1
|
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
|
2
|
Esteves C, Palma SICJ, Costa HMA, Alves C, Santos GMC, Ramou E, Carvalho AL, Alves V, Roque ACA. Tackling Humidity with Designer Ionic Liquid-Based Gas Sensing Soft Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107205. [PMID: 34873762 PMCID: PMC7613046 DOI: 10.1002/adma.202107205] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/12/2021] [Indexed: 05/13/2023]
Abstract
Relative humidity is simultaneously a sensing target and a contaminant in gas and volatile organic compound (VOC) sensing systems, where strategies to control humidity interference are required. An unmet challenge is the creation of gas-sensitive materials where the response to humidity is controlled by the material itself. Here, humidity effects are controlled through the design of gelatin formulations in ionic liquids without and with liquid crystals as electrical and optical sensors, respectively. In this design, the anions [DCA]- and [Cl]- of room temperature ionic liquids from the 1-butyl-3-methylimidazolium family tailor the response to humidity and, subsequently, sensing of VOCs in dry and humid conditions. Due to the combined effect of the materials formulations and sensing mechanisms, changing the anion from [DCA]- to the much more hygroscopic [Cl]- , leads to stronger electrical responses and much weaker optical responses to humidity. Thus, either humidity sensors or humidity-tolerant VOC sensors that do not require sample preconditioning or signal processing to correct humidity impact are obtained. With the wide spread of 3D- and 4D-printing and intelligent devices, the monitoring and tuning of humidity in sustainable biobased materials offers excellent opportunities in e-nose sensing arrays and wearable devices compatible with operation at room conditions.
Collapse
Affiliation(s)
- Carina Esteves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Susana I C J Palma
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Henrique M A Costa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Cláudia Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Gonçalo M C Santos
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Efthymia Ramou
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Ana Luísa Carvalho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Vitor Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Ana C A Roque
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, 1349-017, Portugal
| |
Collapse
|
3
|
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
|
4
|
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
|
5
|
Chuev GN, Fedotova MV, Valiev M. Renormalized site density functional theory for models of ion hydration. J Chem Phys 2021; 155:064501. [PMID: 34391371 DOI: 10.1063/5.0060249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The development of accurate statistical mechanics models of molecular liquid systems is a problem of great practical and fundamental importance. Site-density functional theory (SDFT) is one of the promising directions in this area, but its success hinges upon the ability to efficiently reconcile the co-existence of two distinct intra- and inter-molecular interaction regimes in a molecular liquid. The renormalized formulation of SDFT (RSDFT), which we have recently developed, resolves this problem by introducing an additional potential field variable that decouples two interaction scales and maps the molecular liquid problem onto the effective simple liquid mixture. This work provides a critical assessment of RSDFT for the hydrated ion system-a problem that historically has always been one of the most difficult cases for SDFT applications. Using a two-site model of water, we perform a comprehensive analysis of hydrated alkali metal and halogen ions, including both structural and free energy based characteristics. The results indicate that RSDFT provides a significant improvement over conventional three-dimensional reference interaction site model implementations and may prove useful in coarse grained simulations based on two-site solvent models.
Collapse
Affiliation(s)
- Gennady N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Marat Valiev
- Molecular Sciences Software Group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| |
Collapse
|
6
|
|
7
|
|
8
|
Chuev GN, Fedotova MV, Valiev M. Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids. J Chem Phys 2020; 152:041101. [PMID: 32007044 DOI: 10.1063/1.5139619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Intra-molecular interactions or chemical bonds represent one of the main distinguishing characteristics of molecular fluids. Development of accurate and practical methods to treat these effects is one of the long standing problems in classical site density functional theory (SDFT). One particular instance when these issues become particularly severe is the case of classical interaction potentials with auxiliary sites or dummy atoms. In this situation, current SDFT implementations, such as the three-dimensional reference interaction site model, lead to nonphysical results. We re-examine this issue in this work using our recent reformulation of SDFT (Valiev and Chuev, J. Stat. Mech.: Theory Exp. 2018, 093201). We put forward a simple practical solution to this problem and illustrate its utility for the case of spherical solutes in diatomic liquids.
Collapse
Affiliation(s)
- Gennady N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Marat Valiev
- Molecular Sciences Software Group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| |
Collapse
|
9
|
Fedotova MV, Kruchinin SE, Chuev GN. Features of local ordering of biocompatible ionic liquids: The case of choline-based amino acid ionic liquids. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.112081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
10
|
Cao S, Konovalov KA, Unarta IC, Huang X. Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute–Solvent Interface. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Kirill A. Konovalov
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Ilona Christy Unarta
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuhui Huang
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- HKUST‐Shenzhen Research Institute Hi‐Tech Park, Nanshan Shenzhen 518057 China
| |
Collapse
|
11
|
Shaukat S, Fedotova MV, Kruchinin SE, Bešter-Rogač M, Podlipnik Č, Buchner R. Hydration and ion association of aqueous choline chloride and chlorocholine chloride. Phys Chem Chem Phys 2019; 21:10970-10980. [DOI: 10.1039/c9cp01016e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Choline hydration occurs predominantly via its hydroxyl group, and weak contact ion pair formation with Cl− is via the onium moiety.
Collapse
Affiliation(s)
- Saadia Shaukat
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marija Bešter-Rogač
- Faculty of Chemistry and Chemical Technology
- Večna pot 113
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology
- Večna pot 113
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Richard Buchner
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| |
Collapse
|