1
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Ginell GM, Emenecker RJ, Lotthammer JM, Usher ET, Holehouse AS. Direct prediction of intermolecular interactions driven by disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597104. [PMID: 38895487 PMCID: PMC11185574 DOI: 10.1101/2024.06.03.597104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.
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Affiliation(s)
- Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Ryan. J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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2
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Asakereh I, Rutbeek NR, Singh M, Davidson D, Prehna G, Khajehpour M. The Streptococcus phage protein paratox is an intrinsically disordered protein. Protein Sci 2024; 33:e5037. [PMID: 38801244 PMCID: PMC11129628 DOI: 10.1002/pro.5037] [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: 01/18/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
The bacteriophage protein paratox (Prx) blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces the ability of Streptococcus to uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the Prx:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that Prx may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of Prx in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions Prx is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces Prx folding. However, the solute stabilized fold is different from the conformation Prx adopts when it is bound to ComR. Furthermore, we have characterized Prx folding thermodynamics and folding kinetics through steady-state fluorescence and stopped flow kinetic measurements. Our results show that Prx is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein Prx is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized fold is likely the predominant form of Prx in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing in Streptococcus, by a combination of conformational selection and induced-fit binding mechanisms.
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Affiliation(s)
- Iman Asakereh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Nicole R. Rutbeek
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Manvir Singh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - David Davidson
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Gerd Prehna
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
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3
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [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: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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4
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Trevitt CR, Yashwanth Kumar DR, Fowler NJ, Williamson MP. Interactions between the protein barnase and co-solutes studied by NMR. Commun Chem 2024; 7:44. [PMID: 38418894 PMCID: PMC10902301 DOI: 10.1038/s42004-024-01127-0] [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: 11/05/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.
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Affiliation(s)
- Clare R Trevitt
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
- Certara UK Ltd, Level 2-Acero, 1 Concourse Way, Sheffield, S1 3BJ, UK
| | | | - Nicholas J Fowler
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
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5
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Hervø-Hansen S, Polák J, Tomandlová M, Dzubiella J, Heyda J, Lund M. Salt Effects on Caffeine across Concentration Regimes. J Phys Chem B 2023; 127:10253-10265. [PMID: 38058160 DOI: 10.1021/acs.jpcb.3c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to salting-in or salting-out of aqueous proteins. Early work of Tanford led to the discovery that the solvation of molecular surface motifs is proportional to the solvent accessible surface area (SASA), and later studies have shown that the proportionality constant varies with the salt concentration and type. Using multiscale computer simulations combined with vapor-pressure osmometry on caffeine-salt solutions, we reveal that this SASA description captures a rich set of molecular driving forces in tertiary solutions at changing solute and osmolyte concentrations. Central to the theoretical work is a new potential energy function that depends on the instantaneous surface area, salt type, and concentration. Used in, e.g., Monte Carlo simulations, this allows for a highly efficient exploration of many-body interactions and the resulting thermodynamics at elevated solute and salt concentrations.
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Affiliation(s)
- Stefan Hervø-Hansen
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Markéta Tomandlová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Joachim Dzubiella
- Physikalisches Institut, Albert-Ludwigs Universität Freiburg, Hermann-Herder-Straße 3, Freiburg Im Breisgau D-79104, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Mikael Lund
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Lund Institute of Advance Neutron and X-ray Science (LINXS), Lund SE 223 70, Sweden
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6
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Niederquell A, Stoyanov E, Kuentz M. Physiological Buffer Effects in Drug Supersaturation - A Mechanistic Study of Hydroxypropyl Cellulose as Precipitation Inhibitor. J Pharm Sci 2023; 112:1897-1907. [PMID: 36813134 DOI: 10.1016/j.xphs.2023.02.013] [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: 10/26/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
Phosphate buffer is predominantly used instead of the more physiological bicarbonate buffer, as the latter requires a technical solution of adequate gas mixing. Recent pioneering work on how bicarbonate buffer affected drug supersaturation revealed interesting effects that call for more mechanistic understanding. Therefore, this study used hydroxypropyl cellulose as a model precipitation inhibitor and real-time desupersaturation testing was conducted with the drugs bifonazole, ezetimibe, tolfenamic acid and triclabendazole. Specific buffer effects for the different compounds were noted and overall, statistical significance was found for the precipitation induction time (p = 0.0088). Interestingly, molecular dynamics simulation revealed a conformational effect of the polymer in the presence of the different buffer types. Subsequent molecular docking trials suggested a stronger interaction energy of drug and polymer in the presence of phosphate compared to bicarbonate buffer (p =0.0010). In conclusion, a better mechanistic understanding of how different buffers affect drug-polymer interactions regarding drug supersaturation was achieved. Further mechanisms may account for the overall buffer effects and additional research on drug supersaturation is certainly needed, but it can already be concluded that bicarbonate buffering should be used more often for in vitro testing in drug development.
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Affiliation(s)
- Andreas Niederquell
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, CH 4132 Muttenz, Switzerland
| | - Edmont Stoyanov
- Nisso Chemical Europe, Berliner Allee 42, 40212, Düsseldorf, Germany
| | - Martin Kuentz
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, CH 4132 Muttenz, Switzerland.
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7
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Sun J, Kleuskens S, Luan J, Wang D, Zhang S, Li W, Uysal G, Wilson DA. Morphogenesis of starfish polymersomes. Nat Commun 2023; 14:3612. [PMID: 37330564 PMCID: PMC10276845 DOI: 10.1038/s41467-023-39305-8] [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: 09/17/2021] [Accepted: 06/06/2023] [Indexed: 06/19/2023] Open
Abstract
The enhanced membrane stability and chemical versatility of polymeric vesicles have made them promising tools in micro/nanoreactors, drug delivery, cell mimicking, etc. However, shape control over polymersomes remains a challenge and has restricted their full potential. Here we show that local curvature formation on the polymeric membrane can be controlled by applying poly(N-isopropylacrylamide) as a responsive hydrophobic unit, while adding salt ions to modulate the properties of poly(N-isopropylacrylamide) and its interaction with the polymeric membrane. Polymersomes with multiple arms are fabricated, and the number of arms could be tuned by salt concentration. Furthermore, the salt ions are shown to have a thermodynamic effect on the insertion of poly(N-isopropylacrylamide) into the polymeric membrane. This controlled shape transformation can provide evidence for studying the role of salt ions in curvature formation on polymeric membranes and biomembranes. Moreover, potential stimuli-responsive non-spherical polymersomes can be good candidates for various applications, especially in nanomedicine.
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Affiliation(s)
- Jiawei Sun
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Sandra Kleuskens
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Jiabin Luan
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Danni Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Shaohua Zhang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Wei Li
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Gizem Uysal
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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8
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Arakawa T, Tomioka Y, Kurosawa Y, Akuta T. Elucidating the mechanisms of additive effects at high concentrations on hydrophobic interaction chromatography. J Chromatogr A 2023; 1702:464091. [PMID: 37269642 DOI: 10.1016/j.chroma.2023.464091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/05/2023]
Abstract
Hydrophobic interaction chromatography (HIC) is a commonly used chromatography technique for purifying proteins. It utilizes salting-out salts to facilitate the binding of native proteins to weakly hydrophobic ligands. There have been three proposed mechanisms for the promoting effects of salting-out salts, which include the dehydration of proteins by salts, cavity theory, and salt exclusion. To evaluate the above three mechanisms, an HIC study was conducted on Phenyl Sepharose using four different additives. These additives included a salting-out salt (NH4)2SO4, sodium phosphate that increases the surface tension of water, a salting-in salt MgCl2, and an amphiphilic protein-precipitant polyethylene glycol (PEG). Results indicated that the first two salts resulted in protein binding, while MgCl2 and PEG led to flow-through. These findings were then used to interpret the three proposed mechanisms, which showed that MgCl2 and PEG deviated from the dehydration mechanism, and MgCl2 also deviated from the cavity theory. The observed effects of these additives on HIC were reasonably well explained for the first time by their interactions with proteins.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
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9
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Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
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Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
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10
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Krall JB, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Structure and Formation of Z-DNA and Z-RNA. Molecules 2023; 28:843. [PMID: 36677900 PMCID: PMC9867160 DOI: 10.3390/molecules28020843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.
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Affiliation(s)
- Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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11
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Takekiyo T, Yamada N, Amo T, Nakazawa CT, Asano A, Ichimura T, Kato M, Yoshimura Y. Dissolution of Amyloid Aggregates by Direct Addition of Alkali Halides. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Effect of electrolytes on the sol-gel phase transitions in a Pluronic F127/carboxymethyl cellulose aqueous system: phase map, rheology and NMR self-diffusion study. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Malicka W, Haag R, Ballauff M. Interaction of Heparin with Proteins: Hydration Effects. J Phys Chem B 2022; 126:6250-6260. [PMID: 35960645 DOI: 10.1021/acs.jpcb.2c04928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a thermodynamic investigation of the interaction of heparin with lysozyme in the presence of potassium glutamate (KGlu). The binding constant Kb is measured by isothermal titration calorimetry (ITC) in a temperature range from 288 to 310 K for concentrations of KGlu between 25 and 175 mM. The free energy of binding ΔGb derived from Kb is strongly decreasing with increasing concentration of KGlu, whereas the dependence of ΔGb on temperature T is found to be small. The decrease of ΔGb can be explained in terms of counterion release: Binding of lysozyme to the strong polyelectrolyte heparin liberates approximately three of the condensed counterions of heparin, thus increasing the entropy of the system. The dependence of ΔGb on T, on the other hand, is traced back to a change of hydration of the protein and the polyelectrolyte upon complex formation. This dependence is quantitatively described by the parameter Δw that depends on T and vanishes at a characteristic temperature T0. A comparison of the complex formation in the presence of KGlu with the one in the presence of NaCl demonstrates that the parameters related to hydration are changed considerably. The characteristic temperature T0 in the presence of KGlu solutions is considerably smaller than that in the presence of NaCl solutions. The change of specific heat Δcp is found to become more negative with increasing salt concentration: This finding agrees with the model-free analysis by the generalized van't Hoff equation. The entire analysis reveals a small but important change of the free energy of binding by hydration. It shows that these ion-specific Hofmeister effects can be modeled quantitatively in terms of a characteristic temperature T0 and a parameter describing the dependence of Δcp on salt concentration.
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Affiliation(s)
- Weronika Malicka
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Matthias Ballauff
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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14
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Yun JN, Koh J. Initial heat analysis in dissociation isothermal titration calorimetry: An analytical tool for thermodynamic dissection of biomolecular condensates. Biochem Biophys Res Commun 2022; 605:127-133. [PMID: 35325654 DOI: 10.1016/j.bbrc.2022.03.063] [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: 03/09/2022] [Accepted: 03/13/2022] [Indexed: 11/18/2022]
Abstract
Multi-domain proteins or intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. Such compartmentalization is considered critical in many cellular processes dynamically modulated by various external signals. However, molecular mechanisms underlying potential regulatory functions of the protein condensates remain obscure due to a limited understanding of the driving forces for their assembly. Here we propose isothermal titration calorimetry (ITC) as an efficient analytical tool to dissociate condensates and measure the corresponding dissociation heat. Subsequent analysis of the initial dissociation heat as a function of total protein concentration allows simple and accurate determination of the thermodynamic parameters for cooperative condensate formations including the dissociation (or condensation) enthalpy and the critical protein concentration. By performing systematic simulations, we further demonstrate that the initial heat analysis is sufficiently robust to quantitatively dissect protein condensates with a broad range of thermodynamic properties. Therefore, our proposed method analyzing the initial heat measured in dissociation ITC provides opportunities to further scrutinize the thermodynamic quantities as functions of solution variables to explore the molecular driving forces of LLPS.
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Affiliation(s)
- Jean Nyoung Yun
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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15
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Asakereh I, Lee K, Francisco OA, Khajehpour M. Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A. Chemphyschem 2022; 23:e202100884. [PMID: 35421259 DOI: 10.1002/cphc.202100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/14/2022] [Indexed: 11/06/2022]
Abstract
This work studies the effects of alkaline-earth cation addition upon the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by DSC analysis. RNase A was chosen because it: a) does not specifically bind Mg 2+ , Ca 2+ and Sr 2+ cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl 2 , CaCl 2 and SrCl 2 addition on the melting point of RNase A. Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to "salt-them-in" the solvent, thereby causing an overall reduction in protein stability. We demonstrate that amide-cation interactions are a major contributor to the observed "Hofmeister Effects" of group II cations in protein folding. Our analysis suggests that protein folding "Hofmeister Effects" of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties through increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.
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Affiliation(s)
- Iman Asakereh
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Katherine Lee
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Olga A Francisco
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Mazdak Khajehpour
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, R3T2N2, Winnipeg, CANADA
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16
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Lu J, Hu O, Gu J, Chen G, Ye D, Hou L, Zhang X, Jiang X. Tough and anti-fatigue double network gelatin/polyacrylamide/DMSO/Na2SO4 ionic conductive organohydrogel for flexible strain sensor. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111099] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Zhao Y, Bharadwaj S, van der Vegt N. Nonadditive ion effects on the coil-globule equilibrium of PNIPAM: A computer simulation study. Phys Chem Chem Phys 2022; 24:10346-10355. [DOI: 10.1039/d2cp00057a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combined effect of a weakly hydrated and a strongly hydrated anion on the lower critical solution temperature (LCST) of poly(N-isopropylacrylamide)(PNIPAM) is nonadditive (Bruce et al. J. Am. Chem. Soc....
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18
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Rogers BA, Okur HI, Yan C, Yang T, Heyda J, Cremer PS. Weakly hydrated anions bind to polymers but not monomers in aqueous solutions. Nat Chem 2022; 14:40-45. [PMID: 34725491 DOI: 10.1038/s41557-021-00805-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Abstract
Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN- accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN- preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity.
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Affiliation(s)
- Bradley A Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Halil I Okur
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Chuanyu Yan
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Tinglu Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Dejvice, Czech Republic
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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19
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Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [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
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
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Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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20
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21
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Sanahuja-Embuena V, Frauholz J, Oruc T, Trzaskus K, Hélix-Nielsen C. Transport mechanisms behind enhanced solute rejection in forward osmosis compared to reverse osmosis mode. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Cai Y, Shi J, Liu F, Li H, Man X, Guan S. Hofmeister
Effect‐Assisted
Strong Natural
Biopolymer‐Based
Hydrogels with
Multi‐Functions. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yaqian Cai
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
| | - Jiachuan Shi
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
| | - Fangzhe Liu
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
| | - Haichao Li
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
| | - Xinya Man
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
| | - Shuang Guan
- Department of Polymeric and Soft Materials Laboratory School of Chemistry and Life Science and Advanced Institute of Materials Science Changchun University of Technology, Changchun Jilin 130012 China
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23
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Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg Top Life Sci 2021; 4:307-329. [PMID: 33078839 DOI: 10.1042/etls20190164] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.
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24
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Abstract
The ubiquity of aqueous solutions in contact with charged surfaces and the realization that the molecular-level details of water-surface interactions often determine interfacial functions and properties relevant in many natural processes have led to intensive research. Even so, many open questions remain regarding the molecular picture of the interfacial organization and preferential alignment of water molecules, as well as the structure of water molecules and ion distributions at different charged interfaces. While water, solutes and charge are present in each of these systems, the substrate can range from living tissues to metals. This diversity in substrates has led to different communities considering each of these types of aqueous interface. In this Review, by considering water in contact with metals, oxides and biomembranes, we show the essential similarity of these disparate systems. While in each case the classical mean-field theories can explain many macroscopic and mesoscopic observations, it soon becomes apparent that such theories fail to explain phenomena for which molecular properties are relevant, such as interfacial chemical conversion. We highlight the current knowledge and limitations in our understanding and end with a view towards future opportunities in the field.
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25
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Katsuto H, Okamoto R, Sumi T, Koga K. Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions. J Phys Chem B 2021; 125:6296-6305. [PMID: 34102058 DOI: 10.1021/acs.jpcb.1c03388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
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Affiliation(s)
- Hiroyuki Katsuto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
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26
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Babu CS, Lim C. Influence of solution ionic strength on the stabilities of M20 loop conformations in apo E. coli dihydrofolate reductase. J Chem Phys 2021; 154:195103. [PMID: 34240890 DOI: 10.1063/5.0048968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interactions among ions and their specific interactions with macromolecular solutes are known to play a central role in biomolecular stability. However, similar effects in the conformational stability of protein loops that play functional roles, such as binding ligands, proteins, and DNA/RNA molecules, remain relatively unexplored. A well-characterized enzyme that has such a functional loop is Escherichia coli dihydrofolate reductase (ecDHFR), whose so-called M20 loop has been observed in three ordered conformations in crystal structures. To explore how solution ionic strengths may affect the M20 loop conformation, we proposed a reaction coordinate that could quantitatively describe the loop conformation and used it to classify the loop conformations in representative ecDHFR x-ray structures crystallized in varying ionic strengths. The Protein Data Bank survey indicates that at ionic strengths (I) below the intracellular ion concentration-derived ionic strength in E. coli (I ≤ 0.237M), the ecDHFR M20 loop tends to adopt open/closed conformations, and rarely an occluded loop state, but when I is >0.237M, the loop tends to adopt closed/occluded conformations. Distance-dependent electrostatic potentials around the most mobile M20 loop region from molecular dynamics simulations of ecDHFR in equilibrated CaCl2 solutions of varying ionic strengths show that high ionic strengths (I = 0.75/1.5M) can preferentially stabilize the loop in closed/occluded conformations. These results nicely correlate with conformations derived from ecDHFR structures crystallized in varying ionic strengths. Altogether, our results suggest caution in linking M20 loop conformations derived from crystal structures solved at ionic strengths beyond that tolerated by E. coli to the ecDHFR function.
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Affiliation(s)
- C Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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27
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Wang C, Biok NA, Nayani K, Wang X, Yeon H, Derek Ma CK, Gellman SH, Abbott NL. Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3288-3298. [PMID: 33683138 DOI: 10.1021/acs.langmuir.0c03255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Hydrophobic interactions mediated by nonpolar molecular fragments in water are influenced by local chemical and physical contexts in ways that are not yet fully understood. Here, we use globally amphiphilic (GA) β-peptides (GA-Lys and GA-Arg) with stable conformations to explore if replacement of β3-homolysine (βLys) with β3-homoarginine (βArg) influences the hydrophobically driven assembly of these peptides in bulk aqueous solution. The studies were conducted in 10 mM triethanolamine buffer at pH 7, where both βLys (ammonium) and βArg (guanidinium) side chains are substantially protonated. Comparisons of light scattering measurements and cryo-electron micrographs before and after the addition of 60 vol% MeOH indicate very different outcomes of the hydrophobically driven assembly of AcY-GA-Lys versus AcY-GA-Arg (AcY denotes an N-acetylated-β3-homotyrosine (βTyr) at each N-terminus). Nuclear magnetic resonance and analytical ultracentrifugation confirm that AcY-GA-Lys assembles into large aggregates in aqueous buffer, whereas AcY-GA-Arg at comparable concentrations forms only small oligomers. Titration of AcY-GA-Arg into aqueous solutions of AcY-GA-Lys reveals that the driving force for AcY-GA-Lys association is far stronger than that for AcY-GA-Arg association. We discuss these results in the light of past experimental observations involving single molecule force measurements with GA β-peptides and hydrophobically driven dimerization of conventional peptides that form a GA α-helix upon dimerization (but do not display the Lys versus Arg trend predicted by extrapolating from the earlier AFM studies with β-peptides). Overall, our results establish that the identity of proximal cationic groups, ammonium versus guanidinium, profoundly modulates the hydrophobically driven self-assembly of conformationally stable β-peptides in bulk aqueous solution.
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Affiliation(s)
- Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
- Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Naomi A Biok
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Karthik Nayani
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
| | - Xiaoguang Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Chi-Kuen Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Nicholas L Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
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28
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Bruce EE, Bui PT, Cao M, Cremer PS, van der Vegt NFA. Contact Ion Pairs in the Bulk Affect Anion Interactions with Poly( N-isopropylacrylamide). J Phys Chem B 2021; 125:680-688. [PMID: 33406822 DOI: 10.1021/acs.jpcb.0c11076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Salt effects on the solubility of uncharged polymers in aqueous solutions are usually dominated by anions, while the role of the cation with which they are paired is often ignored. In this study, we examine the influence of three aqueous metal iodide salt solutions (LiI, NaI, and CsI) on the phase transition temperature of poly(N-isopropylacrylamide) (PNIPAM) by measuring the turbidity change of the solutions. Weakly hydrated anions, such as iodide, are known to interact with the polymer and thereby lead to salting-in behavior at low salt concentration followed by salting-out behavior at higher salt concentration. When varying the cation type, an unexpected salting-out trend is observed at higher salt concentrations, Cs+ > Na+ > Li+. Using molecular dynamics simulations, it is demonstrated that this originates from contact ion pair formation in the bulk solution, which introduces a competition for iodide ions between the polymer and cations. The weakly hydrated cation, Cs+, forms contact ion pairs with I- in the bulk solution, leading to depletion of CsI from the polymer-water interface. Microscopically, this is correlated with the repulsion of iodide ions from the amide moiety.
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Affiliation(s)
- Ellen E Bruce
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Pho T Bui
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mengrui Cao
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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29
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Mendes de Oliveira D, Ben-Amotz D. Spectroscopically Quantifying the Influence of Salts on Nonionic Surfactant Chemical Potentials and Micelle Formation. J Phys Chem Lett 2021; 12:355-360. [PMID: 33355467 DOI: 10.1021/acs.jpclett.0c03349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The influence of two salts (NaSCN and Na2SO4) on the micellization of a nonionic surfactant (1,2-hexanediol) is quantified using Raman multivariate curve resolution spectroscopy, combined with a generalized theoretical analysis of the corresponding chemical potential changes. Although the SCN- and SO42- anions are on opposite ends of the Hofmeister series, they are both found to lower the critical micelle concentration. Our combined spectroscopic and theoretical analysis traces these observations to the fact that in both salt solutions the ions have a greater affinity for (or are less strongly expelled from) the hydration shell of the micelle than the free surfactant monomer, as quantified using the corresponding chemical potentials and Wyman-Tanford coefficients. This probe-free experimental and theoretical analysis strategy may readily be extended to micelle formation processes involving other surfactants, salts, and cosolvents, as well as to other sorts of aggregation and binding processes.
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Affiliation(s)
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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30
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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31
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Moses D, Yu F, Ginell GM, Shamoon NM, Koenig PS, Holehouse AS, Sukenik S. Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment. J Phys Chem Lett 2020; 11:10131-10136. [PMID: 33191750 PMCID: PMC8092420 DOI: 10.1021/acs.jpclett.0c02822] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Intrinsically disordered protein-regions (IDRs) make up roughly 30% of the human proteome and are central to a wide range of biological processes. Given a lack of persistent tertiary structure, all residues in IDRs are, to some extent, solvent exposed. This extensive surface area, coupled with the absence of strong intramolecular contacts, makes IDRs inherently sensitive to their chemical environment. We report a combined experimental, computational, and analytical framework for high-throughput characterization of IDR sensitivity. Our framework reveals that IDRs can expand or compact in response to changes in their solution environment. Importantly, the direction and magnitude of conformational change depend on both protein sequence and cosolute identity. For example, some solutes such as short polyethylene glycol chains exert an expanding effect on some IDRs and a compacting effect on others. Despite this complex behavior, we can rationally interpret IDR responsiveness to solution composition changes using relatively simple polymer models. Our results imply that solution-responsive IDRs are ubiquitous and can provide an additional layer of regulation to biological systems.
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Affiliation(s)
- David Moses
- Chemistry and Chemical Biology Program, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | | | - Patrick S. Koenig
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO
| | - Shahar Sukenik
- Chemistry and Chemical Biology Program, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
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32
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Requejo PF, Velho P, Gómez E, Macedo EA. Study of Liquid–Liquid Equilibrium of Aqueous Two-Phase Systems Based on Ethyl Lactate and Partitioning of Rutin and Quercetin. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c02664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patricia F. Requejo
- Advanced Separation Processes Group, Department of Chemical Engineering, University of Vigo, Campus Lagoas-Marcosende, Vigo 36310, Spain
| | - Pedro Velho
- Associate Laboratory of Separation and Reaction Engineering − Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal
| | - Elena Gómez
- Associate Laboratory of Separation and Reaction Engineering − Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal
| | - Eugénia A. Macedo
- Associate Laboratory of Separation and Reaction Engineering − Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal
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33
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Sissaoui J, Budkina DS, Vauthey E. Probing Liquid Interfaces with Room-Temperature Ionic Liquids Using the Excited-State Dynamics of a Cationic Dye. J Phys Chem B 2020; 124:10546-10555. [PMID: 33147032 DOI: 10.1021/acs.jpcb.0c07803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interfaces with room-temperature ionic liquids (ILs) play key roles in many applications of these solvents, but our understanding of their properties is still limited. We investigate how the addition of ILs in the aqueous subphase affects the adsorption of the cationic dye malachite green at the dodecane/water interface using stationary and time-resolved surface second harmonic generation. We find that the interfacial concentration of malachite green depends crucially on the nature of both anionic and cationic constituents. This concentration reports on the overall charge of the interface, which itself depends on the relative interfacial affinity of the ions. Our results reveal that the addition of ILs to the aqueous subphase has similar effects to the addition of conventional salts. However, the IL cations have a significantly higher propensity to adsorb than small inorganic cations. Furthermore, the IL constituents show a synergistic effect, as the interfacial concentration of each of them also depends on the interfacial affinity of the other.
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Affiliation(s)
- Jihad Sissaoui
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Darya S Budkina
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
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34
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Cheng X, Shkel IA, O'Connor K, Record MT. Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water. Proc Natl Acad Sci U S A 2020; 117:27339-27345. [PMID: 33087561 PMCID: PMC7959557 DOI: 10.1073/pnas.2012481117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and side chains. These processes are perturbed by solutes that interact with these atoms differently than water does. Amide NH···O=C hydrogen bonding and various π-system interactions have been better characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkyl ureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, and C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of 10 pairs of amides selected to complete this dataset. An analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are sp2O-sp2C (lone pair-π, presumably n-π*), sp2C-sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.
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Affiliation(s)
- Xian Cheng
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Kevin O'Connor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - M Thomas Record
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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35
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Bruce EE, Okur HI, Stegmaier S, Drexler CI, Rogers BA, van der Vegt NFA, Roke S, Cremer PS. Molecular Mechanism for the Interactions of Hofmeister Cations with Macromolecules in Aqueous Solution. J Am Chem Soc 2020; 142:19094-19100. [PMID: 33124825 DOI: 10.1021/jacs.0c07214] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion identity and concentration influence the solubility of macromolecules. To date, substantial effort has been focused on obtaining a molecular level understanding of specific effects for anions. By contrast, the role of cations has received significantly less attention and the underlying mechanisms by which cations interact with macromolecules remain more elusive. To address this issue, the solubility of poly(N-isopropylacrylamide), a thermoresponsive polymer with an amide moiety on its side chain, was studied in aqueous solutions with a series of nine different cation chloride salts as a function of salt concentration. Phase transition temperature measurements were correlated to molecular dynamics simulations. The results showed that although all cations were on average depleted from the macromolecule/water interface, more strongly hydrated cations were able to locally accumulate around the amide oxygen. These weakly favorable interactions helped to partially offset the salting-out effect. Moreover, the cations approached the interface together with chloride counterions in solvent-shared ion pairs. Because ion pairing was concentration-dependent, the mitigation of the dominant salting-out effect became greater as the salt concentration was increased. Weakly hydrated cations showed less propensity for ion pairing and weaker affinity for the amide oxygen. As such, there was substantially less mitigation of the net salting-out effect for these ions, even at high salt concentrations.
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Affiliation(s)
- Ellen E Bruce
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Halil I Okur
- Department of Chemistry, and National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey.,Laboratory for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sina Stegmaier
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | | | | | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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36
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August DP, Borsley S, Cockroft SL, Della Sala F, Leigh DA, Webb SJ. Transmembrane Ion Channels Formed by a Star of David [2]Catenane and a Molecular Pentafoil Knot. J Am Chem Soc 2020; 142:18859-18865. [PMID: 33084320 PMCID: PMC7745878 DOI: 10.1021/jacs.0c07977] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A (FeII)6-coordinated triply interlocked ("Star of David") [2]catenane (612 link) and a (FeII)5-coordinated pentafoil (51) knot are found to selectively transport anions across phospholipid bilayers. Allostery, topology, and building block stoichiometry all play important roles in the efficacy of the ionophoric activity. Multiple FeII cation coordination by the interlocked molecules is crucial: the demetalated catenane exhibits no anion binding in solution nor any transmembrane ion transport properties. However, the topologically trivial, Lehn-type cyclic hexameric FeII helicates-which have similar anion binding affinities to the metalated Star of David catenane in solution-also display no ion transport properties. The unanticipated difference in behavior between the open- and closed-loop structures may arise from conformational restrictions in the linking groups that likely enhances the rigidity of the channel-forming topologically complex molecules. The (FeII)6-coordinated Star of David catenane, derived from a hexameric cyclic helicate, is 2 orders of magnitude more potent in terms of ion transport than the (FeII)5-coordinated pentafoil knot, derived from a cyclic pentamer of the same building block. The reduced efficacy is reminiscent of multisubunit protein ion channels assembled with incorrect monomer stoichiometries.
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Affiliation(s)
- David P August
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Stefan Borsley
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Flavio Della Sala
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David A Leigh
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Simon J Webb
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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37
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Ganatra SH, Shaikh VR, Ujjankar AS, Khobragade SD, Tomar PA, Patil KJ. Volume and compressibility changes on mixing solutions of alkali halides/sodium acetate with sodium salt of butyric acid at 298.15 K: Understanding like charge ionic (anion–anion) interactions in water. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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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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39
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40
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Vera RE, Salazar‐Rodríguez F, Marquez R, Forgiarini AM. How the Influence of Different Salts on Interfacial Properties of Surfactant–Oil–Water Systems at Optimum Formulation Matches the Hofmeister Series Ranking. J SURFACTANTS DETERG 2020. [DOI: 10.1002/jsde.12406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ramon E. Vera
- Laboratorio FIRPUniversidad de Los Andes Mérida Av Don Tulio Febres Cordero, Mérida 5101 Venezuela
| | | | - Ronald Marquez
- Laboratorio FIRPUniversidad de Los Andes Mérida Av Don Tulio Febres Cordero, Mérida 5101 Venezuela
| | - Ana M. Forgiarini
- Laboratorio FIRPUniversidad de Los Andes Mérida Av Don Tulio Febres Cordero, Mérida 5101 Venezuela
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41
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Luo C, Wei N, Sun X, Luo F. Fabrication of self‐healable, conductive, and ultra‐strong hydrogel from polyvinyl alcohol and grape seed–extracted polymer. J Appl Polym Sci 2020. [DOI: 10.1002/app.49118] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunhui Luo
- College of Chemistry and Chemical EngineeringNorth Minzu University Yinchuan China
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs CommissionNorth Minzu University Yinchuan China
| | - Ning Wei
- College of Chemistry and Chemical EngineeringNorth Minzu University Yinchuan China
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs CommissionNorth Minzu University Yinchuan China
| | - Xinxin Sun
- College of Chemistry and Chemical EngineeringNorth Minzu University Yinchuan China
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs CommissionNorth Minzu University Yinchuan China
| | - Faliang Luo
- State Key Laboratory of High‐efficiency Utilization of Coal and Green Chemical EngineeringNingxia University Yinchuan China
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42
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Sun X, Luo C, Luo F. Preparation and properties of self-healable and conductive PVA-agar hydrogel with ultra-high mechanical strength. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2019.109465] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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43
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Francisco OA, Glor HM, Khajehpour M. Salt Effects on Hydrophobic Solvation: Is the Observed Salt Specificity the Result of Excluded Volume Effects or Water Mediated Ion-Hydrophobe Association? Chemphyschem 2020; 21:484-493. [PMID: 31944529 DOI: 10.1002/cphc.201901000] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/14/2020] [Indexed: 12/30/2022]
Abstract
The solubility of hydrophobic molecules in water is sensitive to salt addition in an ion-specific manner. Such "salting-out" and "salting-in" properties have been shown to be a major contributor to the measured ion-specific Hofmeister effects that are observed in many biophysical phenomena. Various theoretical models have suggested a number of disparate mechanisms for salting-out (salting-in) of hydrophobic moieties, the most popular of which include preferential interaction, water-mediated association, and electrostriction models. However, a complete molecular level description of this ion-specificity is not yet available. This work investigates the ion-specific nature of hydrophobic solvation by studying how sodium and chloride salts affect the thermodynamics of 1,2-hexanediol micellization. The results of this study are analyzed in terms of scaled-particle theory and we show that salt addition can affect hydrophobic solvation in two modalities: salt addition changes the cavitation free energy; salt addition also influences the solvent-solute interaction energy by changing the hydration of the hydrophobic solute. These two effects are salt specific in nature and we suggest that for small hydrophobic solutes these effects are the main cause of salt-specific Hofmeister effects on their solubility.
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Affiliation(s)
| | - Hayden M Glor
- Department of Chemistry, University of Manitoba, Canada
| | - Mazdak Khajehpour
- University of Manitoba, 468 Parker Bldg., Winnipeg, Manitoba, R3T2 N2, Canada.,Department of Chemistry, University of Manitoba, Canada
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44
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Abstract
Structural disorder is widespread in regulatory protein networks. Weak and transient interactions render disordered proteins particularly sensitive to fluctuations in solution conditions such as ion and crowder concentrations. How this sensitivity alters folding coupled binding reactions, however, has not been fully understood. Here, we demonstrate that salt jointly modulates polymer properties and binding affinities of 5 disordered proteins from a transcription factor network. A combination of single-molecule Förster resonance energy transfer experiments, polymer theory, and molecular simulations shows that all 5 proteins expand with increasing ionic strengths due to Debye-Hückel charge screening. Simultaneously, pairwise affinities between the proteins increase by an order of magnitude within physiological salt limits. A quantitative analysis shows that 50% of the affinity increase can be explained by changes in the disordered state. Disordered state properties therefore have a functional relevance even if these states are not directly involved in biological functions. Numerical solutions of coupled binding equilibria with our results show that networks of homologous disordered proteins can function surprisingly robustly in fluctuating cellular environments, despite the sensitivity of its individual proteins.
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45
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The Hofmeister series: Specific ion effects in aqueous polymer solutions. J Colloid Interface Sci 2019; 555:615-635. [PMID: 31408761 DOI: 10.1016/j.jcis.2019.07.067] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Specific ion effects in aqueous polymer solutions have been under active investigation over the past few decades. The current state-of-the-art research is primarily focused on the understanding of the mechanisms through which ions interact with macromolecules and affect their solution stability. Hence, we herein first present the current opinion on the sources of ion-specific effects and review the relevant studies. This includes a summary of the molecular mechanisms through which ions can interact with polymers, quantification of the affinity of ions for the polymer surface, a thermodynamic description of the effects of salts on polymer stability, as well as a discussion on the different forces that contribute to ion-polymer interplay. Finally, we also highlight future research issues that call for further scrutiny. These include fundamental questions on the mechanisms of ion-specific effects and their correlation with polymer properties as well as a discussion on the specific ion effects in more complex systems such as mixed electrolyte solutions.
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46
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Bruce EE, van der Vegt NFA. Molecular Scale Solvation in Complex Solutions. J Am Chem Soc 2019; 141:12948-12956. [DOI: 10.1021/jacs.9b03469] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ellen E. Bruce
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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47
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Gregory KP, Webber GB, Wanless EJ, Page AJ. Lewis Strength Determines Specific-Ion Effects in Aqueous and Nonaqueous Solvents. J Phys Chem A 2019; 123:6420-6429. [DOI: 10.1021/acs.jpca.9b04004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasimir P. Gregory
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Grant B. Webber
- School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Priority Research Centre for Advanced Particle Processing and Transport, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Erica J. Wanless
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Priority Research Centre for Advanced Particle Processing and Transport, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Alister J. Page
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
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48
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Bruce EE, Bui PT, Rogers BA, Cremer PS, van der Vegt NFA. Nonadditive Ion Effects Drive Both Collapse and Swelling of Thermoresponsive Polymers in Water. J Am Chem Soc 2019; 141:6609-6616. [DOI: 10.1021/jacs.9b00295] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ellen E. Bruce
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, D-64287 Darmstadt, Germany
| | - Pho T. Bui
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bradley A. Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Paul S. Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, D-64287 Darmstadt, Germany
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49
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Charaya H, Li X, Jen N, Chung HJ. Specific Ion Effects in Polyampholyte Hydrogels Dialyzed in Aqueous Electrolytic Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1526-1533. [PMID: 30428669 DOI: 10.1021/acs.langmuir.8b02281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polyampholyte hydrogels (PAHs) constitute a class of physical gels with cross-linking originating from inter- and intrachain ionic cross-linking between countercharged functional groups. In our previous report, we have shown that PAH has the potential to be a gel electrolyte in electrochemical energy storage devices. In this work, we further our understanding of charge-balanced PAH as a host material for gel electrolytes by studying the effect of dialysis on the mechanical properties and ionic conductivities of PAHs, whereas these properties are compared with those of poly(vinyl alcohol) (PVA)-based gel electrolytes. Here, various electrolyte solutions were investigated as dialyzing agents. The ionic species in the electrolytes form ion pairs with countercharged functional groups in PAH, whereas such interactions govern the ionic conductivity and mechanical strength of PAH in various electrolytes. For anions, the trend in ionic interactions follows the Hofmeister series in an exact manner, whereas some anomaly is observed among cations. We anticipate that our study provides a design criterion for fabricating gel electrolytes. In a broader context, this work can shed light on understanding the behavior of PAHs in various operational environments, such as under physiological conditions and in antifouling coatings for biomedical and maritime applications, respectively.
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Affiliation(s)
- Hemant Charaya
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Xinda Li
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Nathan Jen
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Hyun-Joong Chung
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
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50
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Vashchenko O, Kasian N, Budianska L, Brodskii R, Bespalova I, Lisetski L. Adsorption of ions on model phospholipid membranes. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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