1
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Thorat A, Chauhan R, Sartape R, Singh MR, Shah JK. Effect of K + Force Fields on Ionic Conductivity and Charge Dynamics of KOH in Ethylene Glycol. J Phys Chem B 2024; 128:3707-3719. [PMID: 38572661 PMCID: PMC11033864 DOI: 10.1021/acs.jpcb.3c08480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Predicting ionic conductivity is crucial for developing efficient electrolytes for energy storage and conversion and other electrochemical applications. An accurate estimate of ionic conductivity requires understanding complex ion-ion and ion-solvent interactions governing the charge transport at the molecular level. Molecular simulations can provide key insights into the spatial and temporal behavior of electrolyte constituents. However, such insights depend on the ability of force fields to describe the underlying phenomena. In this work, molecular dynamics simulations were leveraged to delineate the impact of force field parameters on ionic conductivity predictions of potassium hydroxide (KOH) in ethylene glycol (EG). Four different force fields were used to represent the K+ ion. Diffusion-based Nernst-Einstein and correlation-based Einstein approaches were implemented to estimate the ionic conductivity, and the predicted values were compared with experimental measurements. The physical aspects, including ion-aggregation, charge distribution, cluster correlation, and cluster dynamics, were also examined. A force field was identified that provides reasonably accurate Einstein conductivity values and a physically coherent representation of the electrolyte at the molecular level.
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Affiliation(s)
- Amey Thorat
- School
of Chemical Engineering, Oklahoma State
University, Stillwater, Oklahoma 74078, United States
| | - Rohit Chauhan
- Department
of Chemical Engineering, University of Illinois
at Chicago, Chicago, Illinois 60608, United States
| | - Rohan Sartape
- Department
of Chemical Engineering, University of Illinois
at Chicago, Chicago, Illinois 60608, United States
| | - Meenesh R. Singh
- Department
of Chemical Engineering, University of Illinois
at Chicago, Chicago, Illinois 60608, United States
| | - Jindal K. Shah
- School
of Chemical Engineering, Oklahoma State
University, Stillwater, Oklahoma 74078, United States
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2
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Watanabe E, Nakajima T, Shinohara A, Kasamatsu Y. Hydration Structure of 102No 2+: A Density Functional Theory-Molecular Dynamics Study. J Phys Chem A 2024; 128:2717-2726. [PMID: 38563068 DOI: 10.1021/acs.jpca.3c08063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The hydration structure of No2+, the divalent cation of nobelium in water, was investigated by ab initio molecular dynamics (MD) simulations. First, a series of benchmark calculations were performed to validate the density functional theory (DFT) calculation methods for a molecule containing a No atom. The DFT-MD simulation of the hydration structure of No2+ was conducted after the MD method was validated by simulating the hydration structures of Ca2+ and Sr2+, whose behavior was previously reported to be similar to that of No2+. The model cluster containing M2+ (M = Ca, Sr, or No) and 32 water molecules was used for DFT-MD simulation. The results showed that the hydration distance of No2+ was intermediate between those of Ca2+ and Sr2+. This trend in the hydration distance is in good agreement with the elution position trend obtained in a previous radiochemical experiment. The calculated No-O bond lengths in the optimized structure of [No(H2O)8]2+ was 2.59 Å, while the average No-O bond length of [No(H2O)8]2+ in water by DFT-MD was 2.55 Å. This difference implies the importance of dynamic solvent effects, considering the second (and further) coordination sphere in the theoretical calculation of solution chemistry for superheavy elements.
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Affiliation(s)
- Eisuke Watanabe
- Graduate School of Science, Osaka University, Machikaneyamacho 1-1, Toyonaka, Osaka 560-0043, Japan
- Nishina Accelerator-based Science Center, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Takahito Nakajima
- Center for Computational Science, RIKEN, Minatojimaminamimachi 7-1-26, Kobe, Hyogo 650-0047, Japan
| | - Atsushi Shinohara
- Institute for Radiation Sciences, Osaka University, Yamadaoka 2-4, Suita 565-0871, Japan
- Osaka Aoyama University, Niina 2-11-1, Minoh, Osaka 562-8580, Japan
| | - Yoshitaka Kasamatsu
- Graduate School of Science, Osaka University, Machikaneyamacho 1-1, Toyonaka, Osaka 560-0043, Japan
- Nishina Accelerator-based Science Center, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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3
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Pfeiffer PB, Ugrina M, Schwierz N, Sigurdson CJ, Schmidt M, Fändrich M. Cryo-EM Analysis of the Effect of Seeding with Brain-derived Aβ Amyloid Fibrils. J Mol Biol 2024; 436:168422. [PMID: 38158175 DOI: 10.1016/j.jmb.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/05/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can be proliferated by seeding in vitro. The proliferation reaction is only efficient for one of the three abundant ex vivo Aβ fibril morphologies, which consists of two peptide stacks, while the inefficiently proliferated fibril morphologies contain four or six peptide stacks. In addition to the seeded fibril structures, we find that de novo nucleated fibril structures can emerge in seeded samples if the seeding reaction is continued over multiple generations. These data imply a competition between de novo nucleation and seed extension and suggest further that seeding favours the outgrowth of fibril morphologies that contain fewer peptide stacks.
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Affiliation(s)
| | - Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Christina J Sigurdson
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0612, USA
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany
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4
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Andreotti G, Baur J, Ugrina M, Pfeiffer PB, Hartmann M, Wiese S, Miyahara H, Higuchi K, Schwierz N, Schmidt M, Fändrich M. Insights into the Structural Basis of Amyloid Resistance Provided by Cryo-EM Structures of AApoAII Amyloid Fibrils. J Mol Biol 2024; 436:168441. [PMID: 38199491 DOI: 10.1016/j.jmb.2024.168441] [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: 10/06/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Amyloid resistance is the inability or the reduced susceptibility of an organism to develop amyloidosis. In this study we have analysed the molecular basis of the resistance to systemic AApoAII amyloidosis, which arises from the formation of amyloid fibrils from apolipoprotein A-II (ApoA-II). The disease affects humans and animals, including SAMR1C mice that express the C allele of ApoA-II protein, whereas other mouse strains are resistant to development of amyloidosis due to the expression of other ApoA-II alleles, such as ApoA-IIF. Using cryo-electron microscopy, molecular dynamics simulations and other methods, we have determined the structures of pathogenic AApoAII amyloid fibrils from SAMR1C mice and analysed the structural effects of ApoA-IIF-specific mutational changes. Our data show that these changes render ApoA-IIF incompatible with the specific fibril morphologies, with which ApoA-II protein can become pathogenic in vivo.
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Affiliation(s)
- Giada Andreotti
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany.
| | - Julian Baur
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Marijana Ugrina
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | | | - Max Hartmann
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Hiroki Miyahara
- Institute for Biomedical Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Keiichi Higuchi
- Institute for Biomedical Science, Shinshu University, Matsumoto 390-8621, Japan; Faculty of Human Health Sciences, Meio University, Nago 905-8585, Japan
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
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5
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Limaye A, Suvlu D, Willard AP. Water molecules mute the dependence of the double-layer potential profile on ionic strength. Faraday Discuss 2024; 249:267-288. [PMID: 37830233 DOI: 10.1039/d3fd00114h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
We present the results of molecular dynamics simulations of a nanoscale electrochemical cell. The simulations include an aqueous electrolyte solution with varying ionic strength (i.e., concentrations ranging from 0-4 M) between a pair of metallic electrodes held at constant potential difference. We analyze these simulations by computing the electrostatic potential profile of the electric double-layer region and find it to be nearly independent of ionic concentration, in stark contrast to the predictions of standard continuum-based theories. We attribute this lack of concentration dependence to the molecular influences of water molecules at the electrode-solution interface. These influences include the molecular manifestation of water's dielectric response, which tends to drown out the comparatively weak screening requirement of the ions. To support our analysis, we decompose water's interfacial response into three primary contributions: molecular layering, intrinsic (zero-field) orientational polarization, and the dipolar dielectric response.
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Affiliation(s)
- Aditya Limaye
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| | - Dylan Suvlu
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| | - Adam P Willard
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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6
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Ugrina M, Burkhart I, Müller D, Schwalbe H, Schwierz N. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Res 2024; 52:87-100. [PMID: 37986217 PMCID: PMC10783511 DOI: 10.1093/nar/gkad1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
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Affiliation(s)
- Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
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7
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Philipp J, Dabkowska A, Reiser A, Frank K, Krzysztoń R, Brummer C, Nickel B, Blanchet CE, Sudarsan A, Ibrahim M, Johansson S, Skantze P, Skantze U, Östman S, Johansson M, Henderson N, Elvevold K, Smedsrød B, Schwierz N, Lindfors L, Rädler JO. pH-dependent structural transitions in cationic ionizable lipid mesophases are critical for lipid nanoparticle function. Proc Natl Acad Sci U S A 2023; 120:e2310491120. [PMID: 38055742 PMCID: PMC10723131 DOI: 10.1073/pnas.2310491120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/28/2023] [Indexed: 12/08/2023] Open
Abstract
Lipid nanoparticles (LNPs) are advanced core-shell particles for messenger RNA (mRNA) based therapies that are made of polyethylene glycol (PEG) lipid, distearoylphosphatidylcholine (DSPC), cationic ionizable lipid (CIL), cholesterol (chol), and mRNA. Yet the mechanism of pH-dependent response that is believed to cause endosomal release of LNPs is not well understood. Here, we show that eGFP (enhanced green fluorescent protein) protein expression in the mouse liver mediated by the ionizable lipids DLin-MC3-DMA (MC3), DLin-KC2-DMA (KC2), and DLinDMA (DD) ranks MC3 ≥ KC2 > DD despite similar delivery of mRNA per cell in all cell fractions isolated. We hypothesize that the three CIL-LNPs react differently to pH changes and hence study the structure of CIL/chol bulk phases in water. Using synchrotron X-ray scattering a sequence of ordered CIL/chol mesophases with lowering pH values are observed. These phases show isotropic inverse micellar, cubic Fd3m inverse micellar, inverse hexagonal [Formula: see text] and bicontinuous cubic Pn3m symmetry. If polyadenylic acid, as mRNA surrogate, is added to CIL/chol, excess lipid coexists with a condensed nucleic acid lipid [Formula: see text] phase. The next-neighbor distance in the excess phase shows a discontinuity at the Fd3m inverse micellar to inverse hexagonal [Formula: see text] transition occurring at pH 6 with distinctly larger spacing and hydration for DD vs. MC3 and KC2. In mRNA LNPs, DD showed larger internal spacing, as well as retarded onset and reduced level of DD-LNP-mediated eGFP expression in vitro compared to MC3 and KC2. Our data suggest that the pH-driven Fd3m-[Formula: see text] transition in bulk phases is a hallmark of CIL-specific differences in mRNA LNP efficacy.
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Affiliation(s)
- Julian Philipp
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Aleksandra Dabkowska
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Anita Reiser
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Kilian Frank
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Rafał Krzysztoń
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Christiane Brummer
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Bert Nickel
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory Hamburg Outstation c/o Deutsches Elektronen-Synchrotron, Hamburg22607, Germany
| | - Akhil Sudarsan
- Institute of Physics, University of Augsburg, Augsburg86159, Germany
| | - Mohd Ibrahim
- Institute of Physics, University of Augsburg, Augsburg86159, Germany
| | - Svante Johansson
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Pia Skantze
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Urban Skantze
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Sofia Östman
- Animal Sciences and Technologies, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Marie Johansson
- Animal Sciences and Technologies, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Neil Henderson
- Integrated Bioanalysis, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | | | - Bård Smedsrød
- Vascular Biology Research Group, Department of Medical Biology, University of Tromsø, Tromsø9019, Norway
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Augsburg86159, Germany
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Mölndal431 83, Sweden
| | - Joachim O. Rädler
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich80539, Germany
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8
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Smorodina E, Kav B, Fatafta H, Strodel B. Effects of ion type and concentration on the structure and aggregation of the amyloid peptide A β 16 - 22 $$ {\boldsymbol{\beta}}_{16-22} $$. Proteins 2023. [PMID: 37964477 DOI: 10.1002/prot.26635] [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: 07/19/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Among the various factors controlling the amyloid aggregation process, the influences of ions on the aggregation rate and the resulting structures are important aspects to consider, which can be studied by molecular simulations. There is a wide variety of protein force fields and ion models, raising the question of which model to use in such studies. To address this question, we perform molecular dynamics simulations of Aβ16-22 , a fragment of the Alzheimer's amyloid β peptide, using different protein force fields, AMBER99SB-disp (A99-d) and CHARMM36m (C36m), and different ion parameters. The influences of NaCl and CaCl2 at various concentrations are studied and compared with the systems without the addition of ions. Our results indicate a sensitivity of the peptide-ion interactions to the different ion models. In particular, we observe a strong binding of Ca2+ to residue E22 with C36m and also with the Åqvist ion model used together with A99-d, which slightly affects the monomeric Aβ16-22 structures and the aggregation rate, but significantly affects the oligomer structures formed in the aggregation simulations. For example, at high Ca2+ concentrations, there was a switch from an antiparallel to a parallel β-sheet. Such ionic influences are of biological relevance because local ion concentrations can change in vivo and could help explain the polymorphism of amyloid fibrils.
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Affiliation(s)
- Eva Smorodina
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Hebah Fatafta
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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9
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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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10
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Grava M, Ibrahim M, Sudarsan A, Pusterla J, Philipp J, Rädler JO, Schwierz N, Schneck E. Combining molecular dynamics simulations and x-ray scattering techniques for the accurate treatment of protonation degree and packing of ionizable lipids in monolayers. J Chem Phys 2023; 159:154706. [PMID: 37861119 DOI: 10.1063/5.0172552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The pH-dependent change in protonation of ionizable lipids is crucial for the success of lipid-based nanoparticles as mRNA delivery systems. Despite their widespread application in vaccines, the structural changes upon acidification are not well understood. Molecular dynamics simulations support structure prediction but require an a priori knowledge of the lipid packing and protonation degree. The presetting of the protonation degree is a challenging task in the case of ionizable lipids since it depends on pH and on the local lipid environment and often lacks experimental validation. Here, we introduce a methodology of combining all-atom molecular dynamics simulations with experimental total-reflection x-ray fluorescence and scattering measurements for the ionizable lipid Dlin-MC3-DMA (MC3) in POPC monolayers. This joint approach allows us to simultaneously determine the lipid packing and the protonation degree of MC3. The consistent parameterization is expected to be useful for further predictive modeling of the action of MC3-based lipid nanoparticles.
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Affiliation(s)
- Miriam Grava
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Mohd Ibrahim
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Akhil Sudarsan
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Julio Pusterla
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Julian Philipp
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Joachim O Rädler
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
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11
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Tan S, Nguyen MT, Zhang D, Zhong L, Cheng Z, China S, Johnson GE, Prabhakaran V. Electric-Field-Induced Assembly of an Ionic Liquid-Water Interphase Enables Efficient Heavy Metal Electrosorption. ACS APPLIED MATERIALS & INTERFACES 2023; 15:44469-44481. [PMID: 37676918 DOI: 10.1021/acsami.3c07465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Controlling ion desolvation, transport, and charge transfer at the electrode-electrolyte interface (EEI) is critical to enable the rational design of the efficient and selective separation of targeted heavy metals and the decontamination of industrial wastewater. The main challenge is to sufficiently resolve and interrogate the desolvation of solvated metal ions and their subsequent electroreduction at the EEI and establish pathways to modulate these intermediate steps to achieve efficient energy transfer for targeted reactive separations. Herein, we obtained a predictive understanding of modulating the desolvation and electrosorption of Pb2+ cations using the hydrophobic ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIMCl) in aqueous electrolyte. We revealed the formation of a compact interphase layer consisting of EMIMCl-Pb complexes under an applied electric field using operando electrochemical Raman spectroscopy, atomic force microscopy, and electrochemical impedance spectroscopy measurements combined with classical molecular dynamics simulations. A lower negative potential was shown to result in the formation of a well-oriented layer with the positive imidazolium ring of EMIMCl lying perpendicular to the electrode and the hydrophobic alkyl chain extending into the bulk electrolyte. This oriented layer, which formed from a dilute concentration of EMIMCl added to the electrolyte, was demonstrated to facilitate desolvation of incoming solvated Pb2+ cations and decrease the charge transfer resistance for Pb electrodeposition, which has important implications for the selective removal of Pb from contaminated mixtures. Overall, our findings open up new opportunities to modulate ion desolvation using hydrophobic ionic liquids in aqueous electrolytes for efficient heavy-metal separation.
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Affiliation(s)
- Shuai Tan
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Manh-Thuong Nguyen
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Difan Zhang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Lirong Zhong
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Zezhen Cheng
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Swarup China
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Grant E Johnson
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Venkateshkumar Prabhakaran
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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12
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Sharma K, Banerjee S, Savran D, Rajes C, Wiese S, Girdhar A, Schwierz N, Lee C, Shorter J, Schmidt M, Guo L, Fändrich M. Cryo-EM Structure of the Full-length hnRNPA1 Amyloid Fibril. J Mol Biol 2023; 435:168211. [PMID: 37481159 PMCID: PMC10530274 DOI: 10.1016/j.jmb.2023.168211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein that is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis and multisystem proteinopathy. In this study, we have used cryo-electron microscopy to investigate the three-dimensional structure of amyloid fibrils from full-length hnRNPA1 protein. We find that the fibril core is formed by a 45-residue segment of the prion-like low-complexity domain of the protein, whereas the remaining parts of the protein (275 residues) form a fuzzy coat around the fibril core. The fibril consists of two fibril protein stacks that are arranged into a pseudo-21 screw symmetry. The ordered core harbors several of the positions that are known to be affected by disease-associated mutations, but does not encompass the most aggregation-prone segments of the protein. These data indicate that the structures of amyloid fibrils from full-length proteins may be more complex than anticipated by current theories on protein misfolding.
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Affiliation(s)
- Kartikay Sharma
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany.
| | - Sambhasan Banerjee
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany. https://twitter.com/@SAMBHASANBANERJ
| | - Dilan Savran
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Cedric Rajes
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Amandeep Girdhar
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | - Christopher Lee
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/@shorterlab
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
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13
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Li M, Lv L, Fang T, Hao L, Li S, Dong S, Wu Y, Dong X, Liu H. Self-Consistent Implementation of a Solvation Free Energy Framework to Predict the Salt Solubilities of Six Alkali Halides. J Chem Theory Comput 2023; 19:5586-5601. [PMID: 37471389 DOI: 10.1021/acs.jctc.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
To assess the salt solubilities of six alkali halides in aqueous systems, we proposed a thermodynamic cycle and an efficient molecular modeling methodology. The Gibbs free energy changes for vaporization, dissociation, and dissolution were calculated using the experimental data of ionic thermodynamic properties obtained from the NBS tables. Additionally, the Marcus' and Tissandier's solvation free energy data for Li+, Na+, K+, Cl-, and Br- ions were compared with the conventional solvation free energies by substituting into our self-consistent thermodynamic cycle. Furthermore, Tissandier's absolute solvation free energy data were used as the training set to refit the Lennard-Jones parameters of OPLS-AA force field for ions. To predict salt solubilities, an assumption of a pseudo-solvent was proposed to characterize the coupling work of a solute with its environment from infinitely diluted to saturated solutions, indicating that the Gibbs energy change of solvation process is a function of ionic strength. Following the self-consistency of the cycle, the newly derived formulas were used to determine the salt solubilities by interpolating the intersection of Gibbs free energy of dissolution and the zero free energy line. The refined ion parameters can also predict the structure and thermodynamic properties of aqueous electrolyte solutions, such as densities, pair correlation functions, hydration numbers, mean activity coefficients, vapor pressures, and the radial dependences of the net charge at 298.15 K and 1 bar. Our method can be used to characterize the solid-liquid equilibria of ions or charged particles in aqueous systems. Furthermore, for highly concentrated strong electrolyte systems, it is essential to introduce accurate water models and polarizable force fields.
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Affiliation(s)
- Miyi Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Liqiang Lv
- College of Chemical Engineering, Shijiazhuang University, Hebei, Shijiazhuang 050035, China
| | - Tao Fang
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Long Hao
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Shenhui Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Shoulong Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Yufeng Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Xiao Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Helei Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
- Key Laboratory of Low-Carbon Conversion Science & Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences (Shanghai Advanced Research Institute, Chinese Academy of Sciences), Shanghai 201210, China
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14
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Ibrahim M, Gilbert J, Heinz M, Nylander T, Schwierz N. Structural insights on ionizable Dlin-MC3-DMA lipids in DOPC layers by combining accurate atomistic force fields, molecular dynamics simulations and neutron reflectivity. NANOSCALE 2023. [PMID: 37377412 DOI: 10.1039/d3nr00987d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Ionizable lipids such as the promising Dlin-MC3-DMA (MC3) are essential for the successful design of lipid nanoparticles (LNPs) as drug delivery agents. Combining molecular dynamics simulations with experimental data, such as neutron reflectivity experiments and other scattering techniques, is essential to provide insights into the internal structure of LNPs, which is not fully understood to date. However, the accuracy of the simulations relies on the choice of force field parameters and high-quality experimental data is indispensable to verify the parametrization. For MC3, different parameterizations in combination with the CHARMM and the Slipids force fields have recently emerged. Here, we complement the existing efforts by providing parameters for cationic and neutral MC3 compatible with the AMBER Lipid17 force field. Subsequently, we carefully assess the accuracy of the different force fields by providing a direct comparison to neutron reflectivity experiments of mixed lipid bilayers consisting of MC3 and DOPC at different pHs. At low pH (cationic MC3) and at high pH (neutral MC3) the newly developed MC3 parameters in combination with AMBER Lipid17 for DOPC give good agreement with the experiments. Overall, the agreement is similar compared to the Park-Im parameters for MC3 in combination with the CHARMM36 force field for DOPC. The Ermilova-Swenson MC3 parameters in combination with the Slipids force field underestimate the bilayer thickness. While the distribution of cationic MC3 is very similar, the different force fields for neutral MC3 reveal distinct differences ranging from strong accumulation in the membrane center (current MC3/AMBER Lipid17 DOPC), over mild accumulation (Park-Im MC3/CHARMM36 DOPC) to surface accumulation (Ermilova-Swenson MC3/Slipids DOPC). These pronounced differences highlight the importance of accurate force field parameters and their experimental validation.
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Affiliation(s)
- Mohd Ibrahim
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jennifer Gilbert
- Physical Chemistry, Department of Chemistry Lund University, P.O Box 124, SE-22100 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
| | - Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry Lund University, P.O Box 124, SE-22100 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
- LINXS Institute of Advanced Neutron and X-Ray Science, Scheelevägen 19, 223 70, Lund, Sweden
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon, Republic of Korea
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany.
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15
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Huang J, Fu Z, Sun CF, Deng W. Surfactant Additives Containing Hydrophobic Fluorocarbon Chains and Hydrophilic Sulfonate Anion for Highly Reversible Zn Anode. Molecules 2023; 28:molecules28104177. [PMID: 37241917 DOI: 10.3390/molecules28104177] [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: 04/07/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Aqueous zinc-ion batteries (AZIBs) show enormous potential as a large-scale energy storage technique. However, the growth of Zn dendrites and serious side reactions occurring at the Zn anode hinder the practical application of AZIBs. For the first time, we reported a fluorine-containing surfactant, i.e., potassium perfluoro-1-butanesulfonate (PPFBS), as an additive to the 2 M ZnSO4 electrolyte. Benefitting from its hydrophilic sulfonate anion and hydrophobic long fluorocarbon chain, PPFBS can promote the uniform distribution of Zn2+ flux at the anode/electrolyte interface, allowing the Zn/Zn cell to cycle for 2200 h. Furthermore, PPFBS could inhibit side reactions due to the existence of the perfluorobutyl sulfonate (C4F9SO3-) adsorption layer and the presence of C4F9SO3- in the solvation structure of Zn2+. The former can reduce the amount of H2O molecules and SO42- in contact with the Zn anode and C4F9SO3- entering the Zn2+-solvation structure by replacing SO42-. The Zn/Cu cell exhibits a superior average CE of 99.47% over 500 cycles. When coupled with the V2O5 cathode, the full cell shows impressive cycle stability. This work provides a simple, effective, and economical solution to the common issues of the Zn anode.
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Affiliation(s)
- Jinxian Huang
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Key Laboratory of Nanomaterials, and State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhao Fu
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Key Laboratory of Nanomaterials, and State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Chuan-Fu Sun
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Key Laboratory of Nanomaterials, and State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Wenzhuo Deng
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Key Laboratory of Nanomaterials, and State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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16
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Walhout PK, He Z, Dutagaci B, Nawrocki G, Feig M. Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions. J Phys Chem B 2022; 126:10256-10272. [PMID: 36440862 PMCID: PMC9813770 DOI: 10.1021/acs.jpcb.2c06281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyelectrolytes continue to find wide interest and application in science and engineering, including areas such as water purification, drug delivery, and multilayer thin films. We have been interested in the dynamics of small molecules in a variety of polyelectrolyte (PE) environments; in this paper, we report simulations and analysis of the small dye molecule rhodamine B (RB) in several very simple polyelectrolyte solutions. Translational diffusion of the RB zwitterion has been measured in fully atomistic, 2 μs long molecular dynamics simulations in four different polyelectrolyte solutions. Two solutions contain the common polyanion sodium poly(styrene sulfonate) (PSS), one with a 30-mer chain and the other with 10 trimers. The other two solutions contain the common polycation poly(allyldimethylammonium) chloride (PDDA), one with two 15-mers and the other with 10 trimers. RB diffusion was also simulated in several polymer-free solutions to verify its known experimental value for the translational diffusion coefficient, DRB, of 4.7 × 10-6 cm2/s at 300 K. RB diffusion was slowed in all four simulated PE solutions, but to varying degrees. DRB values of 3.07 × 10-6 and 3.22 × 10-6 cm2/s were found in PSS 30-mer and PSS trimer solutions, respectively, whereas PDDA 15-mer and trimer solutions yielded values of 2.19 × 10-6 and 3.34 × 10-6 cm2/s. Significant associations between RB and the PEs were analyzed and interpreted via a two-state diffusion model (bound and free diffusion) that describes the data well. Crowder size effects and anomalous diffusion were also analyzed. Finally, RB translation along the polyelectrolytes during association was characterized.
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Affiliation(s)
| | - Zhe He
- Wheaton College, Chemistry Department, 501 College Ave, Wheaton, IL 60187
| | - Bercem Dutagaci
- Michigan State University, Biochemistry and Molecular Biology, 603 Wilson Road, Room 218, East Lansing, MI 48824
| | - Grzegorz Nawrocki
- Michigan State University, Biochemistry and Molecular Biology, 603 Wilson Road, Room 218, East Lansing, MI 48824
| | - Michael Feig
- Michigan State University, Biochemistry and Molecular Biology, 603 Wilson Road, Room 218, East Lansing, MI 48824
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17
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Cruz-León S, Schwierz N. RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. J Phys Chem B 2022; 126:8646-8654. [PMID: 36260822 PMCID: PMC9639116 DOI: 10.1021/acs.jpcb.2c04488] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li+, Na+, K+, Cs+, Ca2+, Sr2+, and Ba2+, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.
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Affiliation(s)
- Sergio Cruz-León
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438Frankfurt am Main, Germany
| | - Nadine Schwierz
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438Frankfurt am Main, Germany,Institute
of Physics, University of Augsburg, Universitätsstraße 1, 86159Augsburg, Germany,E-mail:
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18
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Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts. J Mol Biol 2022; 434:167788. [PMID: 35963460 PMCID: PMC10042644 DOI: 10.1016/j.jmb.2022.167788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 12/24/2022]
Abstract
Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure-function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed collective variables and metadynamics efforts, to establish a simple metadynamics protocol, which utilizes only one collective variable, based on multiple tertiary contacts, to characterize the underlying free energy landscape of any RNA molecule. We develop a modified collective variable, the tertiary contacts distance (QTC), which can probe the formation and breakage of all or selectively chosen tertiary contacts of the RNA. The SAM-I riboswitch in the presence of three ionic and substrate conditions was investigated and validated against the structure ensemble previously generated using SAXS experiments. This efficient and easy to implement all-atom MD simulation based approach incorporating metadynamics to study RNA conformational dynamics can also be transferred to any other type of biomolecule.
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19
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Pethes I. Towards the correct microscopic structure of aqueous CsCl solutions with a comparison of classical interatomic potential models. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Fan K, Zhang Y, Qiu Y, Zhang H. Impacts of targeting different hydration free energy references on the development of ion potentials. Phys Chem Chem Phys 2022; 24:16244-16262. [PMID: 35758314 DOI: 10.1039/d2cp01237e] [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
Hydration free energy (HFE) as the most important solvation parameter is often targeted in ion model development, even though the reported values differ by dozens of kcal mol-1 mainly due to the experimentally undetermined HFE of the proton ΔG°(H+). The choice of ΔG°(H+) obviously affects the hydration of single ions and the relative HFE between the ions with different (magnitude or sign) charges, and the impacts of targeted HFEs on the ion solvation and ion-ion interactions are largely unrevealed. Here we designed point charge models of K+, Mg2+, Al3+, and Cl- ions targeting a variety of HFE references and then investigated the HFE influences on the simulations of dilute and concentrated ion solutions and of the salt ion pairs in gas, liquid, and solid phases. Targeting one more property of ion-water oxygen distances (IOD) leaves the ion-water binding distance invariant, while the binding strength increases with the decreasing (more negative) HFE of ions as a result of a decrease in ΔG°(H+) for the cation and an increase in ΔG°(H+) for the anion. The increase in ΔG°(H+) leads to strengthened cation-anion interactions and thus to close ion-ion contacts, low osmotic pressures, and small activity derivatives in concentrated ion solutions as well as too stable ion pairs of the salts in different phases. The ion diffusivity and water exchange rates around the ions are simply not HFE dependent but rather more complex. Targeting both the aqueous IOD and salt crystal properties of KCl was also attempted and the comparison between different models indicates the complexity and challenge in obtaining a balanced performance between different phases using classical force fields. Our results also support that a real ΔG°(H+) value of -259.8 kcal mol-1 recommended by Hünenberger and Reif guides ion models to reproduce ion-water and ion-ion interactions reasonably at relatively low salt concentrations. Simulations of a metalloprotein show that a relatively more positive ΔG°(H+) for Mg2+ model is better for a reasonable description of the metal binding network.
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Affiliation(s)
- Kun Fan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
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21
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The lung surfactant activity probed with molecular dynamics simulations. Adv Colloid Interface Sci 2022; 304:102659. [PMID: 35421637 DOI: 10.1016/j.cis.2022.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 01/17/2023]
Abstract
The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.
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22
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Cruz-León S, Vanderlinden W, Müller P, Forster T, Staudt G, Lin YY, Lipfert J, Schwierz N. Twisting DNA by salt. Nucleic Acids Res 2022; 50:5726-5738. [PMID: 35640616 PMCID: PMC9177979 DOI: 10.1093/nar/gkac445] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ < K+ < Rb+ < Ba2+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Peter Müller
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Tobias Forster
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Georgina Staudt
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Yi-Yun Lin
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience (CeNS), LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
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23
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Torres Cabán C, Yang M, Lai C, Yang L, Subach FV, Smith BO, Piatkevich KD, Boyden ES. Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies. ACS Sens 2022; 7:1336-1346. [PMID: 35427452 PMCID: PMC9150168 DOI: 10.1021/acssensors.1c02201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/09/2022] [Indexed: 12/31/2022]
Abstract
Genetically encoded potassium indicators lack optimal binding affinity for monitoring intracellular dynamics in mammalian cells. Through structure-guided design and genome mining of potassium binding proteins, we developed green fluorescent potassium indicators with a broad range of binding affinities. KRaION1 (K+ ratiometric indicator for optical imaging based on mNeonGreen 1), based on the insertion of a potassium binding protein, Kbp, from E. coli (Ec-Kbp) into the fluorescent protein mNeonGreen, exhibits an isotonically measured Kd of 69 ± 10 mM (mean ± standard deviation used throughout). We identified Ec-Kbp's binding site using NMR spectroscopy to detect protein-thallium scalar couplings and refined the structure of Ec-Kbp in its potassium-bound state. Guided by this structure, we modified KRaION1, yielding KRaION1/D9N and KRaION2, which exhibit isotonically measured Kd's of 138 ± 21 and 96 ± 9 mM. We identified four Ec-Kbp homologues as potassium binding proteins, which yielded indicators with isotonically measured binding affinities in the 39-112 mM range. KRaIONs functioned in HeLa cells, but the Kd values differed from the isotonically measured case. We found that, by tuning the experimental conditions, Kd values could be obtained that were consistent in vitro and in vivo. We thus recommend characterizing potassium indicator Kd in the physiological context of interest before application.
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Affiliation(s)
- Cristina
C. Torres Cabán
- McGovern
Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Media Arts & Sciences, MIT, Cambridge, Massachusetts 02139, United States
| | - Minghan Yang
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
- College
of Physics, Jilin University, Changchun, Jilin 130012, China
| | - Cuixin Lai
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Lina Yang
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Fedor V. Subach
- Complex
of NBICS Technologies, National Research
Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Brian O. Smith
- Institute
of Molecular, Cell & Systems Biology, College of Medical Veterinary
& Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Kiryl D. Piatkevich
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Edward S. Boyden
- McGovern
Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Media Arts & Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Koch
Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
- Department
of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts 02139, United States
- K.
Lisa Yang Center for Bionics, MIT, Cambridge, Massachusetts 02139, United States
- Center
for Neurobiological Engineering, MIT, Cambridge, Massachusetts 02139, United States
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24
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Fakharzadeh A, Zhang J, Roland C, Sagui C. Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. Nucleic Acids Res 2022; 50:4860-4876. [PMID: 35536254 PMCID: PMC9122592 DOI: 10.1093/nar/gkac339] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022] Open
Abstract
The expansion of d(CGG) trinucleotide repeats (TRs) lies behind several important neurodegenerative diseases. Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.
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Affiliation(s)
- Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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25
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Cullati SN, Chaikuad A, Chen JS, Gebel J, Tesmer L, Zhubi R, Navarrete-Perea J, Guillen RX, Gygi SP, Hummer G, Dötsch V, Knapp S, Gould KL. Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Mol Cell 2022; 82:2006-2020.e8. [DOI: 10.1016/j.molcel.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/27/2022] [Accepted: 03/01/2022] [Indexed: 12/01/2022]
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26
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Grotz KK, Schwierz N. Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E. J Chem Phys 2022; 156:114501. [DOI: 10.1063/5.0087292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.
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Affiliation(s)
- Kara K. Grotz
- Theoretical Biophysics, Max Planck Institute of Biophysics, Germany
| | - Nadine Schwierz
- Theoretical Biophysics, Max Planck Institute of Biophysics, Germany
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27
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Tang J, Luo Q, Zeng D, Zhang N. Thermodynamic and Kinetic Studies on the Conversion of Solvent-Shared to Contact Ion Pairs in Sparingly Soluble MF 2 (M = Mg 2+ and Ca 2+) Aqueous Solutions: Implications for Understanding Supersaturated Behavior and Association Constant Determination. J Phys Chem B 2022; 126:1566-1578. [PMID: 35167281 DOI: 10.1021/acs.jpcb.1c09135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thermodynamic and kinetic behaviors of Mg2+-F- ion pairing in aqueous solution are investigated theoretically and experimentally and are contrasted to those of Ca2+-F-. Thermodynamically, similar to CaFx(H2O)142-x (x = 1 and 2), MgF(H2O)y+ (y = 14-20) contact ion pairs (CIPs) are more stable than their solvent-shared ion pairs (SSIPs), whereas the CIPs and SSIPs of MF2(H2O)y are almost isoenergetic. However, in kinetics, the conversion of SSIPs to CIPs for M2+-F- (M = Mg2+ and Ca2+) ion pairing must overcome a high energy barrier due to the strong hydration of Mg2+ and F-. The kinetics dominate after the thermodynamics and kinetics are balanced, which hinders the formation of M2+-F- CIPs in practical MF2 aqueous solutions (less than or equal to saturated concentrations). This result is also supported by the 19F nuclear magnetic resonance spectra of saturated MF2 solutions. Although the interaction between Mg2+ and F- is slightly stronger than that between Ca2+ and F- due to the smaller radius of Mg2+, the formation of Mg2+-F- CIPs needs to go through two rate-limiting steps, the dehydration and entrance of F- (i.e., via exchange mode) with a higher energy barrier, due to the ability of strongly bound water molecules and rigorous octahedral coordinated configuration of Mg2+, while the formation of Ca2+-F- CIPs only goes through a single rate-limiting step, the entrance of F- (i.e., via swinging mode) with a lower energy barrier, due to the flexible coordination configuration of Ca2+. This is responsible for precipitation in MgF2 aqueous solution requiring a larger supersaturation degree and a lower precipitation rate than in CaF2. These kinetic factors lead to the association constants previously reported for MF+ determined by a fluoride ion-selective electrode (ISE) combined with the titration method, where the MF2 solutions were always unsaturated at the titration end point, which actually corresponds to those of the ligand process going from completely free M2+ and F- to their SSIPs. A possible strategy to accurately determine the association constants of MF+ and MF2(aq) CIPs by fluoride ISEs is proposed. The present results suggest that judging the formation of M2+-F- CIPs in practical solutions from a theoretical calculation perspective requires significant consideration of the kinetic factors, except for the thermodynamic factors.
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Affiliation(s)
- Jianfeng Tang
- College of Science, Central South University of Forestry and Technology, Changsha, Hunan 410004, P. R. China
| | - Qiongqiong Luo
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Dewen Zeng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Ning Zhang
- College of Science, Central South University of Forestry and Technology, Changsha, Hunan 410004, P. R. China
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28
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Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins 2022; 90:372-384. [PMID: 34455628 PMCID: PMC8944931 DOI: 10.1002/prot.26227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP-1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2-mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP-1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6-31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP-1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12-6-4 nonbonded interaction model in MD simulations and optimization with a SCC-DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc-metalloenzyme systems.
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Affiliation(s)
- Silvia Gervasoni
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Franco Vairoletti
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores 2124, Montevideo, Uruguay
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29
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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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30
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Grotz KK, Schwierz N. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. J Chem Theory Comput 2022; 18:526-537. [PMID: 34881568 PMCID: PMC8757469 DOI: 10.1021/acs.jctc.1c00791] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Magnesium is essential in many vital processes. To correctly describe Mg2+ in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput. 2021, 17, 2530-2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg2+ parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg2+ force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 106 to 108 exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg2+, or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs.
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Affiliation(s)
- Kara K. Grotz
- Department of Theoretical
Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Nadine Schwierz
- Department of Theoretical
Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
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31
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Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding. Nat Commun 2022; 13:85. [PMID: 35013242 PMCID: PMC8748726 DOI: 10.1038/s41467-021-27688-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022] Open
Abstract
Several studies showed that seeding of solutions of monomeric fibril proteins with ex vivo amyloid fibrils accelerated the kinetics of fibril formation in vitro but did not necessarily replicate the seed structure. In this research we use cryo-electron microscopy and other methods to analyze the ability of serum amyloid A (SAA)1.1-derived amyloid fibrils, purified from systemic AA amyloidosis tissue, to seed solutions of recombinant SAA1.1 protein. We show that 98% of the seeded fibrils remodel the full fibril structure of the main ex vivo fibril morphology, which we used for seeding, while they are notably different from unseeded in vitro fibrils. The seeded fibrils show a similar proteinase K resistance as ex vivo fibrils and are substantially more stable to proteolytic digestion than unseeded in vitro fibrils. Our data support the view that the fibril morphology contributes to determining proteolytic stability and that pathogenic amyloid fibrils arise from proteolytic selection.
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32
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Sundaria A, Liberta F, Savran D, Sarkar R, Rodina N, Peters C, Schwierz N, Haupt C, Schmidt M, Reif B. SAA fibrils involved in AA amyloidosis are similar in bulk and by single particle reconstitution: A MAS solid-state NMR study. J Struct Biol X 2022; 6:100069. [PMID: 35924280 PMCID: PMC9340516 DOI: 10.1016/j.yjsbx.2022.100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
AA amyloidosis is one of the most prevalent forms of systemic amyloidosis and affects both humans and other vertebrates. In this study, we compare MAS solid-state NMR data with a recent cryo-EM study of fibrils involving full-length murine SAA1.1. We address the question whether the specific requirements for the reconstitution of an amyloid fibril structure by cryo-EM can potentially yield a bias towards a particular fibril polymorph. We employ fibril seeds extracted from in to vivo material to imprint the fibril structure onto the biochemically produced protein. Sequential assignments yield the secondary structure elements in the fibril state. Long-range DARR and PAR experiments confirm largely the topology observed in the ex-vivo cryo-EM study. We find that the β-sheets identified in the NMR experiments are similar to the β-sheets found in the cryo-EM study, with the exception of amino acids 33–42. These residues cannot be assigned by solid-state NMR, while they adopt a stable β-sheet in the cryo-EM structure. We suggest that the differences between MAS solid-state NMR and cryo-EM data are a consequence of a second conformer involving residues 33–42. Moreover, we were able to characterize the dynamic C-terminal tail of SAA in the fibril state. The C-terminus is flexible, remains detached from the fibrils, and does not affect the SAA fibril structure as confirmed further by molecular dynamics simulations. As the C-terminus can potentially interact with other cellular components, binding to cellular targets can affect its accessibility for protease digestion.
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33
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Qiu Y, Jiang Y, Zhang Y, Zhang H. Rational Design of Nonbonded Point Charge Models for Monovalent Ions with Lennard-Jones 12-6 Potential. J Phys Chem B 2021; 125:13502-13518. [PMID: 34860517 DOI: 10.1021/acs.jpcb.1c09103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ions are of central importance in nature, and a variety of potential models was proposed to model ions in different phases for an in-depth exploration of ion-related systems. Here, we developed point charge models of 14 monovalent ions with the traditional 12-6 Lennard-Jones (LJ) potential for use in conjunction with 11 water models of TIP3P, OPC3, SPC/E, SPC/Eb, TIP3P-FB, a99SB-disp, TIP4P-Ew, OPC, TIP4P/2005, TIP4P-D, and TIP4P-FB. The designed models reproduced the real hydration free energy (HFE) of ions and the ion-oxygen distance (IOD) in the first hydration shell accurately and simultaneously, a performance similar to the previously reported 12-6-4 LJ-type ion models (12-6 LJ plus an attractive C4 term for cations or a repulsive one for anions). This work, along with our previous work on di-, tri-, and tetravalent metal cations (J. Chem. Inf. Model. 2021, 61, 4031-4044; J. Chem. Inf. Model. 2021, 61, 4613-4629), demonstrates the feasibility of the simple 12-6 LJ potential in ion modeling. In order for the 12-6 LJ potential to reproduce both the HFE and IOD, the LJ R parameters need to be close to Shannon's ionic radii for the highly charged cations and to the Stokes's van der Waals (vdW) radii for the monovalent ions. With an additional C4 term, the R parameters of 12-6-4 LJ ion models agree well with the Stokes's vdW radii and have a more physical meaning. It appears that the C4 term can be merged into the 12-6 LJ potential by a rational tuning of R and the LJ well depth. Simulations of the osmotic coefficients of alkali chloride solutions and the properties of gaseous and solid alkali halides indicate the necessity of further optimizing ion-ion interactions via, for instance, targeting more properties or using a more physical (polarizable) model.
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Affiliation(s)
- Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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34
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Calcium alginate and barium alginate hydrogel filtration membrane coated on fibers for molecule/ion separation. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118761] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Falkner S, Schwierz N. Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field. J Chem Phys 2021; 155:084503. [PMID: 34470357 DOI: 10.1063/5.0060896] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on the water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+-water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and the ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations.
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Affiliation(s)
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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36
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Pappalardo RR, Caralampio DZ, Martínez JM, Sánchez Marcos E. Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy. Inorg Chem 2021; 60:13578-13587. [PMID: 34387993 PMCID: PMC8512670 DOI: 10.1021/acs.inorgchem.1c01888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physicochemical properties of the three heaviest alkaline-earth cations, Sr2+, Ba2+, and Ra2+ in water have been studied by means of classical molecular dynamics (MD) simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The polarizable and flexible model of water MCDHO2 was adopted. The theoretical-experimental comparison of structural, dynamical, energetic, and spectroscopical properties of Sr2+ and Ba2+ aqueous solutions is satisfactory, which supports the methodology developed. This good behavior allows a reasonable reliability for the predicted Ra2+ physicochemical data not experimentally determined yet. Simulated extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge spectroscopy spectra have been computed from the snapshots of the MD simulations and compared with the experimental information available for Sr2+ and Ba2+. For the Ra2+ case, the Ra L3-edge EXAFS spectrum is proposed. Structural and dynamical properties of the aqua ions for the three cations have been obtained and analyzed. Along the [M(H2O)n]m+ series, the M-O distance for the first-hydration shell is 2.57, 2.81, and 2.93 Å for Sr2+, Ba2+, and Ra2+, respectively. The hydration number also increases when one is going down along the group: 8.1, 9.4, and 9.8 for Sr2+, Ba2+, and Ra2+, respectively. Whereas [Sr(H2O)8]2+ is a typical aqua ion with a well-defined structure, the Ba2+ and Ra2+ hydration provides a picture exhibiting an average between the ennea- and the deca-hydration. These results show a similar chemical behavior of Ba2+ and Ra2+ aqueous solutions and support experimental studies on the removal of Ra-226 of aquifers by different techniques, where Ra2+ is replaced by Ba2+. A comparison of the heavy alkaline ions, Rb+ and Cs+, with the heavy alkaline-earth ions is made.
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Affiliation(s)
- Rafael R Pappalardo
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - Daniel Z Caralampio
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - José M Martínez
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
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Uematsu Y. Electrification of water interface. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33. [PMID: 34280896 DOI: 10.1088/1361-648x/ac15d5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/19/2021] [Indexed: 05/04/2023]
Abstract
The surface charge of a water interface determines many fundamental processes in physical chemistry and interface science, and it has been intensively studied for over a hundred years. We summarize experimental methods to characterize the surface charge densities developed so far: electrokinetics, double-layer force measurements, potentiometric titration, surface-sensitive nonlinear spectroscopy, and surface-sensitive mass spectrometry. Then, we elucidate physical ion adsorption and chemical electrification as examples of electrification mechanisms. In the end, novel effects on surface electrification are discussed in detail. We believe that this clear overview of state of the art in a charged water interface will surely help the fundamental progress of physics and chemistry at interfaces in the future.
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Affiliation(s)
- Yuki Uematsu
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
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38
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Zhang Y, Jiang Y, Peng J, Zhang H. Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential. J Chem Inf Model 2021; 61:4031-4044. [PMID: 34313132 DOI: 10.1021/acs.jcim.1c00580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exploring a metal-involved biochemical process at a molecular level often requires a reliable description of metal properties in aqueous solution by classical nonbonded models. An additional C4 term for considering ion-induced dipole interactions was previously proposed to supplement the widely used Lennard-Jones 12-6 potential (known as the 12-6-4 LJ-type model) with good accuracy. Here, we demonstrate an alternative to modeling divalent metal cations (M2+) with the traditional 12-6 LJ potential by developing nonbonded point charge models for use with 11 water models: TIP3P, SPC/E, SPC/Eb, TIP4P-Ew, TIP4P-D, and TIP4P/2005 and the more recent OPC3, TIP3P-FB, OPC, TIP4P-FB, and a99SB-disp. Our designed models simultaneously reproduce the experimental hydration free energy, ion-oxygen distance, and coordination number in the first hydration shell accurately for most of the metal cations, an accuracy equivalent to that of the complex 12-6-4 LJ-type and double exponential potential models. A systematic comparison with the existing M2+ models is presented as well in terms of effective ion radii, diffusion constants, water exchange rates, and ion-water interactions. Molecular dynamics simulations of metal substitution in Escherichia coli glyoxalase I variants show the great potential of our new models for metalloproteins.
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Affiliation(s)
- Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park 16802, Pennsylvania, United States
| | - Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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Loche P, Steinbrunner P, Friedowitz S, Netz RR, Bonthuis DJ. Transferable Ion Force Fields in Water from a Simultaneous Optimization of Ion Solvation and Ion-Ion Interaction. J Phys Chem B 2021; 125:8581-8587. [PMID: 34292738 PMCID: PMC8389903 DOI: 10.1021/acs.jpcb.1c05303] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The poor performance
of many existing nonpolarizable ion force
fields is typically blamed on either the lack of explicit polarizability,
the absence of charge transfer, or the use of unreduced Coulomb interactions.
However, this analysis disregards the large and mostly unexplored
parameter range offered by the Lennard-Jones potential. We use a global
optimization procedure to develop water-model-transferable force fields
for the ions K+, Na+, Cl–,
and Br– in the complete parameter space of all Lennard-Jones
interactions using standard mixing rules. No extra-thermodynamic assumption
is necessary for the simultaneous optimization of the four ion pairs.
After an optimization with respect to the experimental solvation free
energy and activity, the force fields reproduce the concentration-dependent
density, ionic conductivity, and dielectric constant with high accuracy.
The force field is fully transferable between simple point charge/extended
and transferable intermolecular potential water models. Our results
show that a thermodynamically consistent force field for these ions
needs only Lennard-Jones and standard Coulomb interactions.
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Affiliation(s)
- Philip Loche
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Sean Friedowitz
- Department of Materials Science and Engineering, Stanford University, Stanford 94305, California, United States
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Douwe Jan Bonthuis
- Institute of Theoretical and Computational Physics, Graz University of Technology, 8010 Graz, Austria
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40
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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Cruz-León S, Grotz KK, Schwierz N. Extended magnesium and calcium force field parameters for accurate ion-nucleic acid interactions in biomolecular simulations. J Chem Phys 2021; 154:171102. [PMID: 34241062 DOI: 10.1063/5.0048113] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Magnesium and calcium play an essential role in the folding and function of nucleic acids. To correctly describe their interactions with DNA and RNA in biomolecular simulations, an accurate parameterization is crucial. In most cases, the ion parameters are optimized based on a set of experimental solution properties such as solvation free energies, radial distribution functions, water exchange rates, and activity coefficient derivatives. However, the transferability of such bulk-optimized ion parameters to quantitatively describe biomolecular systems is limited. Here, we extend the applicability of our previous bulk-optimized parameters by including experimental binding affinities toward the phosphate oxygen on nucleic acids. In particular, we systematically adjust the combination rules that are an integral part of the pairwise interaction potentials of classical force fields. This allows us to quantitatively describe specific ion binding to nucleic acids without changing the solution properties in the most simple and efficient way. We show the advancement of the optimized Lorentz combination rule for two representative nucleic acid systems. For double-stranded DNA, the optimized combination rule for Ca2+ significantly improves the agreement with experiments, while the standard combination rule leads to unrealistically distorted DNA structures. For the add A-riboswitch, the optimized combination rule for Mg2+ improves the structure of two specifically bound Mg2+ ions as judged by the experimental distance to the binding site. Including experimental binding affinities toward specific ion binding sites on biomolecules, therefore, provides a promising perspective to develop a more accurate description of metal cations for biomolecular simulations.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Kara K Grotz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
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Grotz KK, Cruz-León S, Schwierz N. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties. J Chem Theory Comput 2021; 17:2530-2540. [PMID: 33720710 PMCID: PMC8047801 DOI: 10.1021/acs.jctc.0c01281] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 12/31/2022]
Abstract
Magnesium ions play an essential role in many vital processes. To correctly describe their interactions in molecular dynamics simulations, an accurate parametrization is crucial. Despite the importance and considerable scientific effort, current force fields based on the commonly used 12-6 Lennard-Jones interaction potential fail to reproduce a variety of experimental solution properties. In particular, no parametrization exists so far that simultaneously reproduces the solvation free energy and the distance to the water oxygens in the first hydration shell. Moreover, current Mg2+ force fields significantly underestimate the rate of water exchange leading to unrealistically slow exchange kinetics. In order to make progress in the development of improved models, we systematically optimize the Mg2+ parameters in combination with the TIP3P water model in a much larger parameter space than previously done. The results show that a long-ranged interaction potential and modified Lorentz-Berthelot combination rules allow us to accurately reproduce multiple experimental properties including the solvation free energy, the distances to the oxygens of the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, the self-diffusion coefficient, and the binding affinity to the phosphate oxygen of RNA. Matching this broad range of thermodynamic properties, we present two sets of optimal parameters: MicroMg yields water exchange on the microsecond timescale in agreement with experiments. NanoMg yields water exchange on the nanosecond timescale facilitating the direct observation of ion-binding events. As shown for the example of the add A-riboswitch, the optimized parameters correctly reproduce the structure of specifically bound ions and permit the de novo prediction of Mg2+-binding sites in biomolecular simulations.
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Affiliation(s)
- Kara K. Grotz
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Sergio Cruz-León
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
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43
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Man VH, Wu X, He X, Xie XQ, Brooks BR, Wang J. Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent. J Chem Theory Comput 2021; 17:1086-1097. [PMID: 33503371 DOI: 10.1021/acs.jctc.0c01267] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A double exponential (DE) functional form for Lennard-Jones (LJ) interactions, proposed in our previous study, has many advantages over LJ potentials including a natural softcore characteristic for the convenience of the pathway-based free-energy calculations, fast convergence, and flexibility in use. In this work, we put the first step on the application of the DE functional form by identifying a DE potential, coined DE-TIP3P, for molecular simulations using the TIP3P water model. The developed DE-TIP3 potential was better than LJ potential in reproducing the experimental water properties. Afterward, we developed the nonbonded models of 15 divalent metal ions, which frequently appear and play vital roles in biological systems, to be consistent with the DE-TIP3P potential and TIP3P water model. Our nonbonded models were as good as the complicated nonbonded dummy cationic models by Jiang et al. and the nonbonded 12-6-4 LJ models by Li and Merz in reproducing the experimental properties of those ions. Moreover, our nonbonded models achieved a better performance than the compromise (CM) LJ models and 12-6-4 LJ models, developed by Li and Merz, in reproducing the properties of MgCl2 in aqueous solution.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, Maryland 20892, United States
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, Maryland 20892, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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44
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Baryiames CP, Ma E, Baiz CR. Ions Slow Water Dynamics at Nonionic Surfactant Interfaces. J Phys Chem B 2020; 124:11895-11900. [DOI: 10.1021/acs.jpcb.0c09086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher P. Baryiames
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Emily Ma
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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45
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Gholamjani Moghaddam K, Giudetti G, Sipma W, Faraji S. Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex. Phys Chem Chem Phys 2020; 22:26944-26954. [PMID: 33206064 DOI: 10.1039/d0cp04392c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.
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Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proc Natl Acad Sci U S A 2020; 117:27132-27140. [PMID: 33067392 PMCID: PMC7959525 DOI: 10.1073/pnas.2004563117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The desmosome is a major cell–cell junction connecting cells in tissues under high mechanical load. Currently, while structures of the constituent cadherins are known, the desmosome architecture has remained elusive. The primary reason is the high plasticity of the cadherins. As many other cellular structures, their high flexibility cannot be easily addressed by conventional structural techniques that rely on averaging many identical structures. For this, we combine high-end cryo-electron tomography with large-scale molecular dynamics simulations to produce a molecular model of the desmosome that integrates new with decades-old observations, accounts for the remarkable biophysical properties, and maps the intermolecular interactions. Desmosomes are cell–cell junctions that link tissue cells experiencing intense mechanical stress. Although the structure of the desmosomal cadherins is known, the desmosome architecture—which is essential for mediating numerous functions—remains elusive. Here, we recorded cryo-electron tomograms (cryo-ET) in which individual cadherins can be discerned; they appear variable in shape, spacing, and tilt with respect to the membrane. The resulting sub-tomogram average reaches a resolution of ∼26 Å, limited by the inherent flexibility of desmosomes. To address this challenge typical of dynamic biological assemblies, we combine sub-tomogram averaging with atomistic molecular dynamics (MD) simulations. We generate models of possible cadherin arrangements and perform an in silico screening according to biophysical and structural properties extracted from MD simulation trajectories. We find a truss-like arrangement of cadherins that resembles the characteristic footprint seen in the electron micrograph. The resulting model of the desmosomal architecture explains their unique biophysical properties and strength.
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47
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p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nat Chem Biol 2020; 16:1078-1086. [DOI: 10.1038/s41589-020-0600-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
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48
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Schwierz N. Kinetic pathways of water exchange in the first hydration shell of magnesium. J Chem Phys 2020; 152:224106. [PMID: 32534547 DOI: 10.1063/1.5144258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg2+ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg2+, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations.
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Affiliation(s)
- Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt Am Main, Germany
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49
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Cruz-León S, Schwierz N. Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5979-5989. [PMID: 32366101 PMCID: PMC7304902 DOI: 10.1021/acs.langmuir.0c00851] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A large variety of physicochemical properties involving RNA depends on the type of metal cation present in solution. In order to gain microscopic insight into the origin of these ion specific effects, we apply molecular dynamics simulations to describe the interactions of metal cations and RNA. For the three most common ion binding sites on RNA, we calculate the binding affinities and exchange rates of eight different mono- and divalent metal cations. Our results reveal that binding sites involving phosphate groups preferentially bind metal cations with high charge density (such as Mg2+) in inner-sphere conformations while binding sites involving N7 or O6 atoms preferentially bind cations with low charge density (such as K+). The binding affinity therefore follows a direct Hofmeister series at the backbone but is reversed at the nucleobases leading to a high selectivity of ion binding sites on RNA. In addition, the exchange rates for cation binding cover almost 5 orders of magnitude, leading to a vastly different time scale for the lifetimes of contact pairs. Taken together, the site-specific binding affinities and the specific lifetime of contact pairs provide the microscopic explanation of ion specific effects observed in a wide variety of macroscopic RNA properties. Finally, combining the results from atomistic simulations with extended Poisson-Boltzmann theory allows us to predict the distribution of metal cations around double-stranded RNA at finite concentrations and to reproduce the results of ion counting experiments with good accuracy.
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50
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Dočkal J, Lísal M, Moučka F. Molecular Force Field Development for Aqueous Electrolytes: 2. Polarizable Models Incorporating Crystalline Chemical Potential and Their Accurate Simulations of Halite, Hydrohalite, Aqueous Solutions of NaCl, and Solubility. J Chem Theory Comput 2020; 16:3677-3688. [DOI: 10.1021/acs.jctc.0c00161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Dočkal
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
| | - Martin Lísal
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
| | - Filip Moučka
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
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