making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations, making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+, and K+) in the folding of a small RNA hairpin motif (5'-ucCAAAga-3') using unbiased all-atom molecular dynamics simulations. The advantage of studying this system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, the spatial organization of electronegative nucleobase atoms drives the site-specific binding of the metal ions. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in a Mg2+ solution. We show that the rigid network of Mg2+-coordinated water molecules facilitates the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal-sensing mechanisms in large metalloriboswitches and also provide useful insights into the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
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Affiliation(s)
- Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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Abstract
The electrostatic response underlying the 3D-RISM theory and its general relationship to models in which the solvent is represented in terms of a dielectric continuum are examined. It is found that the theory provides a coherent picture of solvation, although its behavior is not entirely consistent with the trends that are expected in the limit of a large solute. The electrostatic discrepancy is due to the nature of the isotropic pair additive site-site correlation function associated with the susceptibility response of the uniform fluid. The influence of the discrepancy in the magnitude of the solvation free energy is negligible for a solvent with a large dielectric constant.
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Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637-1454, United States
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