1
|
Wong LN, Brunner M, Imberti S, Warr GG, Atkin R. Bulk Nanostructure of Mixtures of Choline Arginate, Choline Lysinate, and Water. J Phys Chem B 2024. [PMID: 38691762 DOI: 10.1021/acs.jpcb.4c01482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Neutron diffraction with empirical potential structure refinement was used to investigate the bulk liquid nanostructure of mixtures of choline arginate (Ch[Arg]), choline lysinate (Ch[Lys]), and water at mole ratios of 1Ch[Arg]:1Ch[Lys]:6H2O (balanced), 1Ch[Arg]:1Ch[Lys]:20H2O (balanced dilute), 3Ch[Arg]:1Ch[Lys]:12H2O (Arg- rich), and 1Ch[Arg]:3Ch[Lys]:12H2O (Lys- rich). The Arg- and Lys- anions tend not to associate due to electrostatic repulsion between charge groups and weak anion-anion attractions. This means that the local ion structures around the anions in these mixtures resemble the parent single-component systems. The bulk liquid nanostructure varies with the Arg-:Lys- ratio. In the Lys--rich mixture (1Ch[Arg]:3Ch[Lys]:12H2O), Lys- side chains cluster into a continuous apolar domain separated from a charged domain of polar groups. In the balanced mixture (1Ch[Arg]:1Ch[Lys]:6H2O), Lys- side chains form discrete apolar aggregates within a continuous polar domain of Arg-, Ch+, and water, and in the Arg--rich mixture (3Ch[Arg]:1Ch[Lys]:12H2O), the distribution of Lys- and Arg- is nearly homogeneous. Finally, in the balance dilute system (1Ch[Arg]:1Ch[Lys]:20H2O), a percolating water domain forms.
Collapse
Affiliation(s)
- Lucas N Wong
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Manuel Brunner
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Silvia Imberti
- UKRI, STFC, ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Gregory G Warr
- School of Chemistry and University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rob Atkin
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| |
Collapse
|
2
|
Fedotova MV, Chuev GN. The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands. Int J Mol Sci 2024; 25:3697. [PMID: 38612508 PMCID: PMC11011341 DOI: 10.3390/ijms25073697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus-host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.
Collapse
Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., 142290 Pushchino, Russia
| |
Collapse
|
3
|
Cao S, Qiu Y, Unarta IC, Goonetilleke EC, Huang X. The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules. J Phys Chem B 2022; 126:8632-8645. [PMID: 36282904 DOI: 10.1021/acs.jpcb.2c04431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation model to compute the structural and thermodynamic properties of biomolecules in aqueous solutions. However, it remains challenging for existing 3DRISM methods to correctly predict water distributions around negatively charged solute molecules. In this paper, we first show that this challenge is mainly due to the orientation of water molecules in the first solvation shell of the negatively charged solute molecules. To properly consider this orientational preference, position-dependent two-body intramolecular correlations of solvent need to be included in the 3DRISM theory, but direct evaluations of these position-dependent two-body intramolecular correlations remain numerically intractable. To address this challenge, we introduce the Ion-Dipole Correction (IDC) to the 3DRISM theory, in which we incorporate the orientation preference of water molecules via an additional solute-solvent interaction term (i.e., the ion-dipole interaction) while keeping the formulism of the 3DRISM equation unchanged. We prove that this newly introduced IDC term is equivalent to an effective direct correlation function which can effectively consider the orientation effect that arises from position dependent two-body correlations. We first quantitatively validate our 3DRISM-IDC theory combined with the PSE3 closure on Cl-, [ClO]- (a two-site anion), and [NO2]- (a three-site anion). For all three anions, we show that our 3DRISM-IDC theory significantly outperforms the 3DRISM theory in accurately predicting the solvation structures in comparison to MD simulations, including RDFs and 3D water distributions. Furthermore, we have also demonstrated that the 3DRISM-IDC can improve the accuracy of hydration free-energy calculation for Cl-. We further demonstrate that our 3DRISM-IDC theory yields significant improvements over the 3DRISM theory when applied to compute the solvation structures for various negatively charged solute molecules, including adenosine triphosphate (ATP), a short peptide containing 19 residues, a DNA hairpin containing 24 nucleotides, and a riboswitch RNA molecule with 77 nucleotides. We expect that our 3DRISM-IDC-PSE3 solvation model holds great promise to be widely applied to study solvation properties for nucleic acids and other biomolecules containing negatively charged functional groups.
Collapse
Affiliation(s)
- Siqin Cao
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Yunrui Qiu
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Ilona C Unarta
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Eshani C Goonetilleke
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Xuhui Huang
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| |
Collapse
|
4
|
Wang S, Li Z, Wang H, Yuan C, Liu K, Yuan M, Wang Y. Study on the structure and properties of choline chloride toughened polylactide composites. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-022-04499-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
5
|
Chai K, Lu X, Zhou Y, Liu H, Wang G, Jing Z, Zhu F, Han L. Hydrogen bonds in aqueous choline chloride solutions by DFT calculations and X-ray scattering. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex. Molecules 2022; 27:molecules27030799. [PMID: 35164065 PMCID: PMC8839245 DOI: 10.3390/molecules27030799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
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.
Collapse
|
7
|
Kruchinin SE, Fedotova MV. Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions. J Phys Chem B 2021; 125:11219-11231. [PMID: 34597044 DOI: 10.1021/acs.jpcb.1c05117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu--Glu- pairing. Namely, the RISM data indicate Glu--Glu- binding by NH3+-COO- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.
Collapse
Affiliation(s)
- Sergey E Kruchinin
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| |
Collapse
|