1
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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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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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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4
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Light TP, Corbett KM, Metrick MA, MacDonald G. Hofmeister Ion-Induced Changes in Water Structure Correlate with Changes in Solvation of an Aggregated Protein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1360-1369. [PMID: 26760222 DOI: 10.1021/acs.langmuir.5b04489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RecA is a naturally aggregating Escherichia coli protein that catalyzes the strand exchange reaction utilized in DNA repair. Previous studies have shown that the presence of salts influence RecA activity, aggregation, and stability and that salts stabilize RecA in an inverse-anionic Hofmeister series. Here we utilized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and circular dichroism (CD) to investigate how various Hofmeister salts alter the water structure and RecA solvation and aggregation. Spectroscopic studies performed in water and deuterium oxide suggest that salts alter water O-(1)H and O-(2)H stretch and bend vibrations as well as protein amide I (or I') and amide II (or II') vibrations. Anions have a much larger influence on water vibrations than cations. Water studies also show increased water-water and/or water-ion interactions in the presence of strongly hydrated SO4(2-) salts and evidence for decreased interactions with weakly hydrated Cl(-) and ClO4(-) salts. Salt-water difference infrared spectra show that kosmotropic salts are more hydrated than chaotropic salts. Interestingly, this is the opposite trend to the changes in protein solvation. Infrared spectra of RecA show that vibrations associated with protein desolvation were observed in the presence of SO4(2-) salts. Conversely, vibrations associated with protein solvation were observed in the presence of Cl(-) and ClO4(-) salts. Difference infrared studies on the dehydration of model proteins aided in identifying changes in RecA-solvent interactions. This study provides evidence that salt-induced changes in water vibrations correlate to changes in protein solvent interactions and thermal stability.
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Affiliation(s)
- Taylor P Light
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Karen M Corbett
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Michael A Metrick
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gina MacDonald
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
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5
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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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6
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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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7
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Ion specific influences on the stability and unfolding transitions of a naturally aggregating protein; RecA. Biophys Chem 2012; 163-164:56-63. [DOI: 10.1016/j.bpc.2012.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/13/2012] [Accepted: 02/18/2012] [Indexed: 10/28/2022]
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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Kolombet VA. A study by RISM method of the features of the environment dielectric response on the hydration of monatomic ions. RUSS J GEN CHEM+ 2010. [DOI: 10.1134/s1070363210080062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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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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16
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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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17
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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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18
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Kalcher I, Horinek D, Netz RR, Dzubiella J. Ion specific correlations in bulk and at biointerfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:424108. [PMID: 21715843 DOI: 10.1088/0953-8984/21/42/424108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.
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Affiliation(s)
- I Kalcher
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
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19
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Chuev GN, Fedorov MV. Reference interaction site model study of self-aggregating cyanine dyes. J Chem Phys 2009; 131:074503. [DOI: 10.1063/1.3211948] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fedorov MV, Goodman JM, Schumm S. To Switch or Not To Switch: The Effects of Potassium and Sodium Ions on α-Poly-l-glutamate Conformations in Aqueous Solutions. J Am Chem Soc 2009; 131:10854-6. [DOI: 10.1021/ja9030374] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D04103 Leipzig, Germany, Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K., and Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands
| | - Jonathan M. Goodman
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D04103 Leipzig, Germany, Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K., and Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands
| | - Stephan Schumm
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D04103 Leipzig, Germany, Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K., and Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands
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