1
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Nishio T, Sugino K, Yoshikawa Y, Matsumoto M, Oe Y, Sadakane K, Yoshikawa K. K+ promotes the favorable effect of polyamine on gene expression better than Na. PLoS One 2020; 15:e0238447. [PMID: 32881909 PMCID: PMC7470421 DOI: 10.1371/journal.pone.0238447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+. PRINCIPAL FINDINGS It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge. CONCLUSION AND SIGNIFICANCE We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kaito Sugino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | | | - Yohei Oe
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan
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2
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Tolmachev DA, Boyko OS, Lukasheva NV, Martinez-Seara H, Karttunen M. Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections. J Chem Theory Comput 2019; 16:677-687. [DOI: 10.1021/acs.jctc.9b00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- D. A. Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - O. S. Boyko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - N. V. Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - H. Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
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3
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Kroeger T, Frieg B, Zhang T, Hansen FK, Marmann A, Proksch P, Nagel-Steger L, Groth G, Smits SHJ, Gohlke H. EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay. PLoS One 2017; 12:e0177024. [PMID: 28472107 PMCID: PMC5417642 DOI: 10.1371/journal.pone.0177024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is widely used in the life sciences as chelating ligand of metal ions. However, formation of supramolecular EDTA aggregates at pH > 8 has been reported, which may lead to artifactual assay results. When applied as a buffer component at pH ≈ 10 in differential scanning fluorimetry (TSA) using SYPRO Orange as fluorescent dye, we observed a sharp change in fluorescence intensity about 20°C lower than expected for the investigated protein. We hypothesized that this change results from SYPRO Orange/EDTA interactions. TSA experiments in the presence of SYPRO Orange using solutions that contain EDTA-Na+ but no protein were performed. The TSA experiments provide evidence that suggests that at pH > 9, EDTA4- interacts with SYPRO Orange in a temperature-dependent manner, leading to a fluorescence signal yielding a "denaturation temperature" of ~68°C. Titrating Ca2+ to SYPRO Orange and EDTA solutions quenched fluorescence. Ethylene glycol tetraacetic acid (EGTA) behaved similarly to EDTA. Analytical ultracentrifugation corroborated the formation of EDTA aggregates. Molecular dynamics simulations of free diffusion of EDTA-Na+ and SYPRO Orange of in total 27 μs suggested the first structural model of EDTA aggregates in which U-shaped EDTA4- arrange in an inverse bilayer-like manner, exposing ethylene moieties to the solvent, with which SYPRO Orange interacts. We conclude that EDTA aggregates induce a SYPRO Orange-based fluorescence in TSA. These results make it relevant to ascertain that future TSA results are not influenced by interference between EDTA, or EDTA-related molecules, and the fluorescent dye.
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Affiliation(s)
- Tobias Kroeger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tao Zhang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Finn K. Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Marmann
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Proksch
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H. J. Smits
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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4
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Okur HI, Hladílková J, Rembert KB, Cho Y, Heyda J, Dzubiella J, Cremer PS, Jungwirth P. Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions. J Phys Chem B 2017; 121:1997-2014. [PMID: 28094985 DOI: 10.1021/acs.jpcb.6b10797] [Citation(s) in RCA: 411] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.
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Affiliation(s)
- Halil I Okur
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Jana Hladílková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic.,Division of Theoretical Chemistry, Lund University , P.O.B. 124, SE-22100 Lund, Sweden
| | | | - Younhee Cho
- Department of Chemistry, Texas A&M University , College Station 77843, Texas, United States
| | - Jan Heyda
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, 16628 Prague 6, Czech Republic
| | - Joachim Dzubiella
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Institut für Physik, Humboldt-Universität zu Berlin , Newtonstrasse 15, 12489 Berlin, Germany
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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5
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Ruggiero MT, Sibik J, Erba A, Zeitler JA, Korter TM. Quantification of cation–anion interactions in crystalline monopotassium and monosodium glutamate salts. Phys Chem Chem Phys 2017; 19:28647-28652. [DOI: 10.1039/c7cp05544g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific anion–cation orbital interactions lead to the large structural and spectral differences observed in crystalline monosodium and monopotassium glutamates.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemistry
- Syracuse University
- 1-104 Center for Science and Technology
- Syracuse
- USA
| | - Juraj Sibik
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Alessandro Erba
- Dipartimento di Chimica and Centre of Excellence Nanostructured Interfaces and Surfaces, Universita di Torino
- Torino
- Italy
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Timothy M. Korter
- Department of Chemistry
- Syracuse University
- 1-104 Center for Science and Technology
- Syracuse
- USA
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6
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Marchand G, Soetens JC, Jacquemin D, Bopp PA. Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution. J Chem Phys 2015; 143:224505. [DOI: 10.1063/1.4937156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Gabriel Marchand
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France
| | - Jean-Christophe Soetens
- Institut des Sciences Moléculaires (ISM), Université de Bordeaux, Bât A12, FR-33405 Talence Cedex, France
| | - Denis Jacquemin
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France
| | - Philippe A. Bopp
- Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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7
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Church AT, Hughes ZE, Walsh TR. Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters. RSC Adv 2015. [DOI: 10.1039/c5ra11268k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca2+, and introduce a modification that can recover experimentally-determined binding free energies for these systems.
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Affiliation(s)
- Andrew T. Church
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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8
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Terekhova I, Chibunova E, Kumeev R, Kruchinin S, Fedotova M, Kozbiał M, Wszelaka-Rylik M, Gierycz P. Specific and nonspecific effects of biologically active inorganic salts on inclusion complex formation of cyclodextrins with aromatic carboxylic acids. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.09.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Shen H, Cheng W, Zhang FS. Structural conservation of the short α-helix in modified higher and lower polarity water solutions. RSC Adv 2015. [DOI: 10.1039/c4ra14739a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Which conformation is preferred when the polarity of water molecules is scaled byEP=ELJ+S2EC?
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Affiliation(s)
- Hao Shen
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Wei Cheng
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
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10
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Liu X, Li H, Li R, Xie D, Ni J, Wu L. Strong non-classical induction forces in ion-surface interactions: general origin of Hofmeister effects. Sci Rep 2014; 4:5047. [PMID: 24854224 PMCID: PMC7365329 DOI: 10.1038/srep05047] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/06/2014] [Indexed: 11/25/2022] Open
Abstract
Hofmeister effects continue to defy all-encompassing theories and their origin
is still a matter of debate. We observed strong Hofmeister effects in
Ca2+/Na+ exchange on a
permanently charged surface over a wide range of ionic strengths. They could not be
attributed to dispersion forces, classical induction forces, ionic size, or
hydration effects. We demonstrated that another stronger force was active in the
ion-surface interactions and which would create Hofmeister effects in general. The
strength of this force was up to 104 times that of the
classical induction force and could be comparable to the Coulomb force. Coulomb,
dispersion and hydration effects appeared to be interwined to affect the force. The
presence of the observed strong non-classical induction force implied that energies
of non-valence electrons of ions/atoms at the interface might be heavily
underestimated in current theories and possibly just those underestimated energies
of non-valence electrons determined Hofmeister effects.
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Affiliation(s)
- Xinmin Liu
- Chongqing key laboratory of soil multi-scale interfacial process, College of Resources and Environment, Southwest University, Chongqing 400715, CHINA
| | - Hang Li
- Chongqing key laboratory of soil multi-scale interfacial process, College of Resources and Environment, Southwest University, Chongqing 400715, CHINA
| | - Rui Li
- Chongqing key laboratory of soil multi-scale interfacial process, College of Resources and Environment, Southwest University, Chongqing 400715, CHINA
| | - Deti Xie
- Chongqing key laboratory of soil multi-scale interfacial process, College of Resources and Environment, Southwest University, Chongqing 400715, CHINA
| | - Jiupai Ni
- Chongqing key laboratory of soil multi-scale interfacial process, College of Resources and Environment, Southwest University, Chongqing 400715, CHINA
| | - Laosheng Wu
- Department of Environmental Sciences, University of California, Riverside, CA 92501, USA
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11
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Asciutto EK, Gaborek T, Madura JD. Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614400045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Equilibrium peptide conformations in solution, especially in the presence of salts, has been of interest for several decades. The fundamental interactions that determine the dominant peptide conformations in solution have been experimentally and computationally probed; however, a unified understanding has not yet emerged. In a previous study, we performed metadynamics simulations on the heptapeptide AEAAAEA in Sodium Chloride ( NaCl ) and Potassium Chloride ( KCl ) solutions at concentrations ranging from 0.5–2.0 M. Using a three-dimensional collective variable coordinate system, we computed the free energy landscapes in each saline environment as well as in pure water. We found that the presence of Na + and K + ions induces some changes in the stability of the conformers that define the state space, but does not alter the overall energetics between conformers and does not favor helical conformations. We investigate here, how the presence of salts ( NaCl and KCl ) affects the glutamic–glutamic interaction and its consequences on the stability of each equilibrium conformation. We perform this study through fixed backbone simulations for the most populated conformations identified in our previous work: the α-helix, 310-helix, π-helix, the extended polyproline II (PPII) and 2.51-helix conformations. It was found that for each conformation, there exists stable substates determined by the glutamic acid side-chains distance and orientation, and that Na + and K + cations (de)stabilize preferentially each conformation. It was also found that intramolecular single water mediated hydrogen bonds play a crucial role in the observed (de) stabilization of each equilibrium conformation.
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Affiliation(s)
- Eliana K. Asciutto
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15219, USA
| | - Timothy Gaborek
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15219, USA
| | - Jeffry D. Madura
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15219, USA
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12
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Shen H, Cheng W, Zhang FS. Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022717. [PMID: 25353518 DOI: 10.1103/physreve.89.022717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 06/04/2023]
Abstract
The structure of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in explicit aqueous solutions with mixed inorganic salts (NaCl and KCl) is investigated by using molecular simulations. The concentration of Na(+), c(Na(+)), varies from 0.0M to 1.0M, whereas the concentration of K(+) is 1-c(Na(+)). The simulated peptide is very sensitive to the change of concentration ratio between Na(+) and K(+). When the concentration ratio between Na^{+} and K^{+} is changed from 0.5/0.5, the structure of the peptide becomes loose or disordered. This specific phenomenon is confirmed via checking the changes of helix parameters and mapping the free energy along different coordinates. The higher normalized probability of forming direct and indirect salt bridges between residues Glu7(+) and Lys11(+) and the smallest probability of forming ringlike structures should be responsible for the stabilized helix structure in the 0.5 Na(+)/0.5 K(+) solution. Furthermore, a noticeable conformational transition from an extended helix to an α helix is found in the 0.5 Na(+)/0.5 K(+) solution, where a local ion cloud shows that some Na(+) ions in the inner shells are still directly binding with the peptide, while K(+) in the outer shells are moving into the inner shells, keeping the peptide in the collapsed state.
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Affiliation(s)
- Hao Shen
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China
| | - Wei Cheng
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China and Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China
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13
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Yoda T, Sugita Y, Okamoto Y. Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations. Proteins 2013; 82:933-43. [PMID: 24214490 DOI: 10.1002/prot.24467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/26/2013] [Accepted: 10/29/2013] [Indexed: 11/07/2022]
Abstract
We have investigated effects of salt ions on folding events of a helical miniprotein chicken villin headpiece subdomain HP36. Low concentrations of ions alter electrostatic interactions between charged groups of a protein and can change the populations of conformers. Here, we compare two data sets of folding simulations of HP36 in explicit water solvent with or without ions. For efficient sampling of the conformational space of HP36, the multicanonical replica-exchange molecular dynamics method was employed. Our analyses suggest that salt alters salt-bridging nature of the protein at later stages of folding at room temperature. Especially, more nonnative, nonlocal salt bridges are formed at near-native conformations in pure water. Our analyses also show that such salt-bridge formation hinders the fully native hydrophobic-core packing at the final stages of folding.
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Affiliation(s)
- Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama, Shiga, 526-0829, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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14
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Xu W, Song A, Dong S, Chen J, Hao J. A systematic investigation and insight into the formation mechanism of bilayers of fatty acid/soap mixtures in aqueous solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:12380-12388. [PMID: 24028317 DOI: 10.1021/la403008d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Vesicles are the most common form of bilayer structures in fatty acid/soap mixtures in aqueous solutions; however, a peculiar bilayer structure called a "planar sheet" was found for the first time in the mixtures. In the past few decades, considerable research has focused on the formation theory of bilayers in fatty acid/soap mixtures. The hydrogen bond theory has been widely accepted by scientists to explain the formation of bilayers. However, except for the hydrogen bond, no other driving forces were proposed systematically. In this work, three kinds of weak interactions were investigated in detail, which could perfectly demonstrate the formation mechanism of bilayer structures in the fatty acid/soap mixtures in aqueous solutions. (i) The influence of hydrophobic interaction was detected by changing the chain length of fatty acid (C(n)H(2n+1)COOH), in which n = 10 to 18, the phase behavior was investigated, and the phase region was presented. With the help of cryogenic transmission electron microscopy (cryo-TEM) observations, deuterium nuclear magnetic resonance ((2)H NMR), and X-ray diffraction (XRD) measurements, the vesicles and planar sheets were determined. The chain length of C(n)H(2n+1)COOH has an important effect on the physical state of the hydrophobic chain, resulting in an obvious difference in the viscoelasticity of the solution samples. (ii) The existence of hydrogen bonds between fatty acids and their soaps in aqueous solutions was demonstrated by Fourier transform infrared (FT-IR) spectroscopy and molecule dynamical simulation. From the pH measurements, the pH ranges of the bilayer formation were at the pKa values of fatty acids, respectively. (iii) Counterions can be embedded in the stern layer of the bilayers and screen the electrostatic repulsion between the COO(-) anionic headgroups. FT-IR characterization demonstrated a bidentate bridging coordination mode between counterions and carboxylates. The conductivity measurements provided the degree of counterion binding (β = 0.854), indicating the importance of the counterions.
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Affiliation(s)
- Wenlong Xu
- Key Laboratory of Colloid and Interface Chemistry and Key Laboratory of Special Aggregated Materials, Shandong University, Ministry of Education , Jinan 250100, P. R. China
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15
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α-Cyclodextrin/aminobenzoic acid binding in salt solutions at different pH: Dependence on guest structure. Int J Biol Macromol 2013; 57:255-8. [DOI: 10.1016/j.ijbiomac.2013.03.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/11/2013] [Accepted: 03/09/2013] [Indexed: 11/19/2022]
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16
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Tomé LIN, Pinho SP, Jorge M, Gomes JRB, Coutinho JAP. Salting-in with a salting-out agent: explaining the cation specific effects on the aqueous solubility of amino acids. J Phys Chem B 2013; 117:6116-28. [PMID: 23638911 DOI: 10.1021/jp4021307] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although the understanding of ion specific effects on the aqueous solubilities of biomolecules is crucial for the development of many areas of biochemistry and life sciences, a consensual and well-supported molecular picture of the phenomena has not yet been established. Mostly, the influence of cations and the nature of the molecular interactions responsible for the reversal of the Hofmeister trend in aqueous solutions of amino acids and proteins are still defectively understood. Aiming at contributing to the understanding of the molecular-level mechanisms governing the cation specific effects on the aqueous solubilities of biocompounds, experimental solubility measurements and classical molecular dynamics simulations were performed for aqueous solutions of three amino acids (alanine, valine, and isoleucine), in the presence of a series of inorganic salts. The evidence gathered suggests that the mechanism by which salting-in inducing cations operate in aqueous solutions of amino acids is different from that of anions, and allows for a novel and consistent molecular description of the effect of the cation on the solubility based on specific interactions of the cations with the negatively charged moieties of the biomolecules.
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Affiliation(s)
- Luciana I N Tomé
- CICECO, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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17
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Naini CA, Thomas M, Franzka S, Frost S, Ulbricht M, Hartmann N. Hofmeister Effect of Sodium Halides on the Switching Energetics of Thermoresponsive Polymer Brushes. Macromol Rapid Commun 2013; 34:417-22. [DOI: 10.1002/marc.201200681] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 11/27/2012] [Indexed: 12/15/2022]
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18
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Gaborek TJ, Chipot C, Madura JD. Conformational free-energy landscapes for a peptide in saline environments. Biophys J 2012; 103:2513-20. [PMID: 23260053 DOI: 10.1016/j.bpj.2012.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/26/2012] [Accepted: 11/01/2012] [Indexed: 10/27/2022] Open
Abstract
The conformations that proteins adopt in solution are a function of both their primary structure and surrounding aqueous environment. Recent experimental and computational work on small peptides, e.g., polyK, polyE, and polyR, have highlighted an interesting and unusual behavior in the presence of aqueous ions such as ClO₄⁻, Na⁺, and K⁺. Notwithstanding the aforementioned studies, as of this writing, the nature of the driving force induced by the presence of ions and its role on the conformational stability of peptides remains only partially understood. Molecular-dynamics simulations have been performed on the heptapeptide AEAAAEA in NaCl and KCl solutions at concentrations of 0.5, 1.0, and 2.0 M. Metadynamics in conjunction with a three-dimensional model reaction coordinate was used to sample the conformational space of the peptide. All simulations were run for 2 μs. Free-energy landscapes were computed over the model reaction coordinate for the peptide in each saline assay as well as in the absence of ions. Circular dichroism spectra were also calculated from each trajectory. In the presence of Na⁺ and K⁺ ions, no increase in helicity is observed with respect to the conformation in pure water.
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Affiliation(s)
- Timothy J Gaborek
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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19
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Roy S, Javid N, Sefcik J, Halling PJ, Ulijn RV. Salt-induced control of supramolecular order in biocatalytic hydrogelation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16664-70. [PMID: 23116236 DOI: 10.1021/la303388s] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biocatalytic action and specific ion effects are both known to have dramatic effects on molecular self-assembly and hydrogelation. In this paper, we demonstrate that these effects are highly cooperative. Biocatalytic hydrogelation of Fmoc peptides in the presence of salts combines kinetic (through enzymatic catalysis) and thermodynamic (specific ion and protein templating) contributions when applied in combination. Spectroscopic data (obtained by fluorescence spectroscopy and circular dichroism) revealed that hydrophobic interactions are greatly affected, giving rise to differential chiral organization and supramolecular structure formation. The kinetic effects of catalytic action could be removed from the system by applying a heat/cool cycle, giving insight into the thermodynamic influence of both protein and salt on these systems and showing that the effects of catalysis, templating, and salts are cooperative. The variable molecular interactions are expressed as variable material properties, such as thermal stability and mechanical strength of the final gel-phase material. To gain more insight into the role of the enzyme, beyond catalysis, in the underlying mechanism, static light scattering is performed, which indicates the different mode of aggregation of the enzyme molecules in the presence of different salts in aqueous solution that may play a role to direct the assembly via templating. Overall, the results show that the combination of specific salts and enzymatic hydrogelation can give rise to complex self-assembly behaviors that may be exploited to tune hydrogel properties.
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Affiliation(s)
- Sangita Roy
- WestCHEM/Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom.
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20
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Ottosson N, Romanova AO, Söderström J, Björneholm O, Öhrwall G, Fedorov MV. Molecular Sinkers: X-ray Photoemission and Atomistic Simulations of Benzoic Acid and Benzoate at the Aqueous Solution/Vapor Interface. J Phys Chem B 2012; 116:13017-23. [DOI: 10.1021/jp300956j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Niklas Ottosson
- Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Anastasia O. Romanova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D
04103, Leipzig, Germany
| | - Johan Söderström
- Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Olle Björneholm
- Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Gunnar Öhrwall
- MAX-lab, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D
04103, Leipzig, Germany
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21
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Ratkova EL. A semiempirical model for estimating the hydration free energy of neutral nonpolar compounds. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412100196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Roy S, Javid N, Frederix PWJM, Lamprou DA, Urquhart AJ, Hunt NT, Halling PJ, Ulijn RV. Dramatic Specific-Ion Effect in Supramolecular Hydrogels. Chemistry 2012; 18:11723-31. [DOI: 10.1002/chem.201201217] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 11/06/2022]
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23
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Sergiievskyi VP, Frolov AI. A universal bridge functional for infinitely diluted solutions: A case study for Lennard-Jones spheres of different diameters. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412080122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Collins KD. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions. Biophys Chem 2012; 167:43-59. [DOI: 10.1016/j.bpc.2012.04.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 01/13/2023]
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25
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Hasuike M, Kuroki S, Satoh M. Double conformational transition of alkali metal poly(l-glutamate)s in aqueous ethanol. Biophys Chem 2012; 165-166:48-55. [DOI: 10.1016/j.bpc.2012.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 11/25/2022]
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26
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Tomé LIN, Jorge M, Gomes JRB, Coutinho JAP. Molecular Dynamics Simulation Studies of the Interactions between Ionic Liquids and Amino Acids in Aqueous Solution. J Phys Chem B 2012; 116:1831-42. [DOI: 10.1021/jp209625e] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luciana I. N. Tomé
- CICECO, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Miguel Jorge
- LSRE—Laboratory of Separation
and Reaction Engineering—Associate Laboratory LSRE/LCM, Faculdade
de Engenharia, Universidade do Porto, Rua
Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - José R. B. Gomes
- CICECO, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- CICECO, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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27
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Simón L, Goodman JM. Hydrogen-bond stabilization in oxyanion holes: grand jeté to three dimensions. Org Biomol Chem 2012; 10:1905-13. [PMID: 22273994 DOI: 10.1039/c2ob06717j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently reported crystallographic evidence that the hydrogen bonds which can stabilize oxygen-centered negative charge within enzyme oxyanion holes are rarely found in the place they should be expected on the basis of the analysis of small-molecule crystal structures. We investigated this phenomenon using calculations on simplified active site models. A recent paper suggested that several aspects of the analysis required further exploration. In this paper we: (i) review the results of our crystallographic study; (ii) report molecular dynamics studies which investigate the effect of protein movement; (iii) report ONIOM calculations which trace the reaction coordinate for an oxyanion hole reaction in the presence of a complete enzyme active site. These results show that the limitations of gas phase calculations on simplified models do not invalidate our comparison of competing active site geometries. These new results reaffirm the conclusion that oxyanion holes are not usually stabilized by planar arrangements of H-bonds, and that this sub-optimal transition state stabilization leads to better overall catalysis.
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Affiliation(s)
- Luis Simón
- Facultad de Ciencias Químicas, Universidad de Salamanca, Plaza de los Caídos 1-5, Salamanca, E37004, Spain.
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28
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Frolov AI, Arif RN, Kolar M, Romanova AO, Fedorov MV, Rozhin AG. Molecular mechanisms of salt effects on carbon nanotube dispersions in an organic solvent (N-methyl-2-pyrrolidone). Chem Sci 2012. [DOI: 10.1039/c1sc00232e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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29
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Conformation of poly-L-glutamate is independent of ionic strength. Biophys Chem 2011; 162:1-5. [PMID: 22236769 DOI: 10.1016/j.bpc.2011.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/08/2011] [Accepted: 11/12/2011] [Indexed: 11/23/2022]
Abstract
CD and UV resonance Raman measurements surprisingly find that the charge screening of even 2 M concentrations of NaCl and KCl does not alter the unfolded PPII and 2.5(1)-helix conformations of poly-L-glutamate. These salts appear to be excluded from the region between the side chain charges and the peptide backbone. Furthermore, no direct ion pairing occurs between these salts and the side chain carboxylates.
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30
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Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol 2011; 63:1139-200. [PMID: 21279359 PMCID: PMC3113640 DOI: 10.1007/s00285-011-0402-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 12/24/2010] [Indexed: 10/18/2022]
Abstract
Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature.
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Affiliation(s)
- Zhan Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Nathan A. Baker
- Pacific Northwest National Laboratory,
902 Battelle Boulevard P.O. Box 999, MSIN K7-28, Richland, WA 99352 USA
| | - G. W. Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
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31
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Kolombet VA. Calculation of the hydration energy of polyvalent metal ions by the RISM method. RUSS J INORG CHEM+ 2011. [DOI: 10.1134/s0036023611080110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Sergiievskyi VP. Model for calculating the free energy of hydration of bioactive compounds based on integral equation theory of liquids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111020382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Potoyan DA, Papoian GA. Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. J Am Chem Soc 2011; 133:7405-15. [PMID: 21517079 DOI: 10.1021/ja1111964] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ∼3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.
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Affiliation(s)
- Davit A Potoyan
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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34
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Sergiievskyi VP, Hackbusch W, Fedorov MV. Multigrid solver for the reference interaction site model of molecular liquids theory. J Comput Chem 2011; 32:1982-92. [DOI: 10.1002/jcc.21783] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/22/2011] [Accepted: 02/09/2011] [Indexed: 11/12/2022]
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35
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Cherstvy AG. DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions? J Phys Chem B 2011; 115:4286-94. [DOI: 10.1021/jp2003479] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. G. Cherstvy
- Institute of Complex Systems, ICS-2, Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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36
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Kolombet VA, Frolov AI. Na+/K+ selectivity in the formation of ion pairs in aqueous solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793110060011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Cherstvy AG, Winkler RG. Polyelectrolyte adsorption onto oppositely charged interfaces: unified approach for plane, cylinder, and sphere. Phys Chem Chem Phys 2011; 13:11686-93. [DOI: 10.1039/c1cp20749k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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38
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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39
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Looping charged elastic rods: applications to protein-induced DNA loop formation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:69-80. [PMID: 20963409 DOI: 10.1007/s00249-010-0628-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 10/18/2022]
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40
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von Hansen Y, Kalcher I, Dzubiella J. Ion Specificity in α-Helical Folding Kinetics. J Phys Chem B 2010; 114:13815-22. [DOI: 10.1021/jp107495f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yann von Hansen
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
| | - Immanuel Kalcher
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
| | - Joachim Dzubiella
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
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41
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Terekhova IV, Romanova AO, Kumeev RS, Fedorov MV. Selective Na+/K+ Effects on the Formation of α-Cyclodextrin Complexes with Aromatic Carboxylic Acids: Competition for the Guest. J Phys Chem B 2010; 114:12607-13. [DOI: 10.1021/jp1063512] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irina V. Terekhova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D 04103, Leipzig, Germany, and Institute of Solution Chemistry of Russian Academy of Science, Academicheskaya 1, 153045, Ivanovo, Russia
| | - Anastasia O. Romanova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D 04103, Leipzig, Germany, and Institute of Solution Chemistry of Russian Academy of Science, Academicheskaya 1, 153045, Ivanovo, Russia
| | - Roman S. Kumeev
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D 04103, Leipzig, Germany, and Institute of Solution Chemistry of Russian Academy of Science, Academicheskaya 1, 153045, Ivanovo, Russia
| | - Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D 04103, Leipzig, Germany, and Institute of Solution Chemistry of Russian Academy of Science, Academicheskaya 1, 153045, Ivanovo, Russia
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42
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Frolov AI, Rozhin AG, Fedorov MV. Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms. Chemphyschem 2010; 11:2612-6. [DOI: 10.1002/cphc.201000231] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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43
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Dzubiella J. Molecular Insights into the Ion-Specific Kinetics of Anionic Peptides. J Phys Chem B 2010; 114:7098-103. [DOI: 10.1021/jp1010814] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Joachim Dzubiella
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
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44
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Kolombet VA, Sergievskii VP. The special features of the thermodynamic characteristics of hydration of univalent ions according to the reference interaction site model. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410090025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Dzubiella J. Salt-Specific Stability of Short and Charged Alanine-Based α-Helices. J Phys Chem B 2009; 113:16689-94. [DOI: 10.1021/jp9077932] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joachim Dzubiella
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
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