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Sharma H, Dar TA, Wijayasinghe YS, Sahoo D, Poddar NK. Nano-Osmolyte Conjugation: Tailoring the Osmolyte-Protein Interactions at the Nanoscale. ACS OMEGA 2023; 8:47367-47379. [PMID: 38144115 PMCID: PMC10733987 DOI: 10.1021/acsomega.3c07248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/26/2023]
Abstract
Osmolytes are small organic compounds accumulated at higher concentrations in the cell under various stress conditions like high temperature, high salt, high pressure, etc. Osmolytes mainly include four major classes of compounds including sugars, polyols, methylamines, and amino acids and their derivatives. In addition to their ability to maintain protein stability and folding, these osmolytes, also termed as chemical chaperones, can prevent protein misfolding and aggregation. Although being efficient protein folders and stabilizers, these osmolytes exhibit certain unavoidable limitations such as nearly molar concentrations of osmolytes being required for their effect, which is quite difficult to achieve inside a cell or in the extracellular matrix due to nonspecificity and limited permeability of the blood-brain barrier system and reduced bioavailability. These limitations can be overcome to a certain extent by using smart delivery platforms for the targeted delivery of osmolytes to the site of action. In this context, osmolyte-functionalized nanoparticles, termed nano-osmolytes, enhance the protein stabilization and chaperone efficiency of osmolytes up to 105 times in certain cases. For example, sugars, polyols, and amino acid functionalized based nano-osmolytes have shown tremendous potential in preventing protein aggregation. The enhanced potential of nano-osmolytes can be attributed to their high specificity at low concentrations, high tunability, amphiphilicity, multivalent complex formation, and efficient drug delivery system. Keeping in view the promising potential of nano-osmolytes conjugation in tailoring the osmolyte-protein interactions, as compared to their molecular forms, the present review summarizes the recent advancements of the nano-osmolytes that enhance the protein stability/folding efficiency and ability to act as artificial chaperones with increased potential to prevent protein misfolding disorders. Some of the potential nano-osmolyte aggregation inhibitors have been highlighted for large-scale screening with future applications in aggregation disorders. The synthesis of nano-osmolytes by numerous approaches and future perspectives are also highlighted.
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Affiliation(s)
- Hemlata Sharma
- Department
of Biosciences, Manipal University Jaipur, Jaipur-Ajmer Express Highway, Dehmi
Kalan, Near GVK Toll Plaza, Jaipur, Rajasthan 303007, India
| | - Tanveer Ali Dar
- Department
of Clinical Biochemistry, University of
Kashmir, Srinagar 190006, Jammu and Kashmir India
| | | | - Dibakar Sahoo
- School
of Physics, Sambalpur University, Jyoti Vihar, Burla 768019, Odisha, India
| | - Nitesh Kumar Poddar
- Department
of Biosciences, Manipal University Jaipur, Jaipur-Ajmer Express Highway, Dehmi
Kalan, Near GVK Toll Plaza, Jaipur, Rajasthan 303007, India
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2
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Ji D, Kim J. Trend of Developing Aqueous Liquid and Gel Electrolytes for Sustainable, Safe, and High-Performance Li-Ion Batteries. NANO-MICRO LETTERS 2023; 16:2. [PMID: 37930432 PMCID: PMC10628089 DOI: 10.1007/s40820-023-01220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Current lithium-ion batteries (LIBs) rely on organic liquid electrolytes that pose significant risks due to their flammability and toxicity. The potential for environmental pollution and explosions resulting from battery damage or fracture is a critical concern. Water-based (aqueous) electrolytes have been receiving attention as an alternative to organic electrolytes. However, a narrow electrochemical-stability window, water decomposition, and the consequent low battery operating voltage and energy density hinder the practical use of aqueous electrolytes. Therefore, developing novel aqueous electrolytes for sustainable, safe, high-performance LIBs remains challenging. This Review first commences by summarizing the roles and requirements of electrolytes-separators and then delineates the progression of aqueous electrolytes for LIBs, encompassing aqueous liquid and gel electrolyte development trends along with detailed principles of the electrolytes. These aqueous electrolytes are progressed based on strategies using superconcentrated salts, concentrated diluents, polymer additives, polymer networks, and artificial passivation layers, which are used for suppressing water decomposition and widening the electrochemical stability window of water of the electrolytes. In addition, this Review discusses potential strategies for the implementation of aqueous Li-metal batteries with improved electrolyte-electrode interfaces. A comprehensive understanding of each strategy in the aqueous system will assist in the design of an aqueous electrolyte and the development of sustainable and safe high-performance batteries.
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Affiliation(s)
- Donghwan Ji
- School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of NanoEngineering, University of California San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Jaeyun Kim
- School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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3
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Khan S, Siraj S, Shahid M, Haque MM, Islam A. Osmolytes: Wonder molecules to combat protein misfolding against stress conditions. Int J Biol Macromol 2023; 234:123662. [PMID: 36796566 DOI: 10.1016/j.ijbiomac.2023.123662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
The proper functioning of any protein depends on its three dimensional conformation which is achieved by the accurate folding mechanism. Keeping away from the exposed stress conditions leads to cooperative unfolding and sometimes partial folding, forming the structures like protofibrils, fibrils, aggregates, oligomers, etc. leading to several neurodegenerative diseases like Parkinson's disease, Alzheimer's, Cystic fibrosis, Huntington, Marfan syndrome, and also cancers in some cases, too. Hydration of proteins is necessary, which may be achieved by the presence of organic solutes called osmolytes within the cell. Osmolytes belong to different classes in different organisms and play their role by preferential exclusion of osmolytes and preferential hydration of water molecules and achieves the osmotic balance in the cell otherwise it may cause problems like cellular infection, cell shrinkage leading to apoptosis and cell swelling which is also the major injury to the cell. Osmolyte interacts with protein, nucleic acids, intrinsically disordered proteins by non-covalent forces. Stabilizing osmolytes increases the Gibbs free energy of the unfolded protein and decreases that of folded protein and vice versa with denaturants (urea and guanidinium hydrochloride). The efficacy of each osmolyte with the protein is determined by the calculation of m value which reflects its efficiency with protein. Hence osmolytes can be therapeutically considered and used in drugs.
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Affiliation(s)
- Sobia Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Seerat Siraj
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, P.O. Box: 173, Al Kharj, Saudi Arabia
| | | | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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4
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Pradhan S, Rath R, Biswas M. GB1 Dimerization in Crowders: A Multiple Resolution Approach. J Chem Inf Model 2023; 63:1570-1577. [PMID: 36858485 DOI: 10.1021/acs.jcim.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In-cell protein-protein association, which is crucial in enzyme catalysis and polymerization, occurs in an environment that is highly heterogeneous and crowded. The crowder molecules exclude the reactant molecules from occupying certain regions of the cell, resulting in changes in the reaction thermodynamics and kinetics. Recent studies, both experiment and simulations, revealed that the nature of the interaction between crowder and protein species, in particular the soft interactions, plays an important role in crowder induced effects on protein association. To this end, from a simulation perspective, it is important to decipher the level of structural resolution in a protein-crowder model that can faithfully capture the influence of crowding on protein association. Here, we investigate the dimerization of model system GB1 in the presence of lysozyme crowders at two structural resolutions. The lower resolution model assumes both protein and crowder species as spherical beads, similar to the analytical scaled particle theory model, whereas the higher resolution model retains residue specific structural details for protein and crowder species. From the higher resolution model, it is found that GB1 dimer formation is destabilized in the presence of lysozyme crowders, and the destabilization is more for the side-by-side dimer compared to the domain-swapped dimer, in qualitative agreement with experimental findings. However, the low resolution CG model predicts stabilization of the dimers in the presence of the lysozyme crowder, similar to the SPT model. Our results indicate a nontrivial role of the choice of model resolution in computer simulation studies investigating crowder induced effects.
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Affiliation(s)
- Sweta Pradhan
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Rajendra Rath
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Mithun Biswas
- National Institute of Technology Rourkela, Rourkela 769008, India
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5
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Ren H, Li S, Wang B, Zhang Y, Wang T, Lv Q, Zhang X, Wang L, Han X, Jin F, Bao C, Yan P, Zhang N, Wang D, Cheng T, Liu H, Dou S. Molecular-Crowding Effect Mimicking Cold-Resistant Plants to Stabilize the Zinc Anode with Wider Service Temperature Range. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208237. [PMID: 36239267 DOI: 10.1002/adma.202208237] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Growth of dendrites, the low plating/stripping efficiency of Zn anodes, and the high freezing point of aqueous electrolytes hinder the practical application of aqueous Zn-ion batteries. Here, a zwitterionic osmolyte-based molecular crowding electrolyte is presented, by adding betaine (Bet, a by-product from beet plant) to the aqueous electrolyte, to solve the abovementioned problems. Substantive verification tests, density functional theory calculations, and ab initio molecular dynamics simulations consistently reveal that side reactions and growth of Zn dendrites are restrained because Bet can break Zn2+ solvation and regulate oriented 2D Zn2+ deposition. The Bet/ZnSO4 electrolyte enables superior reversibility in a Zn-Cu half-cell to achieve a high Coulombic efficiency >99.9% for 900 cycles (≈1800 h), and dendrite-free Zn plating/stripping in Zn-Zn cells for 4235 h at 0.5 mA cm-2 and 0.5 mAh cm-2 . Furthermore, a high concentration of Bet lowers the freezing point of the electrolyte to -92 °C via the molecular-crowding effect, which ensures the stable operation of the aqueous batteries at -30 °C. This innovative concept of such a molecular crowding electrolyte will inject new vitality into the development of multifunctional aqueous electrolytes.
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Affiliation(s)
- Huaizheng Ren
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Sai Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Bo Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Yanyan Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu, 215123, China
| | - Tian Wang
- Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Department of Chemistry & Laser Chemistry Institute, Fudan University, Shanghai, 200433, China
| | - Qiang Lv
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiangyu Zhang
- Department of Biochemical Engineering, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiao Han
- Institute of Microstructure and Properties of Advanced Materials, Beijing University of Technology, Beijing, 100124, China
| | - Fan Jin
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Changyuan Bao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Pengfei Yan
- Institute of Microstructure and Properties of Advanced Materials, Beijing University of Technology, Beijing, 100124, China
| | - Nan Zhang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Dianlong Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Tao Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu, 215123, China
| | - Huakun Liu
- Institute for Superconducting & Electronic Materials, Australian Institute of Innovative Materials, University of Wollongong, Wollongong, New South Wales, 2500, Australia
- Institute of Energy Material Science, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Shixue Dou
- Institute for Superconducting & Electronic Materials, Australian Institute of Innovative Materials, University of Wollongong, Wollongong, New South Wales, 2500, Australia
- Institute of Energy Material Science, University of Shanghai for Science and Technology, Shanghai, 200093, China
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6
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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7
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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8
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Titus AR, Madeira PP, Ferreira LA, Belgovskiy AI, Mann EK, Mann JA, Meyer WV, Smart AE, Uversky VN, Zaslavsky BY. Arrangement of Hydrogen Bonds in Aqueous Solutions of Different Globular Proteins. Int J Mol Sci 2022; 23:ijms231911381. [PMID: 36232682 PMCID: PMC9570128 DOI: 10.3390/ijms231911381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/07/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
This work presents the first evidence that dissolved globular proteins change the arrangement of hydrogen bonds in water, with different proteins showing quantitatively different effects. Using ATR-FTIR (attenuated total reflection—Fourier transform infrared) spectroscopic analysis of OH-stretch bands, we obtain quantitative estimates of the relative amounts of the previously reported four subpopulations of water structures coexisting in a variety of aqueous solutions. Where solvatochromic dyes can measure the properties of solutions of non-ionic polymers, the results correlate well with ATR-FTIR measurements. In protein solutions to which solvatochromic dye probes cannot be applied, NMR (nuclear magnetic resonance) spectroscopy was used for the first time to estimate the hydrogen bond donor acidity of water. We found strong correlations between the solvent acidity and arrangement of hydrogen bonds in aqueous solutions for several globular proteins. Even quite similar proteins are found to change water properties in dramatically different ways.
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Affiliation(s)
- Amber R. Titus
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA
| | - Pedro P. Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal
| | | | | | | | - Jay Adin Mann
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH 44242, USA
| | | | | | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-974-5816
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9
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Speer SL, Stewart CJ, Sapir L, Harries D, Pielak GJ. Macromolecular Crowding Is More than Hard-Core Repulsions. Annu Rev Biophys 2022; 51:267-300. [PMID: 35239418 DOI: 10.1146/annurev-biophys-091321-071829] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon L Speer
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Claire J Stewart
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA;
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, USA; .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina, USA.,Lineberger Cancer Research Center, University of North Carolina at Chapel Hill, North Carolina, USA
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10
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Kumar CU, Suryavanshi U, Sontake V, Reddy PY, Sankhala RS, Swamy MJ, Reddy GB. Effect of Sorbitol on Alpha-Crystallin Structure and Function. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:131-140. [PMID: 35508910 DOI: 10.1134/s0006297922020055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Loss of eye lens transparency due to cataract is the leading cause of blindness all over the world. While aggregation of lens crystallins is the most common endpoint in various types of cataracts, chaperone-like activity (CLA) of α-crystallin preventing protein aggregation is considered to be important for maintaining the eye lens transparency. Osmotic stress due to increased accumulation of sorbitol under hyperglycemic conditions is believed to be one of the mechanisms for diabetic cataract. In addition, compromised CLA of α-crystallin in diabetic cataract has been reported. However, the effect of sorbitol on the structure and function of α-crystallin has not been elucidated yet. Hence, in the present exploratory study, we described the effect of varying concentrations of sorbitol on the structure and function of α-crystallin. Alpha-crystallin purified from the rat lens was incubated with varying concentrations of sorbitol in the dark under sterile conditions for up to 5 days. At the end of incubation, structural properties and CLA were evaluated by spectroscopic methods. Interestingly, different concentrations of sorbitol showed contrasting results: at lower concentrations (5 and 50 mM) there was a decrease in CLA and subtle alterations in secondary and tertiary structure but not at higher concentrations (500 mM). Though, these results shed a light on the effect of sorbitol on α-crystallin structure-function, further studies are required to understand the mechanism of the observed effects and their implication to cataractogenesis.
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Affiliation(s)
- Ch Uday Kumar
- Biochemistry Division, National Institute of Nutrition, Hyderabad, 500007, India.
| | | | - Vishwaraj Sontake
- Biochemistry Division, National Institute of Nutrition, Hyderabad, 500007, India.
| | - P Yadagiri Reddy
- Biochemistry Division, National Institute of Nutrition, Hyderabad, 500007, India.
| | | | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad, 500046, India.
| | - G Bhanuprakash Reddy
- Biochemistry Division, National Institute of Nutrition, Hyderabad, 500007, India.
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11
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Wang Z, Qi J, Goddard JM. Concentrated sugar solutions protect lactase from thermal inactivation. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Hydrogen Bond Arrangement Is Shown to Differ in Coexisting Phases of Aqueous Two-Phase Systems. Biomolecules 2021; 11:biom11121787. [PMID: 34944431 PMCID: PMC8698934 DOI: 10.3390/biom11121787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/25/2022] Open
Abstract
Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation.
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13
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da Silva N, Ferreira LA, Belgovskiy AI, Madeira PP, Teixeira JA, Mann EK, Adin Mann J, Meyer WV, Smart AE, Chernyak VY, Uversky VN, Zaslavsky BY. Effects of different solutes on the physical chemical properties of aqueous solutions via rearrangement of hydrogen bonds in water. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Camino JD, Gracia P, Cremades N. The role of water in the primary nucleation of protein amyloid aggregation. Biophys Chem 2021; 269:106520. [PMID: 33341693 DOI: 10.1016/j.bpc.2020.106520] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022]
Abstract
The understanding of the complex conformational landscape of amyloid aggregation and its modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating some of the molecular basis of pathology in amyloid related diseases, and for developing and evaluating effective disease-specific therapeutics to reduce or eliminate the underlying sources of toxicity in these diseases. Interactions of proteins with solvating water have been long considered to be fundamental in mediating their function and folding; however, the relevance of water in the process of protein amyloid aggregation has been largely overlooked. Here, we provide a perspective on the role water plays in triggering primary amyloid nucleation of intrinsically disordered proteins (IDPs) based on recent experimental evidences. The initiation of amyloid aggregation likely results from the synergistic effect between both protein intermolecular interactions and the properties of the water hydration layer of the protein surface. While the self-assembly of both hydrophobic and hydrophilic IDPs would be thermodynamically favoured due to large water entropy contributions, large desolvation energy barriers are expected, particularly for the nucleation of hydrophilic IDPs. Under highly hydrating conditions, primary nucleation is slow, being facilitated by the presence of nucleation-active surfaces (heterogeneous nucleation). Under conditions of poor water activity, such as those found in the interior of protein droplets generated by liquid-liquid phase separation, however, the desolvation energy barrier is significantly reduced, and nucleation can occur very rapidly in the bulk of the solution (homogeneous nucleation), giving rise to structurally distinct amyloid polymorphs. Water, therefore, plays a key role in modulating the transition free energy of amyloid nucleation, thus governing the initiation of the process, and dictating the type of preferred primary nucleation and the type of amyloid polymorph generated, which could vary depending on the particular microenvironment that the protein molecules encounter in the cell.
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Affiliation(s)
- José D Camino
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Pablo Gracia
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
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15
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Xie J, Liang Z, Lu YC. Molecular crowding electrolytes for high-voltage aqueous batteries. NATURE MATERIALS 2020; 19:1006-1011. [PMID: 32313263 DOI: 10.1038/s41563-020-0667-y] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
Developing low-cost and eco-friendly aqueous electrolytes with a wide voltage window is critical to achieve safe, high-energy and sustainable Li-ion batteries. Emerging approaches using highly concentrated salts (21-55 m (mol kg-1)) create artificial solid-electrode interfaces and improve water stability; however, these approaches raise concerns about cost and toxicity. Molecular crowding is a common phenomenon in living cells where water activity is substantially suppressed by molecular crowding agents through altering the hydrogen-bonding structure. Here we demonstrate a 'molecular crowding' electrolyte using the water-miscible polymer poly(ethylene glycol) as the crowding agent to decrease water activity, thereby achieving a wide electrolyte operation window (3.2 V) with low salt concentration (2 m). Aqueous Li4Ti5O12/LiMn2O4 full cells with stable specific energies between 75 and 110 W h kg-1 were demonstrated over 300 cycles. Online electrochemical mass spectroscopy revealed that common side reactions in aqueous Li-ion batteries (hydrogen/oxygen evolution reactions) are virtually eliminated. This work provides a path for designing high-voltage aqueous electrolytes for low-cost and sustainable energy storage.
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Affiliation(s)
- Jing Xie
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhuojian Liang
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yi-Chun Lu
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
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16
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proc Natl Acad Sci U S A 2020; 117:14194-14201. [PMID: 32522884 DOI: 10.1073/pnas.1920886117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (T m) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.
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17
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McClintic WT, Taylor GJ, Simpson ML, Collier CP. Macromolecular Crowding Affects Voltage-Dependent Alamethicin Pore Formation in Lipid Bilayer Membranes. J Phys Chem B 2020; 124:5095-5102. [DOI: 10.1021/acs.jpcb.0c01650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William T. McClintic
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Graham J. Taylor
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Michael L. Simpson
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - C. Patrick Collier
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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18
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Influence of crowding agents on the dynamics of a multidomain protein in its denatured state: a solvation approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:289-305. [PMID: 32399581 DOI: 10.1007/s00249-020-01435-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/26/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
It is now well appreciated that the crowded intracellular environment significantly modulates an array of physiological processes including protein folding-unfolding, aggregation, and dynamics to name a few. In this work we have studied the dynamics of domain I of the protein human serum albumin (HSA) in its urea-induced denatured states, in the presence of a series of commonly used macromolecular crowding agents. HSA was labeled at Cys-34 (a free cysteine) in domain I with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) to act as a solvation probe. In partially denatured states (2-6 M urea), lower crowder concentrations (~ < 125 g/L) induced faster dynamics, while the dynamics became slower beyond 150 g/L of crowders. We propose that this apparent switch in dynamics is an evidence of a crossover from soft (enthalpic) to hard-core (entropic) interactions between the protein and crowder molecules. That soft interactions are also important for the crowders used here was further confirmed by the appreciable shift in the wavelength of the emission maximum of BADAN, in particular for PEG8000 and Ficoll 70 at concentrations where the excluded volume effect is not dominant.
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19
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Pavlovic M, Plucinski A, Zhang J, Antonietti M, Zeininger L, Schmidt BVKJ. Cascade Kinetics in an Enzyme-Loaded Aqueous Two-Phase System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1401-1408. [PMID: 31977224 PMCID: PMC7307955 DOI: 10.1021/acs.langmuir.0c00186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Indexed: 05/20/2023]
Abstract
Macromolecular crowding plays a critical role in the kinetics of enzymatic reactions. Dynamic compartmentalization of biological components in living cells due to liquid-liquid phase separation represents an important cell regulatory mechanism that can increase enzyme concentration locally and influence the diffusion of substrates. In the present study, we probed partitioning of two enzymes (horseradish-peroxidase and urate-oxidase) in a poly(ethylene glycol)-dextran aqueous two-phase system (ATPS) as a function of salt concentration and ion position in the Hofmeister series. Moreover, we investigated enzymatic cascade reactions and their kinetics within the ATPS, which revealed a strong influence of the ion hydration stemming from the background electrolyte on the partitioning coefficients of proteins following the Hofmeister series. As a result, we were able to realize cross-partitioning of two enzymes because of different protein net charges at a chosen pH. Our study reveals a strong dependency of the enzyme activity on the substrate type and crowding agent interaction on the final kinetics of enzymatic reactions in the ATPS and therefore provides substantial implications en route toward dynamic regulation of reactivity in synthetic protocells.
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Affiliation(s)
- Marko Pavlovic
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Alexander Plucinski
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- School
of Chemistry, University of Glasgow, Joseph Black Building, G128QQ Glasgow, U.K.
| | - Jianrui Zhang
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Markus Antonietti
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Lukas Zeininger
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- E-mail: (L.Z.)
| | - Bernhard V. K. J. Schmidt
- Department
of Colloid Chemistry, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- School
of Chemistry, University of Glasgow, Joseph Black Building, G128QQ Glasgow, U.K.
- E-mail: (B.V.K.J.S.)
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20
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Fan C, Lim LKP, Loh SQ, Ying Lim KY, Upton Z, Leavesley D. Application of “macromolecular crowding” in vitro to investigate the naphthoquinones shikonin, naphthazarin and related analogues for the treatment of dermal scars. Chem Biol Interact 2019; 310:108747. [DOI: 10.1016/j.cbi.2019.108747] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 07/10/2019] [Indexed: 01/05/2023]
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21
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22
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Intrinsic Disorder-Based Emergence in Cellular Biology: Physiological and Pathological Liquid-Liquid Phase Transitions in Cells. Polymers (Basel) 2019; 11:polym11060990. [PMID: 31167414 PMCID: PMC6631845 DOI: 10.3390/polym11060990] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
The visible outcome of liquid-liquid phase transitions (LLPTs) in cells is the formation and disintegration of various proteinaceous membrane-less organelles (PMLOs). Although LLPTs and related PMLOs have been observed in living cells for over 200 years, the physiological functions of these transitions (also known as liquid-liquid phase separation, LLPS) are just starting to be understood. While unveiling the functionality of these transitions is important, they have come into light more recently due to the association of abnormal LLPTs with various pathological conditions. In fact, several maladies, such as various cancers, different neurodegenerative diseases, and cardiovascular diseases, are known to be associated with either aberrant LLPTs or some pathological transformations within the resultant PMLOs. Here, we will highlight both the physiological functions of cellular liquid-liquid phase transitions as well as the pathological consequences produced through both dysregulated biogenesis of PMLOs and the loss of their dynamics. We will also discuss the potential downstream toxic effects of proteins that are involved in pathological formations.
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23
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Zegarra FC, Homouz D, Gasic AG, Babel L, Kovermann M, Wittung-Stafshede P, Cheung MS. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico. J Phys Chem B 2019; 123:3607-3617. [PMID: 30963769 DOI: 10.1021/acs.jpcb.9b00782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
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Affiliation(s)
- Fabio C Zegarra
- Department of Physics , University of Houston , Houston 77204 , United States
| | - Dirar Homouz
- Department of Physics , University of Houston , Houston 77204 , United States.,Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Andrei G Gasic
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Lucas Babel
- Department of Physics , University of Houston , Houston 77204 , United States
| | | | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
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24
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Turoverov KK. The unfolding of iRFP713 in a crowded milieu. PeerJ 2019; 7:e6707. [PMID: 30993043 PMCID: PMC6459179 DOI: 10.7717/peerj.6707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/02/2019] [Indexed: 01/07/2023] Open
Abstract
The exploring of biological processes in vitro under conditions of macromolecular crowding is a way to achieve an understanding of how these processes occur in vivo. In this work, we study the unfolding of the fluorescent probe iRFP713 in crowded environment in vitro. Previously, we showed that the unfolding of the dimeric iRFP713 is accompanied by the formation of a compact monomer and an intermediate state of the protein. In the intermediate state, the macromolecules of iRFP713 have hydrophobic clusters exposed to the surface of the protein and are prone to aggregation. Concentrated solutions of polyethylene glycol (PEG-8000), Dextran-40 and Dextran-70 with a molecular mass of 8000, 40000 and 70000 Da, respectively, were used to model the conditions for macromolecular crowding. A limited available space provided by all the crowding agents used favors to the enhanced aggregation of iRFP713 in the intermediate state at the concentration of guanidine hydrochloride (GdnHCl), at which the charge of protein surface is neutralized by the guanidine cations. This is in line with the theory of the excluded volume. In concentrated solutions of the crowding agents (240–300 mg/ml), the stabilization of the structure of iRFP713 in the intermediate state is observed. PEG-8000 also enhances the stability of iRFP713 in the monomeric compact state, whereas in concentrated solutions of Dextran-40 and Dextran-70 the resistance of the protein in the monomeric state against GdnHCl-induced unfolding decreases. The obtained data argues for the excluded volume effect being not the only factor that contributes the behavior of biological molecules in a crowded milieu. Crowding agents do not affect the structure of the native dimer of iRFP713, which excludes the direct interactions between the target protein and the crowding agents. PEGs of different molecular mass and Dextran-40/Dextran-70 are known to influence the solvent properties of water. The solvent dipolarity/polarizability and basicity/acidity in aqueous solutions of these crowding agents vary in different ways. The change of the solvent properties in aqueous solutions of crowding agents might impact the functioning of a target protein.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
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25
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26
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Perturbation of water structure by water-polymer interactions probed by FTIR and polarized Raman spectroscopy. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Madeira PP, Loureiro JA, Freire MG, Coutinho JAP. Solvatochromism as a new tool to distinguish structurally similar compounds. J Mol Liq 2019; 274:740-745. [PMID: 30936594 DOI: 10.1016/j.molliq.2018.11.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
It is here reported a new concept based on solvatochromism to distinguish structurally similar compounds in aqueous solutions by the analysis of the stabilization of electronic excited states. The sensitivity of this approach to differentiate similar organic compounds, such as structural isomers or compound differing in the number of methylene groups, or proteins with conformational changes induced by being or not bound to cofactors, differing in two amino acids substitutions, or differing in their glycosylation profile, is demonstrated. The sensitivity of the proposed approach, based on the solvatochromic method, opens the path to its use as an auxiliary analytical tool in biomedical diagnosis/prognosis or in quality control of biologic-based drugs.
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Affiliation(s)
- Pedro P Madeira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Joana A Loureiro
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto 4500-465, Portugal
| | - Mara G Freire
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A P Coutinho
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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28
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da Silva NR, Ferreira LA, Teixeira JA, Uversky VN, Zaslavsky BY. Effects of sodium chloride and sodium perchlorate on properties and partition behavior of solutes in aqueous dextran-polyethylene glycol and polyethylene glycol-sodium sulfate two-phase systems. J Chromatogr A 2019; 1583:28-38. [DOI: 10.1016/j.chroma.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022]
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29
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo. Cell Mol Life Sci 2018; 75:3907-3929. [PMID: 30066087 PMCID: PMC11105604 DOI: 10.1007/s00018-018-2894-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022]
Abstract
Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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30
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Ferreira LA, Walczyk Mooradally A, Zaslavsky B, Uversky VN, Graether SP. Effect of an Intrinsically Disordered Plant Stress Protein on the Properties of Water. Biophys J 2018; 115:1696-1706. [PMID: 30297135 DOI: 10.1016/j.bpj.2018.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Dehydrins are plant proteins that are able to protect plants from various forms of dehydrative stress such as drought, cold, and high salinity. Dehydrins can prevent enzymes from losing activity after freeze/thaw treatments. Previous studies had suggested that the dehydrins function by a molecular shield effect, essentially preventing a denatured enzyme from aggregating with another enzyme. Therefore, the larger the dehydrin, the larger the shield and theoretically the more effective the protection. Although this relationship holds for smaller dehydrins, it fails to explain why larger dehydrins are less efficient than would be predicted from their size. Using solvatochromic dyes to probe the solvent features of water, we first confirm that the dehydrins do not bind the dyes, which would interfere with interpretation of the data. We then show that the dehydrins have an effect on three solvent properties of water (dipolarity/polarizability, hydrogen-bond donor acidity and hydrogen-bond acceptor basicity), which can contribute to the protective mechanism of these proteins. Interpretation of these data suggests that although polyethylene glycol and dehydrins have similar protective effects, dehydrins may more efficiently modify the hydrogen-bonding ability of bulk water to prevent enzyme denaturation. This possibly explains why dehydrins recover slightly more enzyme activity than polyethylene glycol.
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Affiliation(s)
| | | | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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31
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Ferreira L, Uversky V, Zaslavsky B. Modified binodal model describes phase separation in aqueous two-phase systems in terms of the effects of phase-forming components on the solvent features of water. J Chromatogr A 2018; 1567:226-232. [DOI: 10.1016/j.chroma.2018.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/27/2018] [Accepted: 07/02/2018] [Indexed: 11/27/2022]
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32
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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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Ferreira LA, Uversky VN, Zaslavsky BY. Phase equilibria, solvent properties, and protein partitioning in aqueous polyethylene glycol-600-trimethylamine N-oxide and polyethylene glycol-600-choline chloride two-phase systems. J Chromatogr A 2018; 1535:154-161. [DOI: 10.1016/j.chroma.2018.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
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Zaslavsky BY, Uversky VN. In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles. Biochemistry 2018; 57:2437-2451. [PMID: 29303563 DOI: 10.1021/acs.biochem.7b01215] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.
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Affiliation(s)
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
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