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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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2
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Kundu A, Mamatkulov SI, Brünig FN, Bonthuis DJ, Netz RR, Elsaesser T, Fingerhut BP. Short-Range Cooperative Slow-down of Water Solvation Dynamics Around SO 4 2--Mg 2+ Ion Pairs. ACS PHYSICAL CHEMISTRY AU 2022; 2:506-514. [PMID: 36465835 PMCID: PMC9706802 DOI: 10.1021/acsphyschemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg2+ and SO4 2- ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics. Here, we introduce asymmetric SO4 2- stretching vibrations as new and most specific local probes of solvation dynamics that allow to access ion hydration dynamics at the dilute concentration (0.2 M) of a native electrolyte environment. Highly sensitive heterodyne 2D-IR spectroscopy in the fingerprint region of the SO4 2- ions around 1100 cm-1 reveals a specific slow-down of solvation dynamics for hydrated MgSO4 and for Na2SO4 in the presence of Mg2+ ions, which manifests as a retardation of spectral diffusion compared to aqueous Na2SO4 solutions in the absence of Mg2+ ions. Extensive molecular dynamics and density functional theory QM/MM simulations provide a microscopic view of the observed ultrafast dephasing and hydration dynamics. They suggest a molecular picture where the slow-down of hydration dynamics arises from the structural peculiarities of solvent-shared SO4 2--Mg2+ ion pairs.
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Affiliation(s)
- Achintya Kundu
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
| | - Shavkat I. Mamatkulov
- Institute
of Material Sciences of Uzbekistan Academy of Sciences, Tashkent100084, Uzbekistan
| | | | - Douwe Jan Bonthuis
- Institute
of Theoretical and Computational Physics, Graz University of Technology, Graz8010, Austria
| | - Roland R. Netz
- Fachbereich
Physik, Freie Universität Berlin, Berlin14195, Germany
| | - Thomas Elsaesser
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
| | - Benjamin P. Fingerhut
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
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3
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Graham TR, Nienhuis ET, Reynolds JG, Marcial J, Loring JS, Rosso KM, Pearce CI. Sodium site occupancy and phosphate speciation in natrophosphate are invariant to changes in NaF and Na 3PO 4 concentration. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00868h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of multimodal characterization of Natrophosphate suggests that the crystalline structure is preserved across a range of synthesis conditions.
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Affiliation(s)
- Trent R. Graham
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Emily T. Nienhuis
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Jacob G. Reynolds
- Washington River Protection Solutions, LLC, Richland, Washington 99352, USA
| | - Jose Marcial
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - John S. Loring
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Kevin M. Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Carolyn I. Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164, USA
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Fingerhut BP. The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface. Chem Commun (Camb) 2021; 57:12880-12897. [PMID: 34816825 PMCID: PMC8640580 DOI: 10.1039/d1cc05367a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022]
Abstract
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.
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Avila Salazar DA, Bellstedt P, Miura A, Oi Y, Kasuga T, Brauer DS. Unravelling the dissolution mechanism of polyphosphate glasses by 31P NMR spectroscopy: ligand competition and reactivity of intermediate complexes. Dalton Trans 2021; 50:3966-3978. [PMID: 33646216 DOI: 10.1039/d0dt03381b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate glass dissolution can be tailored via compositional and subsequent structural changes, which is of interest for biomedical applications such as therapeutic ion delivery. Here, solid-state 31P nuclear magnetic resonance characterisation of 45P2O5-xCaO - (55 -x)Na2O glasses was correlated with dissolution studies using time-dependent liquid 31P NMR spectroscopy and quantitative chemical analysis. Glasses dissolved congruently in aqueous media, and the first dissolution stage was the hydration of phosphate chains. In deionised water and Tris buffer (pH0 7.4 or 7.9), trimetaphosphate rings and orthophosphates were the predominant species in solution, indicating relatively fast degradation. By contrast, long phosphate chains were identified in EDTA (pH0 10.0). Besides pH differences, coordination of phosphate species by metal cations appears to play a catalytic role in the hydrolysis mechanism via turning phosphorus atoms into suitable electrophiles for the subsequent nucleophilic attack by water. Hydrolysis rates were proportional to phosphate complex stability, with stronger complexes for chains than for rings. A competition between solvent and phosphate species for the metal ion occurred in the order EDTA > Tris > deionised water.
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Affiliation(s)
- Dahiana A Avila Salazar
- Otto Schott Institute of Materials Research, Friedrich Schiller University, Fraunhoferstr. 6, 07743 Jena, Germany.
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Schauss J, Kundu A, Fingerhut BP, Elsaesser T. Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations. J Phys Chem B 2021; 125:740-747. [PMID: 33284610 PMCID: PMC7848891 DOI: 10.1021/acs.jpcb.0c08966] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Ions interacting with hydrated RNA
play a central role in defining
its secondary and tertiary structure. While spatial arrangements of
ions, water molecules, and phosphate groups have been inferred from
X-ray studies, the role of electrostatic and other noncovalent interactions
in stabilizing compact folded RNA structures is not fully understood
at the molecular level. Here, we demonstrate that contact ion pairs
of magnesium (Mg2+) and phosphate groups embedded in local
water shells stabilize the tertiary equilibrium structure of transfer
RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA
from Escherichia coli, we follow the
population of Mg2+ sites close to phosphate groups of the
ribose-phosphodiester backbone step by step, combining linear and
nonlinear infrared spectroscopy of phosphate vibrations with molecular
dynamics simulations and ab initio vibrational frequency calculations.
The formation of up to six Mg2+/phosphate contact pairs
per tRNA and local field-induced reorientations of water molecules
balance the phosphate–phosphate repulsion in nonhelical parts
of tRNA, thus stabilizing the folded structure electrostatically.
Such geometries display limited sub-picosecond fluctuations in the
arrangement of water molecules and ion residence times longer than
1 μs. At higher Mg2+ excess, the number of contact
ion pairs per tRNA saturates around 6 and weakly interacting ions
prevail. Our results suggest a predominance of contact ion pairs over
long-range coupling of the ion atmosphere and the biomolecule in defining
and stabilizing the tertiary structure of tRNA.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
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7
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Friedrichs G, Hansen N. Congratulations to Friedrich Temps: a multifaceted career in Physical Chemistry. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2020-5001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Gernot Friedrichs
- Institut für Physikalische Chemie , Christian-Albrechts-Universität zu Kiel , Max-Eyth-Strasse 1 , D-24118 Kiel , Germany
| | - Nils Hansen
- Combustion Research Facility, Sandia National Laboratories , Livermore , CA 94550 , USA
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