1
|
Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024; 63:1621-1635. [PMID: 38607680 PMCID: PMC11223479 DOI: 10.1021/acs.biochem.3c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood. PEG may impact protein conformation and dynamics, thus its function. In the present study, the effects of PEG molecules of various molecular weights and concentrations on the conformation and dynamics of Ec ProRS were investigated using a combined experimental and computational approach including intrinsic tryptophan fluorescence spectroscopy, atomic force microscopy, and atomistic molecular dynamic simulations. Results of the present study suggest that lower molecular weight PEGs in the dilute regime have modest effects on the conformational dynamics of Ec ProRS but impact the catalytic function primarily via the excluded volume effect; they form large clusters blocking the active site pocket. In contrast, the larger molecular weight PEGs in dilute to semidilute regimes have a significant impact on the protein's conformational dynamics; they wrap on the protein surface through noncovalent interactions. Thus, lower-molecular-weight PEG molecules impact protein dynamics and function via crowding effects, whereas larger PEGs induce confinement effects. These results have implications for the development of inhibitors for protein targets in a crowded cellular environment.
Collapse
Affiliation(s)
- Jessica Liebau
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Bethany F. Laatsch
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Joshua Rusnak
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Keegan Gunderson
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Brianna Finke
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Kassandra Bargender
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Alex Narkiewicz-Jodko
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Katelyn Weeks
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Murphi T. Williams
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Irina Shulgina
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Karin Musier-Forsyth
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sudeep Bhattacharyya
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| |
Collapse
|
2
|
Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
Collapse
Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| |
Collapse
|
3
|
Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
Collapse
Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
| |
Collapse
|
4
|
Olgenblum GI, Carmon N, Harries D. Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds. J Am Chem Soc 2023; 145:23308-23320. [PMID: 37845197 PMCID: PMC10603812 DOI: 10.1021/jacs.3c08702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.
Collapse
Affiliation(s)
- Gil I Olgenblum
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Neta Carmon
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| |
Collapse
|
5
|
Ribeiro SS, Gnutt D, Azoulay-Ginsburg S, Fetahaj Z, Spurlock E, Lindner F, Kuz D, Cohen-Erez Y, Rapaport H, Israelson A, Gruzman AL, Ebbinghaus S. Intracellular spatially-targeted chemical chaperones increase native state stability of mutant SOD1 barrel. Biol Chem 2023; 404:909-930. [PMID: 37555646 DOI: 10.1515/hsz-2023-0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurological disorder with currently no cure. Central to the cellular dysfunction associated with this fatal proteinopathy is the accumulation of unfolded/misfolded superoxide dismutase 1 (SOD1) in various subcellular locations. The molecular mechanism driving the formation of SOD1 aggregates is not fully understood but numerous studies suggest that aberrant aggregation escalates with folding instability of mutant apoSOD1. Recent advances on combining organelle-targeting therapies with the anti-aggregation capacity of chemical chaperones have successfully reduce the subcellular load of misfolded/aggregated SOD1 as well as their downstream anomalous cellular processes at low concentrations (micromolar range). Nevertheless, if such local aggregate reduction directly correlates with increased folding stability remains to be explored. To fill this gap, we synthesized and tested here the effect of 9 ER-, mitochondria- and lysosome-targeted chemical chaperones on the folding stability of truncated monomeric SOD1 (SOD1bar) mutants directed to those organelles. We found that compound ER-15 specifically increased the native state stability of ER-SOD1bar-A4V, while scaffold compound FDA-approved 4-phenylbutyric acid (PBA) decreased it. Furthermore, our results suggested that ER15 mechanism of action is distinct from that of PBA, opening new therapeutic perspectives of this novel chemical chaperone on ALS treatment.
Collapse
Affiliation(s)
- Sara S Ribeiro
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, D-44780 Bochum, Germany
| | | | - Zamira Fetahaj
- Institute of Physical Chemistry II, Ruhr University, D-44780 Bochum, Germany
| | - Ella Spurlock
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
| | - Felix Lindner
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
| | - Damon Kuz
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
| | - Yfat Cohen-Erez
- Department of Biotechnology Engineering, The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
| | - Hanna Rapaport
- Department of Biotechnology Engineering, The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
| | - Adrian Israelson
- Department of Physiology and Cell Biology, The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
| | - Arie-Lev Gruzman
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), D-38106 Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, D-44780 Bochum, Germany
- Research Center Chemical Sciences and Sustainability, Research Alliance Ruhr, Duisburg, Germany
| |
Collapse
|
6
|
Stewart CJ, Olgenblum GI, Propst A, Harries D, Pielak GJ. Resolving the enthalpy of protein stabilization by macromolecular crowding. Protein Sci 2023; 32:e4573. [PMID: 36691735 PMCID: PMC9942490 DOI: 10.1002/pro.4573] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
Proteins in the cellular milieu reside in environments crowded by macromolecules and other solutes. Although crowding can significantly impact the protein folded state stability, most experiments are conducted in dilute buffered solutions. To resolve the effect of crowding on protein stability, we use 19 F nuclear magnetic resonance spectroscopy to follow the reversible, two-state unfolding thermodynamics of the N-terminal Src homology 3 domain of the Drosophila signal transduction protein drk in the presence of polyethylene glycols (PEGs) of various molecular weights and concentrations. Contrary to most current theories of crowding that emphasize steric protein-crowder interactions as the main driving force for entropically favored stabilization, our experiments show that PEG stabilization is accompanied by significant heat release, and entropy disfavors folding. Using our newly developed model, we find that stabilization by ethylene glycol and small PEGs is driven by favorable binding to the folded state. In contrast, for larger PEGs, chemical or soft PEG-protein interactions do not play a significant role. Instead, folding is favored by excluded volume PEG-protein interactions and an exothermic nonideal mixing contribution from release of confined PEG and water upon folding. Our results indicate that crowding acts through molecular interactions subtler than previously assumed and that interactions between solution components with both the folded and unfolded states must be carefully considered.
Collapse
Affiliation(s)
- Claire J. Stewart
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gil I. Olgenblum
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Ashlee Propst
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Daniel Harries
- Institute of Chemistry & the Fritz Haber Research Center, The Hebrew UniversityJerusalemIsrael
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| |
Collapse
|
7
|
Effects of Molecular Crowding and Betaine on HSPB5 Interactions, with Target Proteins Differing in the Quaternary Structure and Aggregation Mechanism. Int J Mol Sci 2022; 23:ijms232315392. [PMID: 36499725 PMCID: PMC9737104 DOI: 10.3390/ijms232315392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The aggregation of intracellular proteins may be enhanced under stress. The expression of heat-shock proteins (HSPs) and the accumulation of osmolytes are among the cellular protective mechanisms in these conditions. In addition, one should remember that the cell environment is highly crowded. The antiaggregation activity of HSPB5 and the effect on it of either a crowding agent (polyethylene glycol (PEG)) or an osmolyte (betaine), or their mixture, were tested on the aggregation of two target proteins that differ in the order of aggregation with respect to the protein: thermal aggregation of glutamate dehydrogenase and DTT-induced aggregation of lysozyme. The kinetic analysis of the dynamic light-scattering data indicates that crowding can decrease the chaperone-like activity of HSPB5. Nonetheless, the analytical ultracentrifugation shows the protective effect of HSPB5, which retains protein aggregates in a soluble state. Overall, various additives may either improve or impair the antiaggregation activity of HSPB5 against different protein targets. The mixed crowding arising from the presence of PEG and 1 M betaine demonstrates an extraordinary effect on the oligomeric state of protein aggregates. The shift in the equilibrium of HSPB5 dynamic ensembles allows for the regulation of its antiaggregation activity. Crowding can modulate HSPB5 activity by affecting protein-protein interactions.
Collapse
|
8
|
Pastore A, Temussi PA. Crowding revisited: Open questions and future perspectives. Trends Biochem Sci 2022; 47:1048-1058. [PMID: 35691783 DOI: 10.1016/j.tibs.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/12/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects protein stability is an important question heatedly discussed over the past 20 years. Theoretical estimations have suggested a 5-20°C effect of fold stabilisation. This estimate, however, is at variance with what has been verified experimentally that proposes only a limited increase of stability, opening the question whether some of the assumptions taken for granted should be reconsidered. The present review critically analyses the causes of this discrepancy and discusses the limitations and implications of the current concept of crowding.
Collapse
Affiliation(s)
- Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| |
Collapse
|
9
|
Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
Collapse
Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
| |
Collapse
|
10
|
Rivas G, Minton A. Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo. Annu Rev Biochem 2022; 91:321-351. [PMID: 35287477 DOI: 10.1146/annurev-biochem-040320-104151] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain;
| | - Allen Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
| |
Collapse
|
11
|
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: 49] [Impact Index Per Article: 24.5] [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.
Collapse
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
| |
Collapse
|
12
|
Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
Collapse
Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
| |
Collapse
|
13
|
Shukla SK, Mikkola JP. Use of Ionic Liquids in Protein and DNA Chemistry. Front Chem 2020; 8:598662. [PMID: 33425856 PMCID: PMC7786294 DOI: 10.3389/fchem.2020.598662] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.
Collapse
Affiliation(s)
- Shashi Kant Shukla
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
| | - Jyri-Pekka Mikkola
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
- Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland
| |
Collapse
|
14
|
Stadmiller SS, Pielak GJ. Protein-complex stability in cells and in vitro under crowded conditions. Curr Opin Struct Biol 2020; 66:183-192. [PMID: 33285342 DOI: 10.1016/j.sbi.2020.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 11/29/2022]
Abstract
Biology is beginning to appreciate the effects of the crowded and complex intracellular environment on the equilibrium thermodynamics and kinetics of protein folding. The next logical step involves the interactions between proteins. We review quantitative, wet-experiment based efforts aimed at understanding how and why high concentrations of small molecules, synthetic polymers, biologically relevant cosolutes and the interior of living cells affect the energetics of protein-protein interactions. We then address popular theories used to explain the effects and suggest expeditious paths for a more methodical integration of experiment and simulation.
Collapse
Affiliation(s)
- Samantha S Stadmiller
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
15
|
Naidu KT, Rao DK, Prabhu NP. Cryo vs Thermo: Duality of Ethylene Glycol on the Stability of Proteins. J Phys Chem B 2020; 124:10077-10088. [PMID: 33143422 DOI: 10.1021/acs.jpcb.0c06247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Osmolytes are known to stabilize proteins under stress conditions. Thermal denaturation studies on globular proteins (β-lactoglobulin, cytochrome c, myoglobin, α-chymotrypsin) in the presence of ethylene glycol (EG), a polyol class of osmolyte, demonstrate a unique property of EG. EG stabilizes proteins against cold denaturation and destabilizes them during heat-induced denaturation. Further, chemical denaturation experiments performed at room temperature and at a sub-zero temperature (-10 °C) show that EG stabilizes the proteins at subzero temperature but destabilizes them at room temperature. The experiments carried out in the presence of glycerol, however, showed that glycerol stabilizes proteins against all of the denaturing conditions. This differential effect has not been reported for any other polyol class of osmolyte and might be specific to EG. Moreover, molecular dynamics simulations of all of the four proteins were carried out at three different temperatures, 240, 300, and 340 K, in the absence and presence of EG (20 and 40%). The results suggest that EG preferably accumulates around the hydrophobic residues and reduces the hydrophobic hydration of the proteins at a low temperature leading to stabilization of the proteins. At 340 K, the preferential hydration of the proteins is significantly reduced and the preferential binding of EG destabilizes the proteins like common denaturants.
Collapse
Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| |
Collapse
|
16
|
Renzetti S, van den Hoek IA, van der Sman RG. Amino acids, polyols and soluble fibres as sugar replacers in bakery applications: Egg white proteins denaturation controlled by hydrogen bond density of solutions. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.106034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
17
|
Adams LM, Andrews RJ, Hu QH, Schmit HL, Hati S, Bhattacharyya S. Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase. Biophys J 2019; 117:1269-1284. [PMID: 31542226 PMCID: PMC6818166 DOI: 10.1016/j.bpj.2019.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023] Open
Abstract
The effect of molecular crowding on the structure and function of Escherichia coli prolyl-transfer RNA synthetase (Ec ProRS), a member of the aminoacyl-transfer RNA synthetase family, has been investigated using a combined experimental and theoretical method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of molecular crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
Collapse
Affiliation(s)
- Lauren M Adams
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Ryan J Andrews
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Quin H Hu
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Heidi L Schmit
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| |
Collapse
|
18
|
Larimi MG, Mayse LA, Movileanu L. Interactions of a Polypeptide with a Protein Nanopore Under Crowding Conditions. ACS NANO 2019; 13:4469-4477. [PMID: 30925041 PMCID: PMC6482057 DOI: 10.1021/acsnano.9b00008] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Molecular crowding, a ubiquitous feature of the cellular environment, has significant implications in the kinetics and equilibrium of biopolymer interactions. In this study, a single charged polypeptide is exposed to competing forces that drive it into a transmembrane protein pore versus forces that pull it outside. Using single-molecule electrophysiology, we provide compelling experimental evidence that the kinetic details of the polypeptide-pore interactions are substantially affected by high concentrations of less-penetrating polyethylene glycols (PEGs). At a polymer concentration above a critical value, the presence of these neutral macromolecular crowders increases the rate constant of association but decreases the rate constant of dissociation, resulting in a stronger polypeptide-pore interaction. Moreover, a larger-molecular weight PEG exhibits a lower rate constant of association but a higher rate constant of dissociation than those values corresponding to a smaller-molecular weight PEG. These outcomes are in accord with a lower diffusion constant of the polypeptide and higher depletion-attraction forces between the polypeptide and transmembrane protein pore under crowding and confinement conditions.
Collapse
Affiliation(s)
- Motahareh Ghahari Larimi
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Lauren Ashley Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
| |
Collapse
|
19
|
Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents. Phys Chem Chem Phys 2018; 20:29389-29398. [PMID: 30451257 DOI: 10.1039/c8cp04421j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.
Collapse
Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia - 80126 Napoli, Italy.
| | | | | | | |
Collapse
|
20
|
Cheng K, Wu Q, Zhang Z, Pielak GJ, Liu M, Li C. Crowding and Confinement Can Oppositely Affect Protein Stability. Chemphyschem 2018; 19:3350-3355. [DOI: 10.1002/cphc.201800857] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Zeting Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Gary J. Pielak
- Department of Chemistry Department of Biochemistry and Biophysics University of North Carolina, Chapel Hill Chapel Hill, NC 27599-3290 USA
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| |
Collapse
|
21
|
RGM VDS. Progress in understanding of supplemented state diagrams of hydrophilic food materials. Curr Opin Food Sci 2018. [DOI: 10.1016/j.cofs.2018.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
22
|
Budkov YA, Kiselev MG. Flory-type theories of polymer chains under different external stimuli. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:043001. [PMID: 29271365 DOI: 10.1088/1361-648x/aa9f56] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this Review, we present a critical analysis of various applications of the Flory-type theories to a theoretical description of the conformational behavior of single polymer chains in dilute polymer solutions under a few external stimuli. Different theoretical models of flexible polymer chains in the supercritical fluid are discussed and analysed. Different points of view on the conformational behavior of the polymer chain near the liquid-gas transition critical point of the solvent are presented. A theoretical description of the co-solvent-induced coil-globule transitions within the implicit-solvent-explicit-co-solvent models is discussed. Several explicit-solvent-explicit-co-solvent theoretical models of the coil-to-globule-to-coil transition of the polymer chain in a mixture of good solvents (co-nonsolvency) are analysed and compared with each other. Finally, a new theoretical model of the conformational behavior of the dielectric polymer chain under the external constant electric field in the dilute polymer solution with an explicit account for the many-body dipole correlations is discussed. The polymer chain collapse induced by many-body dipole correlations of monomers in the context of statistical thermodynamics of dielectric polymers is analysed.
Collapse
Affiliation(s)
- Yu A Budkov
- Tikhonov Moscow Institute of Electronics and Mathematics, School of Applied Mathematics, National Research University Higher School of Economics, Moscow, Russia. Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
| | | |
Collapse
|
23
|
Senske M, Constantinescu-Aruxandei D, Havenith M, Herrmann C, Weingärtner H, Ebbinghaus S. The temperature dependence of the Hofmeister series: thermodynamic fingerprints of cosolute-protein interactions. Phys Chem Chem Phys 2018; 18:29698-29708. [PMID: 27806138 DOI: 10.1039/c6cp05080h] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e.g. the melting point Tm), we here consider the salt induced shifts of the entire protein 'stability curve' (the temperature dependence of the unfolding free energy change, ΔGu(T)). We found multiple intersections of these curves, pinpointing a widely ignored fact: the Hofmeister cation and anion rankings are temperature dependent. We further developed a novel classification scheme of cosolute effects based on their thermodynamic fingerprints, reaching beyond salt effects to non-electrolytes.
Collapse
Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | | | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Christian Herrmann
- Department of Physical Chemistry I, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Hermann Weingärtner
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Simon Ebbinghaus
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Budkov YA, Kolesnikov AL. Statistical description of co-nonsolvency suppression at high pressures. SOFT MATTER 2017; 13:8362-8367. [PMID: 29116278 DOI: 10.1039/c7sm01637a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present an application of Flory-type theory of a flexible polymer chain dissolved in a binary mixture of solvents to theoretical description of co-nonsolvency. We show that our theoretical predictions are in good quantitative agreement with the recently published MD simulation results for the conformational behavior of a Lennard-Jones flexible chain in a binary mixture of the Lennard-Jones fluids. We show that our theory is able to describe co-nonsolvency suppression through pressure enhancement to extremely high values recently discovered in experiments and reproduced by full atomistic MD simulations. By analysing the co-solvent concentration in the internal polymer volume at different pressure values, we speculate that this phenomenon is caused by the suppression of the co-solvent preferential solvation of the polymer backbone at the rather high pressure imposed. We show that when the co-solvent-induced coil-globule transition takes place, the entropy and enthalpy contributions to the solvation free energy abruptly decrease, while the solvation free energy remains continuous.
Collapse
Affiliation(s)
- Yu A Budkov
- Tikhonov Moscow Institute of Electronics and Mathematics, School of Applied Mathematics, National Research University Higher School of Economics, Tallinskaya St. 34, 123458 Moscow, Russia.
| | | |
Collapse
|
26
|
Ferreira LA, Uversky VN, Zaslavsky BY. Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes. MOLECULAR BIOSYSTEMS 2017; 13:2551-2563. [DOI: 10.1039/c7mb00436b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.
Collapse
Affiliation(s)
| | - V. N. Uversky
- Department of Molecular Medicine
- Morsant College of Medicine
- University of South Florida
- Tampa
- USA
| | | |
Collapse
|
27
|
Rivas G, Minton AP. Macromolecular Crowding In Vitro, In Vivo, and In Between. Trends Biochem Sci 2016; 41:970-981. [PMID: 27669651 DOI: 10.1016/j.tibs.2016.08.013] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer. Finally, we propose strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells.
Collapse
Affiliation(s)
- Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Allen P Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
28
|
Sapir L, Harries D. Macromolecular compaction by mixed solutions: Bridging versus depletion attraction. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
29
|
Sapir L, Stanley CB, Harries D. Properties of Polyvinylpyrrolidone in a Deep Eutectic Solvent. J Phys Chem A 2016; 120:3253-9. [DOI: 10.1021/acs.jpca.5b11927] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liel Sapir
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Christopher B. Stanley
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Daniel Harries
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| |
Collapse
|
30
|
Rodríguez-Ropero F, Hajari T, van der Vegt NFA. Mechanism of Polymer Collapse in Miscible Good Solvents. J Phys Chem B 2015; 119:15780-8. [PMID: 26619003 DOI: 10.1021/acs.jpcb.5b10684] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a physical mechanism for co-nonsolvency of a stimulus-responsive polymer in water/methanol mixed solution based on results obtained with molecular simulations. Even though the phenomenon is well known, the mechanism behind co-nonsolvency is still under debate. Herein, we study co-nonsolvency of poly(N-isopropylacrylamide) (PNiPAM) in methanol aqueous solutions, the most widely studied and experimentally well-characterized system. Our results show that at low alcohol content of the solution methanol preferentially binds to the PNiPAM globule and drives polymer collapse. The energetics of electrostatic, hydrogen bonding, or bridging-type interactions with the globule is found to play no role. Instead, preferential methanol binding results in a significant increase in the globule's configurational entropy, stabilizing methanol-enriched globular structures over wet globular structures in neat water. This mechanism drives the reduction of the lower critical solution temperature with increasing methanol content in the co-nonsolvency regime and eventually leads to polymer collapse. The globule-to-coil re-entrance at high methanol concentrations is instead driven by changes in solvent-excluded volume of the coil and globular states imparted by a decrease in solvent density with increasing methanol content of the solution: with increasing proportion of larger solvent particles (methanol), the entropic (cavity formation) cost of redistributing solvent molecules upon polymer re-entrance becomes smaller. This effect provides a natural explanation for the experimentally observed dependence of the re-entrance transition on chain molecular weight.
Collapse
Affiliation(s)
- Francisco Rodríguez-Ropero
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Timir Hajari
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| |
Collapse
|