1
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Garg M, Sharma D, Kaur G, Rawat J, Goyal B, Kumar S, Kumar R. Factor defining the effects of tetraalkylammonium chloride on stability, folding, and dynamics of horse cytochrome c. Int J Biol Macromol 2024; 276:133713. [PMID: 38986993 DOI: 10.1016/j.ijbiomac.2024.133713] [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: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
This article describes the molecular mechanism by which tetraalkylammonium chloride ([R4N]Cl: R- = methyl (Me), ethyl (Et), propyl (Pr),butyl (Bu)) modulates the stability, folding, and dynamics of cytochrome c (Cyt c). Analysis of [R4N]Cl effects on thermal/chemical denaturations, millisecond refolding/unfolding kinetics, and slow CO-association kinetics of Cyt c without and with denaturant providing some significant results: (i) [R4N]Cl decreasing the unfolding free energy estimated by thermodynamic and kinetic analysis of thermal/chemical denaturation curves and kinetic chevrons (Log kobs-[GdmCl]) of Cyt c, respectively (ii) hydrophobicity of R-group of [R4N]Cl, preferential inclusion of [R4N]Cl at the protein surface, and destabilizing enthalpic attractive interactions of [Me4N]Cl and steric entropic interactions of [Et4N]Cl,[Pr4N]Cl and [Bu4N]Cl with protein contribute to [R4N]Cl-induced decrease thermodynamic stability of Cyt c (iii) [R4N]Cl exhibits an additive effect with denaturant to decrease thermodynamic stability and refolding rates of Cyt c (iv) low concentrations of [R4N]Cl (≤ 0.5 M) constrain the motional dynamics while the higher concentrations (>0.75 M [R4N]Cl) enhance the structural-fluctuations that denture protein (v) hydrophobicity of R-group of [R4N]Cl alters the [denaturant]-dependent conformational stability, refolding-unfolding kinetics, and CO-association kinetics of Cyt c. Furthermore, the MD simulations depicted that the addition of 1.0 M of [R4N]Cl increased the conformational fluctuations in Cyt c leading to decreased structural stability in the order [Me4N]Cl < [Et4N]Cl < [Pr4N]Cl < [Bu4N]Cl consistent with the experimental results.
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Affiliation(s)
- Mansi Garg
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39A, Academy of Scientific & Innovative Research, Chandigarh, India
| | - Gurmeet Kaur
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Jayanti Rawat
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Bhupesh Goyal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Sumit Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Rajesh Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India.
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2
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Ghosh S, Prabhu NP. Heterogeneous Macromolecular crowding effect on nucleation-independent fibril formation of Lysozyme: Spectroscopic analysis of Structure, Stability, and fibrillation rate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124276. [PMID: 38626673 DOI: 10.1016/j.saa.2024.124276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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3
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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.
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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
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4
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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5
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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BBA ADVANCES 2024; 5:100115. [PMID: 38318251 PMCID: PMC10840120 DOI: 10.1016/j.bbadva.2024.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain. Statement of significance For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show in vitro the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, in vivo, diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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6
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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547256. [PMID: 38014150 PMCID: PMC10680572 DOI: 10.1101/2023.06.30.547256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis (Greek for "life without water"). Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and varying amounts of glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. We find that protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Extending on this, we have examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. In all cases, the dried desiccation tolerant life stage of an organism had an increased glass transition temperature relative to its dried desiccation intolerant life stage, and this trend is also seen in all three organisms when considering reduced glass former fragility. These results suggest that while drying of different protective sugars in vitro results in vitrified systems with distinct material properties that correlate with their enzyme-protective capacity, in nature organismal desiccation tolerance relies on a combination of these properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming. Laramie, WY 82071
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7
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [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: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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8
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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.
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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
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9
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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.
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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
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10
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [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: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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11
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Garg H, Rajesh R, Vemparala S. The conformational phase diagram of neutral polymers in the presence of attractive crowders. J Chem Phys 2023; 158:114903. [PMID: 36948827 DOI: 10.1063/5.0140721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Extensive coarse-grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowder densities, the polymer predominantly shows three phases as a function of both intra-polymer and polymer-crowder interactions: (1) weak intra-polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E), (2) strong intra-polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI), and (3) strong polymer-crowder attractive interactions, regardless of intra-polymer interactions, induce a second collapsed or globular conformation that encloses bridging crowders (phase CB). The detailed phase diagram is obtained by determining the phase boundaries delineating the different phases based on an analysis of the radius of gyration as well as bridging crowders. The dependence of the phase diagram on strength of crowder-crowder attractive interactions and crowder density is clarified. We also show that when the crowder density is increased, a third collapsed phase of the polymer emerges for weak intra-polymer attractive interactions. This crowder density-induced compaction is shown to be enhanced by stronger crowder-crowder attraction and is different from the depletion-induced collapse mechanism, which is primarily driven by repulsive interactions. We also provide a unified explanation of the observed re-entrant swollen/extended conformations of the earlier simulations of weak and strongly self-interacting polymers in terms of crowder-crowder attractive interactions.
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Affiliation(s)
- Hitesh Garg
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - R Rajesh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
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12
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Irukuvajjula SS, Reddy JG, Vadrevu R. Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY). Biochemistry 2022; 61:1431-1443. [PMID: 35796609 DOI: 10.1021/acs.biochem.2c00030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
| | - Jithender G Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
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13
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Gorensek-Benitez AH, Kirk B, Myers JK. Protein Fibrillation under Crowded Conditions. Biomolecules 2022; 12:biom12070950. [PMID: 35883507 PMCID: PMC9312947 DOI: 10.3390/biom12070950] [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: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.
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Affiliation(s)
- Annelise H. Gorensek-Benitez
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, CO 80903, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| | - Bryan Kirk
- Department of Biology, Davidson College, Davidson, NC 28035, USA;
| | - Jeffrey K. Myers
- Department of Chemistry, Davidson College, Davidson, NC 28035, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
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14
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Bazmi S, Wallin S. Crowding-induced protein destabilization in the absence of soft attractions. Biophys J 2022; 121:2503-2513. [PMID: 35672949 DOI: 10.1016/j.bpj.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.
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Affiliation(s)
- Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada.
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15
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Stasiulewicz M, Panuszko A, Bruździak P, Stangret J. Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence. J Phys Chem B 2022; 126:2990-2999. [PMID: 35441516 PMCID: PMC9059127 DOI: 10.1021/acs.jpcb.2c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
investigated the influence of stabilizing (N,N,N-trimethylglycine)
and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules
in folded forms (trpzip-1 peptide and hen egg white
lysozyme—hewl) and unfolded protein models
(glycine—GLY and N-methylglycine—NMG)
by means of infrared spectroscopy. GLY and NMG were clearly limited
as minimal models for unfolded proteins and should be treated with
caution. We isolated the spectral share of water changed simultaneously
by the biomacromolecule/model molecule and the osmolyte, which allowed
us to provide unambiguous experimental arguments for the mechanism
of stabilization/destabilization of proteins by osmolytes. In the
case of both types of osmolytes, the decisive factor determining the
equilibrium folded/unfolded state of protein was the enthalpy effect
exerted on the hydration spheres of proteins in both forms. In the
case of stabilizing osmolytes, enthalpy was also favored by entropy,
as the unfolded state of a protein was more entropically destabilized
than the folded state.
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Affiliation(s)
- Marcin Stasiulewicz
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Aneta Panuszko
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Piotr Bruździak
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
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16
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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: 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.
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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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17
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Miranda-Quintana RA, Smiatek J. Electronic Properties of Protein Destabilizers and Stabilizers: Implications for Preferential Binding and Exclusion Mechanisms. J Phys Chem B 2021; 125:11857-11868. [PMID: 34672590 DOI: 10.1021/acs.jpcb.1c06295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the electronic properties of low-weight organic co-solutes by means of conceptual density functional theory calculations. Our results highlight the important role of certain chemical reactivity descriptors such as chemical hardness, electronegativity, nucleofugality, and the electrofugality as important criteria to classify protein stabilizers and destabilizers. Our results imply Lewis basic properties with lower chemical hardness for stabilizers, while destabilizers show higher Lewis acidity with higher chemical hardness. Further consideration of analytical calculations in terms of transfer energies reveals the crucial role of co-solute-protein interactions which significantly change the interaction pattern of the stabilizing or destabilizing species. The corresponding outcomes connect statistical thermodynamics with the electronic properties of co-solutes and also allow us to define general principles for strong stabilizers and destabilizers.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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18
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Keller F, Heuer A, Galla HJ, Smiatek J. Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns. Phys Chem Chem Phys 2021; 23:22936-22946. [PMID: 34622252 DOI: 10.1039/d1cp03052c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We study the interactions between dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in the gel and the fluid phase with ectoine, amino ectoine and water molecules by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations. Our results reveal a pronounced preferential exclusion of both co-solutes from the DPPC lipid bilayer which is stronger for the fluid phase. The corresponding outcomes can be brought into relation with the Kirkwood-Buff theory of solutions in order to provide a thermodynamic rationale for the experimentally observed stabilization of the gel phase. Closely related to preferential exclusion of both co-solutes, our simulations also highlight a preferential hydration behavior as manifested by an increased number of hydrogen bonds between water and DPPC molecules. All results are rationalized by conceptual DFT calculations with regard to differences in the electronic properties between ectoine and amino ectoine.
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Affiliation(s)
- Fabian Keller
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, D-48149 Münster, Germany
| | - Hans-Joachim Galla
- Institute of Biochemistry, University of Münster, D-48149 Münster, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
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19
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Hydration and aggregation in aqueous xylitol solutions in the wide temperature range. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Olgenblum GI, Wien F, Sapir L, Harries D. β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State. J Phys Chem Lett 2021; 12:7659-7664. [PMID: 34351767 DOI: 10.1021/acs.jpclett.1c02379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
From stem cell freeze-drying to organ storage, considerable recent efforts have been directed toward the development of new preservation technologies. A prominent protein stabilizing strategy involves vitrification in glassy matrices, most notably those formed of sugars such as the biologically relevant preservative trehalose. Here, we compare the folding thermodynamics of a model miniprotein in solution and in the glassy state of the sugars trehalose and glucose. Using synchrotron radiation circular dichroism (SRCD), we find that the same native structure persists in solution and glass. However, upon transition to the glass, a completely different, conformationally restricted unfolded state replaces the disordered denatured state found in solution, potentially inhibiting misfolding. Concomitantly, a large exothermic contribution is observed in glass, exposing the stabilizing effect of interactions with the sugar matrix on the native state. Our results shed light on the mechanism of protein stabilization in sugar glass and should aid in future preservation technologies.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
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21
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Garfagnini T, Levi-Kalisman Y, Harries D, Friedler A. Osmolytes and crowders regulate aggregation of the cancer-related L106R mutant of the Axin protein. Biophys J 2021; 120:3455-3469. [PMID: 34087214 DOI: 10.1016/j.bpj.2021.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Protein aggregation is involved in a variety of diseases, including neurodegenerative diseases and cancer. The cellular environment is crowded by a plethora of cosolutes comprising small molecules and biomacromolecules at high concentrations, which may influence the aggregation of proteins in vivo. To account for the effect of cosolutes on cancer-related protein aggregation, we studied their effect on the aggregation of the cancer-related L106R mutant of the Axin protein. Axin is a key player in the Wnt signaling pathway, and the L106R mutation in its RGS domain results in a native molten globule that tends to form native-like aggregates. This results in uncontrolled activation of the Wnt signaling pathway, leading to cancer. We monitored the aggregation process of Axin RGS L106R in vitro in the presence of a wide ensemble of cosolutes including polyols, amino acids, betaine, and polyethylene glycol crowders. Except myo-inositol, all polyols decreased RGS L106R aggregation, with carbohydrates exerting the strongest inhibition. Conversely, betaine and polyethylene glycols enhanced aggregation. These results are consistent with the reported effects of osmolytes and crowders on the stability of molten globular proteins and with both amorphous and amyloid aggregation mechanisms. We suggest a model of Axin L106R aggregation in vivo, whereby molecularly small osmolytes keep the protein as a free soluble molecule but the increased crowding of the bound state by macromolecules induces its aggregation at the nanoscale. To our knowledge, this is the first systematic study on the effect of osmolytes and crowders on a process of native-like aggregation involved in pathology, as it sheds light on the contribution of cosolutes to the onset of cancer as a protein misfolding disease and on the relevance of aggregation in the molecular etiology of cancer.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology and The Alexander Silberman Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel; The Fritz Haber Center, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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22
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Suda K, Suematsu A, Akiyama R. Lateral depletion effect on two-dimensional ordering of bacteriorhodopsins in a lipid bilayer: A theoretical study based on a binary hard-disk model. J Chem Phys 2021; 154:204904. [PMID: 34241177 DOI: 10.1063/5.0044399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 2D ordering of bacteriorhodopsins in a lipid bilayer was studied using a binary hard-disk model. The phase diagrams were calculated taking into account the lateral depletion effects. The critical concentrations of the protein ordering for monomers and trimers were obtained from the phase diagrams. The critical concentration ratio agreed well with the experiment when the repulsive core interaction between the depletants, namely, lipids, was taken into account. The results suggest that the depletion effect plays an important role in the association behaviors of transmembrane proteins.
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Affiliation(s)
- Keiju Suda
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ayumi Suematsu
- Faculty of Science and Engineering, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Ryo Akiyama
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
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23
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Song X, An L, Wang M, Chen J, Liu Z, Yao L. Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions. ACS Chem Biol 2021; 16:864-871. [PMID: 33843182 DOI: 10.1021/acschembio.1c00024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although numerous in vitro studies have shown that osmolytes are capable of stabilizing proteins, their effect on protein folding in vivo has been less understood. In this work, we investigated the effect of osmolytes, including glycerol, sorbitol, betaine, and taurine, on the folding of a protein GB3 variant in E. coli cells using NMR spectroscopy. 400 mM osmolytes were added to E. coli cells; only glycerol stabilizes the folded protein, whereas betaine and taurine considerably destabilize the protein through modulating folding and unfolding rates. Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges. The combination of the two factors causes destabilization of the protein in E. coli cells. These factors counteract the preferential exclusion mechanism that is adopted by osmolytes to stabilize proteins.
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Affiliation(s)
- Xiangfei Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengting Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhijun Liu
- National Facility for Protein Science, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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24
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Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
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Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
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25
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Schnatwinkel J, Herrmann C. The interaction strength of an intrinsically disordered protein domain with its binding partner is little affected by very different cosolutes. Phys Chem Chem Phys 2020; 22:27903-27911. [PMID: 33284914 DOI: 10.1039/d0cp03040f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A common feature of intrinsically disordered proteins (IDPs) is a disorder-to-order transition upon binding to other proteins, which has been tied to multiple benefits, including accelerated association rates or binding with low affinity, yet high specificity. Given the balanced equilibrium concentrations of folded and unfolded state of an IDP we asked the question if changes in the chemical environment, such as the presence of osmolytes or crowding agents, have a strong influence on the interaction of an IDP. Here, we demonstrate the impact of cosolutes on the interaction of the intrinsically disordered transcription factor c-Myb and its binding partner, the kinase-inducible interaction domain (KIX) of the CREB-binding protein. Temperature jump relaxation kinetics and microscale thermophoresis were employed in order to quantify the rate constants and the binding affinity of the c-Myb/KIX complex, respectively, in the presence of various cosolutes. We find the binding free energy of the c-Myb/KIX complex only marginally modulated by cosolutes, whereas the enthalpy and entropy of the interaction are very sensitive to the respective solvent conditions. For different cosolutes we observe substantial changes in enthalpy, both favorable and unfavorable, which are going with entropy changes largely compensating the enthalpy effects in each case. These characteristics might reflect a potential mechanism by which c-Myb offsets changes in the physico-chemical environment to maintain a roughly unaltered binding affinity.
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Affiliation(s)
- Jan Schnatwinkel
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
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26
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Ferreira C, Pinto MF, Macedo-Ribeiro S, Pereira PJB, Rocha FA, Martins PM. Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions. Phys Chem Chem Phys 2020; 22:16143-16149. [PMID: 32638771 DOI: 10.1039/d0cp02469d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When placed in the same environment, biochemically unrelated macromolecules influence each other's biological function through macromolecular crowding (MC) effects. This has been illustrated in vitro by the effects of inert polymers on protein stability, protein structure, enzyme kinetics and protein aggregation kinetics. While a unified way to quantitatively characterize MC is still lacking, we show that the crystal solubility of lysozyme can be used to predict the influence of crowding agents on the catalytic efficiency of this enzyme. In order to capture general enthalpic effects, as well as hard entropic effects that are specific of large molecules, we tested sucrose and its cross-linked polymer Ficoll-70 as additives. Despite the different conditions of pH and ionic strength adopted, both the crystallization and the enzymatic assays point to an entropic contribution of approximately -1 kcal mol-1 caused by MC. Our results demonstrate that the thermodynamic activity of proteins is markedly increased by the reduction of accessible volume caused by the presence of macromolecular cosolutes. Unlike what is observed in protein folding studies, this MC effect cannot be reproduced using equivalent concentrations of monomeric crowding units. Applicable to any crystallizable protein, the thermodynamic interpretation of MC based on crystal solubility is expected to help in elucidating the full extent and importance of hard-type interactions in the crowded environment of the cell.
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Affiliation(s)
- Cecília Ferreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria Filipa Pinto
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal and ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Fernando Alberto Rocha
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Pedro Miguel Martins
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal and IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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27
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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.
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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
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Olgenblum GI, Sapir L, Harries D. Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding. J Chem Theory Comput 2020; 16:1249-1262. [PMID: 31917927 PMCID: PMC7467637 DOI: 10.1021/acs.jctc.9b01071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Trehalose is a naturally occurring disaccharide known to remarkably stabilize biomacromolecules in the biologically active state. The stabilizing effect is typically observed over a large concentration range and affects many macromolecules including proteins, lipids, and DNA. Of special interest is the transition from aqueous solution to the dense and highly concentrated glassy state of trehalose that has been implicated in bioadaptation of different organisms toward desiccation stress. Although several mechanisms have been suggested to link the structure of the low water content glass with its action as an exceptional stabilizer, studies are ongoing to resolve which are most pertinent. Specifically, the role that hydrogen bonding plays in the formation of the glass is not well resolved. Here we model aqueous trehalose mixtures over a wide concentration range, using molecular dynamics simulations with two available force fields. Both force fields indicate glass transition temperatures and osmotic pressures that are close to experimental values, particularly at high trehalose contents. We develop and employ a methodology that allows us to analyze the thermodynamics of hydrogen bonds in simulations at different water contents and temperatures. Remarkably, this analysis is able to link the liquid to glass transition with changes in hydrogen bond characteristics. Most notably, the onset of the glassy state can be quantitatively related to the transition from weakly to strongly correlated hydrogen bonds. Our findings should help resolve the properties of the glass and the mechanisms of its formation in the presence of added macromolecules.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
| | - Liel Sapir
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
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29
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Pal S, Pyne P, Samanta N, Ebbinghaus S, Mitra RK. Thermal stability modulation of the native and chemically-unfolded state of bovine serum albumin by amino acids. Phys Chem Chem Phys 2020; 22:179-188. [DOI: 10.1039/c9cp04887a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cells are crowded with various cosolutes including salts, osmolytes, nucleic acids, peptides and proteins.
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Affiliation(s)
- Saikat Pal
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Partha Pyne
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Nirnay Samanta
- Institute for Physical and Theoretical Chemistry
- TU Braunschweig
- BRICS
- 56 D-38106 Braunschweig
- Germany
| | - Simon Ebbinghaus
- Institute for Physical and Theoretical Chemistry
- TU Braunschweig
- BRICS
- 56 D-38106 Braunschweig
- Germany
| | - Rajib Kumar Mitra
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
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30
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Puster LO, Stanley CB, Uversky VN, Curtis JE, Krueger S, Chu Y, Peterson CB. Characterization of an Extensive Interface on Vitronectin for Binding to Plasminogen Activator Inhibitor-1: Adoption of Structure in an Intrinsically Disordered Region. Biochemistry 2019; 58:5117-5134. [PMID: 31793295 DOI: 10.1021/acs.biochem.9b00605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Small-angle neutron scattering (SANS) measurements were pursued to study human vitronectin, a protein found in tissues and the circulation that regulates cell adhesion/migration and proteolytic cascades that govern hemostasis and pericellular proteolysis. Many of these functions occur via interactions with its binding partner, plasminogen activator inhibitor-1 (PAI-1), the chief inhibitor of proteases that lyse and activate plasminogen. We focused on a region of vitronectin that remains uncharacterized from previous X-ray scattering, nuclear magnetic resonance, and computational modeling approaches and which we propose is involved in binding to PAI-1. This region, which bridges the N-terminal somatomedin B (SMB) domain with a large central β-propeller domain of vitronectin, appears unstructured and has characteristics of an intrinsically disordered domain (IDD). The effect of osmolytes was evaluated using circular dichroism and SANS to explore the potential of the IDD to undergo a disorder-to-order transition. The results suggest that the IDD favors a more ordered structure under osmotic pressure; SANS shows a smaller radius of gyration (Rg) and a more compact fold of the IDD upon addition of osmolytes. To test whether PAI-1 binding is also coupled to folding within the IDD structure, a set of SANS experiments with contrast variation were performed on the complex of PAI-1 with a vitronectin fragment corresponding to the N-terminal 130 amino acids (denoted the SMB-IDD because it contains the SMB domain and IDD in linear sequence). Analysis of the SANS data using the Ensemble Optimization Method confirms that the SMB-IDD adopts a more compact configuration when bound to PAI-1. Calculated structures for the PAI-1:SMB-IDD complex suggest that the IDD provides an interaction surface outside of the primary PAI-1-binding site located within the SMB domain; this binding is proposed to lead to the assembly of higher-order structures of vitronectin and PAI-1 commonly found in tissues.
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Affiliation(s)
- Letitia O Puster
- Department of Biochemistry and Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - 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, Russian Academy of Sciences , Pushchino , Moscow region 142290 , Russia
| | - Joseph E Curtis
- National Institute of Standards and Technology Center for Neutron Research , Gaithersburg , Maryland 20899 , United States
| | - Susan Krueger
- National Institute of Standards and Technology Center for Neutron Research , Gaithersburg , Maryland 20899 , United States
| | - Yuzhuo Chu
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Cynthia B Peterson
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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31
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Das N, Sen P. Size-dependent macromolecular crowding effect on the thermodynamics of protein unfolding revealed at the single molecular level. Int J Biol Macromol 2019; 141:843-854. [DOI: 10.1016/j.ijbiomac.2019.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022]
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32
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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.
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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.
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33
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Cheng K, Wu Q, Jiang L, Liu M, Li C. Protein stability analysis in ionic liquids by 19F NMR. Anal Bioanal Chem 2019; 411:4929-4935. [DOI: 10.1007/s00216-019-01804-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/24/2019] [Accepted: 03/25/2019] [Indexed: 01/16/2023]
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34
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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
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35
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Das N, Sen P. Structural, Functional, and Dynamical Responses of a Protein in a Restricted Environment Imposed by Macromolecular Crowding. Biochemistry 2018; 57:6078-6089. [DOI: 10.1021/acs.biochem.8b00599] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
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36
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Romero-Fernández M, Moreno-Perez S, Martins de Oliveira S, Santamaría RI, Guisan JM, Rocha-Martin J. Preparation of a robust immobilized biocatalyst of β-1,4-endoxylanase by surface coating with polymers for production of xylooligosaccharides from different xylan sources. N Biotechnol 2018; 44:50-58. [DOI: 10.1016/j.nbt.2018.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023]
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37
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Ramirez R, Woodcock J, Kilbey SM. ARGET-ATRP synthesis and swelling response of compositionally varied poly(methacrylic acid-co-N,N-diethylaminoethyl methacrylate) polyampholyte brushes. SOFT MATTER 2018; 14:6290-6302. [PMID: 30014055 DOI: 10.1039/c8sm00882e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Modifying the composition of polyampholytes, which are comprised of charge-positive and charge-negative repeat units, directly contributes to trade-offs between charge and structure, which are externally regulated by solution pH and added salt. Here, the relative ratio of anionic and cationic comonomers is varied to tailor the stimuli-responsiveness of poly(methacrylic acid-co-N,N-diethylaminoethyl methacrylate) (P(MAA-co-DEAEMA)) brushes to changes in solution pH and an added zwitterion. These systems display a strong dependence on excess repeating units of either type and the random incorporation appears to facilitate self-neutralization of charges. Pseudo-living growth with smooth comonomer incorporation is achieved using activators regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP), creating well-defined brushes. In situ ellipsometry measurements of solvated brush thickness indicate that at low and high pH, the brushes display polyelectrolyte behavior with a strong compositional dependence, but at intermediate pH values, the brushes show the characteristic collapse attributed to self-neutralization of polyampholytes. The polyampholyte brushes maintain these patterns of behavior across all compositions and in the presence of an added zwitterion, which contributes additional hydrophobic character as evidenced by decreases in the swollen layer thicknesses. The response of the P(MAA-co-DEAEMA) brushes to the organic osmolyte betaine is consistent with its tendency to stabilize proteins and peptides in a kosmotropic fashion. These studies add perspective to efforts to manipulate sequence in polyampholytic polymers, support broader efforts to tailor interfacial soft films for applications in biotechnology and sensing, and understand aggregation and stability of biological polymers.
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Affiliation(s)
- Rachel Ramirez
- Department of Chemistry, University of Tennessee Knoxville, Tennessee 37996, USA.
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38
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Sukenik S, Salam M, Wang Y, Gruebele M. In-Cell Titration of Small Solutes Controls Protein Stability and Aggregation. J Am Chem Soc 2018; 140:10497-10503. [DOI: 10.1021/jacs.8b04809] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shahar Sukenik
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Mohammed Salam
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
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39
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Govrin R, Schlesinger I, Tcherner S, Sivan U. Regulation of Surface Charge by Biological Osmolytes. J Am Chem Soc 2017; 139:15013-15021. [DOI: 10.1021/jacs.7b07036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Roy Govrin
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Itai Schlesinger
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Shani Tcherner
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Uri Sivan
- Department of Physics and
the Russell Berrie Nanotechnology Institute, Technion−Israel Institute of Technology, Technion City, Haifa 3200003, Israel
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40
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Gorensek-Benitez AH, Smith AE, Stadmiller SS, Perez Goncalves GM, Pielak GJ. Cosolutes, Crowding, and Protein Folding Kinetics. J Phys Chem B 2017; 121:6527-6537. [PMID: 28605189 PMCID: PMC5982521 DOI: 10.1021/acs.jpcb.7b03786] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long accepted as the most important interaction, recent work shows that steric repulsions alone cannot explain the effects of macromolecular cosolutes on the equilibrium thermodynamics of protein stability. Instead, chemical interactions have been shown to modulate, and even dominate, crowding-induced steric repulsions. Here, we use 19F NMR to examine the effects of small and large cosolutes on the kinetics of protein folding and unfolding using the metastable 7 kDa N-terminal SH3 domain of the Drosophila signaling protein drk (SH3), which folds by a two-state mechanism. The small cosolutes consist of trimethylamine N-oxide and sucrose, which increase equilibrium protein stability, and urea, which destabilizes proteins. The macromolecules comprise the stabilizing sucrose polymer, Ficoll, and the destabilizing globular protein, lysozyme. We assessed the effects of these cosolutes on the differences in free energy between the folded state and the transition state and between the unfolded ensemble and the transition state. We then examined the temperature dependence to assess changes in activation enthalpy and entropy. The enthalpically mediated effects are more complicated than suggested by equilibrium measurements. We also observed enthalpic effects with the supposedly inert sucrose polymer, Ficoll, that arise from its macromolecular nature. Assessment of activation entropies shows important contributions from solvent and cosolute, in addition to the configurational entropy of the protein that, again, cannot be gleaned from equilibrium data. Comparing the effects of Ficoll to those of the more physiologically relevant cosolute lysozyme reveals that synthetic polymers are not appropriate models for understanding the kinetics of protein folding in cells.
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Affiliation(s)
| | - Austin E. Smith
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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41
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Smiatek J. Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:233001. [PMID: 28398214 DOI: 10.1088/1361-648x/aa6c9d] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.
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Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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42
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Sapir L, Harries D. Revisiting Hydrogen Bond Thermodynamics in Molecular Simulations. J Chem Theory Comput 2017; 13:2851-2857. [DOI: 10.1021/acs.jctc.7b00238] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and The Fritz Haber
Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber
Research Center, The Hebrew University, Jerusalem 91904, Israel
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43
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Abstract
The effects of small (∼102 Da) and larger (>103 Da) cosolutes on the equilibrium stability of monomeric globular proteins are broadly understood, excluding volume stabilizes proteins and chemical interactions are stabilizing when repulsive, but destabilizing when attractive. Proteins, however, rarely work alone. Here, we investigate the effects of small and large cosolutes on the equilibrium stability of the simplest defined protein-protein interactions, the side-by-side homodimer formed by the A34F variant of the 56-residue B1 domain of protein G. We used 19F nuclear magnetic resonance spectroscopy to quantify the effects of urea, trimethylamine oxide, Ficoll, and more physiologically relevant cosolutes on the dimer dissociation constant. The data reveal the same stabilizing and destabilizing influences from chemical interactions as observed in studies of protein stability. Results with more physiologically relevant molecules such as bovine serum albumin, lysozyme, and reconstituted Escherichia coli cytosol reflect the importance of chemical interactions between these cosolutes and the test protein. Our study serves as a stepping-stone to a more complete understanding of crowding effects on protein-protein interactions.
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Affiliation(s)
- Alex J. Guseman
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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44
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Mansouri AL, Grese LN, Rowe EL, Pino JC, Chennubhotla SC, Ramanathan A, O'Neill HM, Berthelier V, Stanley CB. Folding propensity of intrinsically disordered proteins by osmotic stress. MOLECULAR BIOSYSTEMS 2016; 12:3695-3701. [PMID: 27752679 PMCID: PMC5363718 DOI: 10.1039/c6mb00512h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain α-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. By focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.
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Affiliation(s)
- Amanda L Mansouri
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA
| | - Laura N Grese
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Erica L Rowe
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - James C Pino
- Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Ramanathan
- Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh M O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Valerie Berthelier
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA
| | - Christopher B Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme. Biochem J 2016; 473:3705-3724. [DOI: 10.1042/bcj20160604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
Osmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical denaturation of lysozyme in different solvent conditions to study the molecular mechanism by which two biologically relevant osmolytes, denaturing (urea) and stabilizing (betaine), affect the folding equilibrium. We found that urea interacts favorably with all types of residues via both hydrogen bonds and dispersion forces, and therefore accumulates in a diffuse solvation shell around the protein. This not only provides an enthalpic stabilization of the unfolded state, but also weakens the hydrophobic effect, as hydrophobic forces promote the association of urea with nonpolar residues, facilitating the unfolding. In contrast, we observed that betaine is excluded from the protein backbone and nonpolar side chains, but is accumulated near the basic residues, yielding a nonuniform distribution of betaine molecules at the protein surface. Spatially resolved solvent–protein interaction energies further suggested that betaine behaves in a ligand- rather than solvent-like manner and its exclusion from the protein surface arises mostly from the scarcity of favorable binding sites. Finally, we found that, in the presence of betaine, the reduced ability of water molecules to solvate the protein results in an additional enthalpic contribution to the betaine-induced stabilization.
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Gnutt D, Ebbinghaus S. The macromolecular crowding effect--from in vitro into the cell. Biol Chem 2016; 397:37-44. [PMID: 26351910 DOI: 10.1515/hsz-2015-0161] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/13/2015] [Indexed: 01/18/2023]
Abstract
The influence of the cellular milieu, a complex and crowded solvent, is often neglected when biomolecular structure and function are studied in vitro. To mimic the cellular environment, crowding effects are commonly induced in vitro using artificial crowding agents like Ficoll or dextran. However, it is unclear if such effects are also observed in cellulo. Diverging results on protein stability in living cells point out the need for new quantitative methods to investigate the contributions of excluded volume and nonspecific interactions to the cellular crowding effect. We show how new crowding sensitive probes may be utilized to directly investigate crowding effects in living cells. Moreover, we discuss processes where crowding effects could play a crucial role in molecular cell biology.
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Shkel IA, Knowles DB, Record MT. Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation. Biopolymers 2016; 103:517-27. [PMID: 25924886 DOI: 10.1002/bip.22662] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/24/2015] [Accepted: 04/24/2015] [Indexed: 01/11/2023]
Abstract
Small and large PEGs greatly increase chemical potentials of globular proteins (μ2), thereby favoring precipitation, crystallization, and protein-protein interactions that reduce water-accessible protein surface and/or protein-PEG excluded volume. To determine individual contributions of PEG-protein chemical and excluded volume interactions to μ2 as functions of PEG molality m3 , we analyze published chemical potential increments μ23 = dμ2/dm3 quantifying unfavorable interactions of PEG (PEG200-PEG6000) with BSA and lysozyme. For both proteins, μ23 increases approximately linearly with the number of PEG residues (N3). A 1 molal increase in concentration of PEG -CH2 OCH2 - groups, for any chain-length PEG, increases μBSA by ∼2.7 kcal/mol and μlysozyme by ∼1.0 kcal/mol. These values are similar to predicted chemical interactions of PEG -CH2 OCH2 - groups with these protein components (BSA ∼3.3 kcal/mol, lysozyme ∼0.7 kcal/mol), dominated by unfavorable interactions with amide and carboxylate oxygens and counterions. While these chemical effects should be dominant for small PEGs, larger PEGS are expected to exhibit unfavorable excluded volume interactions and reduced chemical interactions because of shielding of PEG residues in PEG flexible coils. We deduce that these excluded volume and chemical shielding contributions largely compensate, explaining why the dependence of μ23 on N3 is similar for both small and large PEGs.
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Affiliation(s)
- Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706.,Department of Chemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706
| | - D B Knowles
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706.,Department of Chemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706
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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]
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Senske M, Smith AE, Pielak GJ. Protein Stability in Reverse Micelles. Angew Chem Int Ed Engl 2016; 55:3586-9. [DOI: 10.1002/anie.201508981] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/14/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Austin E. Smith
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill NC 27599-3290 USA
| | - Gary J. Pielak
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill NC 27599-3290 USA
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