Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions

Fedotova, M. V.; Kruchinin, Sergey E.

doi:10.1016/j.bpc.2014.04.001

Cited by 45 publications

(35 citation statements)

References 74 publications

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“…The foundations of the 1D-and 3D-RISM theories were described in detail elsewhere 16,20,47,48 including our recent publications, [29][30][31][49][50][51] therefore it may suffice here to give only a brief outline of the aspects relevant to our study.…”

Section: Rism Calculationsmentioning

confidence: 99%

Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids

Bešter‐Rogač

Fedotova

Kruchinin

et al. 2016

Phys. Chem. Chem. Phys.

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The mobility and the mechanism of ion pairing of 1,1 electrolytes in aqueous solutions were investigated systematically on nine imidazolium based ionic liquids (ILs) from 1-methylimidazolium chloride, [MIM][Cl], to 1-dodecyl-3-methylimidazolium chloride, [1,3-DoMIM][Cl], with two isomers 1,2-dimethylimidazolium chloride, [1,2-MMIM][Cl], and 1,3-dimethylimidazolium chloride, [1,3-MMIM][Cl]. Molecular dynamics (MD) simulations, statistical mechanics calculations in the framework of the integral equation theory using one-dimensional (1D-) and three-dimensional (3D-) reference interaction site model (RISM) approaches as well as conductivity measurements were applied. From experiment and MD simulations it was found that the mobility/diffusion coefficients of cations in the limit of infinite dilution decrease with an increasing length of the cation alkyl chain, but not linearly. The aggregation tendency of cations with long alkyl chains at higher IL concentrations impedes their diffusivity. Binding free energies of imidazolium cations with the chloride anion estimated by RISM calculations, MD simulations and experiments reveal that the association of investigated ILs as model 1,1 electrolytes in water solutions is weak but evidently dependent on the molecular structure (alkyl chain length), which also strongly affects the mobility of cations.

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Section: Rism Calculationsmentioning

confidence: 99%

Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids

Bešter‐Rogač

Fedotova

Kruchinin

et al. 2016

Phys. Chem. Chem. Phys.

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“…Namely, the 3DRISM reduces the problem to numerical solution of Ornstein-Zernike integral equations similar to those for simple fluids. The model is very popular for treatment of small bio-rganic solutes [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 ].…”

Section: Introductionmentioning

confidence: 99%

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

Tučs

Bera

et al. 2022

Molecules

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The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

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“…In a theoretical study, Fedotova et al. simulated ion binding between chloride salts and charged groups of the zwitterion glycine and found strong electrostatic interactions between both [12] . A water‐mediated interaction of cations with glycine, in agreement with the Hofmeister series, has also been indirectly proposed by the application of Raman and dielectric spectroscopies [13] .…”

Section: Introductionmentioning

confidence: 92%

“…In the present study, we want to observe the changes in the THz spectrum of solvated glycine upon protonation. Glycine is the simplest of the 20 proteinogenic standard amino acids and has served as a prototype for many hydration studies of zwitterions [12, 14–20] . Under physiological conditions glycine is a zwitterion with a negatively charged carboxyl group and a positively charged amino group.…”

Section: Introductionmentioning

confidence: 99%

Probing Local Electrostatics of Glycine in Aqueous Solution by THz Spectroscopy

Sebastiani

Funke

et al. 2020

Angewandte Chemie

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Based upon precise terahertz (THz) measurements of the solvated amino acid glycine and accompanying ab‐initio molecular‐dynamics simulations, we show that the N‐C‐C‐O open/close mode at 315 cm−1 serves as a sensitive, label‐free probe for the local protonation of the amide group. Experimentally, we can show that this holds not only for glycine but also for diglycine and valine. The approach is more general, since the changes due to protonation result in intensity changes which can be probed by THz time domain (0–50 cm−1) as well as by precise THz‐FT spectroscopy (50–400 cm−1). A detailed analysis allows us to directly correlate the titration spectra with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of a natural amino acid in water in a label‐free manner.

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Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions

Cited by 45 publications

References 74 publications

Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids

Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

Probing Local Electrostatics of Glycine in Aqueous Solution by THz Spectroscopy

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