1
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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2
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Cubuk J, Soranno A. Macromolecular crowding and intrinsically disordered proteins: a polymer physics perspective. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Cubuk
- Washington University in St Louis Biochemistry and Molecular Biophysics UNITED STATES
| | - Andrea Soranno
- Washington University in St Louis Biochemistry and Molecular Biophysics 660 St Euclid Ave 63110 St Louis UNITED STATES
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3
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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: 4] [Impact Index Per Article: 2.0] [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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4
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Abstract
The interior of a cell is a highly packed environment that can be occupied up to 40% by different macromolecules. Such crowded media influence different biochemical processes like protein folding, enzymatic activity, and gene regulation. In this work, we use simulations to study protein stability under the presence of crowding agents that interact with the protein by excluded volume interactions. In general, the presence of crowding agents in the solution enhances the stability of the protein's native state. However, we find that the effects of excluded volume depend not only on crowding occupancy but also the crowders' geometry and size. Specifically, we find that polymeric crowders have stronger influence than spherical crowders and that this effect increases with polymer length, while it decreases with increasing size of spherical crowders. These opposing size effects are explained by the interplay of decreasing excluded volume and demixing, which together determine the change in the entropy of the crowders upon folding of the protein.
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Affiliation(s)
- David Gomez
- Max Planck Institute of Colloids and Interfaces , 14476 Potsdam , Germany
- School of Mechanical Engineering , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Klaus Huber
- Department of Chemistry , University of Paderborn , 33098 Paderborn , Germany
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces , 14476 Potsdam , Germany
- Institute for the Dynamics of Complex Systems , University of Göttingen , 37073 Göttingen , Germany
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5
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Abstract
Comprehensive data about the composition and structure of cellular components have enabled the construction of quantitative whole-cell models. While kinetic network-type models have been established, it is also becoming possible to build physical, molecular-level models of cellular environments. This review outlines challenges in constructing and simulating such models and discusses near- and long-term opportunities for developing physical whole-cell models that can connect molecular structure with biological function.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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6
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Hall D. On the nature of the optimal form of the holdase-type chaperone stress response. FEBS Lett 2019; 594:43-66. [PMID: 31432502 DOI: 10.1002/1873-3468.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 11/08/2022]
Abstract
The holdase paradigm of chaperone action involves preferential binding by the chaperone to the unfolded protein state, thereby preventing it from either, associating with other unstable proteins (to form large dysfunctional aggregates), or being degraded by the proteolytic machinery of the cell/organism. In this paper, we examine the necessary physical constraints imposed upon the holdase chaperone response in a cell-like environment and use these limitations to comment on the likely nature of the optimal form of chaperone response in vivo.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD, USA.,Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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7
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Ionic liquids and protein folding-old tricks for new solvents. Biophys Rev 2019; 11:209-225. [PMID: 30888574 DOI: 10.1007/s12551-019-00509-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/15/2019] [Indexed: 01/19/2023] Open
Abstract
One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. In this short note, we briefly outline the nature of the parameters associated with different empirical and model-based characterization procedures and point out factors which affect their interpretation when using a base solvent different from water. This review principally describes arguments developed by Wakayama et al., Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry, 2019, edited by Y. Kuroda and F. Arisaka; CMC Publishing House. Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.
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8
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Yildirim A, Brenner N, Sutherland R, Feig M. Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. BMC BIOPHYSICS 2018; 11:8. [PMID: 30555686 PMCID: PMC6286541 DOI: 10.1186/s13628-018-0048-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
Abstract
Background Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied extensively, very little is known how cellular crowding affects the conformational sampling of nucleic acids. Results The effect of protein crowding on the conformational preferences of DNA (deoxyribonucleic acid) is described from fully atomistic molecular dynamics simulations of systems containing a DNA dodecamer surrounded by protein crowders. From the simulations, it was found that DNA structures prefer to stay in B-like conformations in the presence of the crowders. The preference for B-like conformations results from non-specific interactions of crowder proteins with the DNA sugar-phosphate backbone. Moreover, the simulations suggest that the crowder interactions narrow the conformational sampling to canonical regions of the conformational space. Conclusions The overall conclusion is that crowding effects may stabilize the canonical features of DNA that are most important for biological function. The results are complementary to a previous study of DNA in reduced dielectric environments where reduced dielectric environments alone led to a conformational shift towards A-DNA. Such a shift was not observed here suggested that the reduced dielectric response of cellular environments is counteracted by non-specific interactions with protein crowders under in vivo conditions. Electronic supplementary material The online version of this article (10.1186/s13628-018-0048-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asli Yildirim
- 1Department of Chemistry, Michigan State University, East Lansing, MI 48824 USA
| | - Nathalie Brenner
- 2Faculty of Mathematics and Natural Sciences, University of Düsseldorf, 40225 Düsseldorf, Germany.,3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
| | - Robert Sutherland
- 3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
| | - Michael Feig
- 3Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, Room BCH 218, East Lansing, MI 48824 USA
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9
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Kumar R, Kumar R, Sharma D, Garg M, Kumar V, Agarwal MC. Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1102-1114. [DOI: 10.1016/j.bbapap.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022]
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10
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Molina JE, Vasquez-Echeverri A, Schwartz DC, Hernández-Ortiz JP. Discrete and Continuum Models for the Salt in Crowded Environments of Suspended Charged Particles. J Chem Theory Comput 2018; 14:4901-4913. [PMID: 30044624 DOI: 10.1021/acs.jctc.8b00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrostatic forces greatly affect the overall dynamics and diffusional activities of suspended charged particles in crowded environments. Accordingly, the concentration of counter- or co-ions in a fluid-''the salt"-determines the range, strength, and order of electrostatic interactions between particles. This environment fosters engineering routes for controlling directed assembly of particles at both the micro- and nanoscale. Here, we analyzed two computational modeling schemes that considered salt within suspensions of charged particles, or polyelectrolytes: discrete and continuum. Electrostatic interactions were included through a Green's function formalism, where the confined fundamental solution for Poisson's equation is resolved by the general geometry Ewald-like method. For the discrete model, the salt was considered as regularized point-charges with a specific valence and size, while concentration fields were defined for each ionic species for the continuum model. These considerations were evolved using Brownian dynamics of the suspended charged particles and the discrete salt ions, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the concentration fields. The salt/particle models were considered as suspensions under slit-confinement conditions for creating crowded "macro-ions", where density distributions and radial distribution functions were used to compare and differentiate computational models. Importantly, our analysis shows that disparate length scales or increased system size presented by the salt and suspended particles are best dealt with using concentration fields to model the ions. These findings were then validated by novel simulations of a semipermeable polyelectrolyte membrane, at the mesoscale, from which ionic channels emerged and enable ion conduction.
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Affiliation(s)
- Jarol E Molina
- Departamento de Materiales y Nanotecnología , Universidad Nacional de Colombia-Medellín , Medellín 050034 , Colombia
| | - Alejandro Vasquez-Echeverri
- Departamento de Materiales y Nanotecnología , Universidad Nacional de Colombia-Medellín , Medellín 050034 , Colombia
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States.,The Biotechnology Center , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Juan P Hernández-Ortiz
- Departamento de Materiales y Nanotecnología , Universidad Nacional de Colombia-Medellín , Medellín 050034 , Colombia.,The Biotechnology Center , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States.,Institute for Molecular Engineering , University of Chicago , Chicago , Illinois 60637 , United States
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11
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Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem 2018; 542:40-57. [DOI: 10.1016/j.ab.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
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12
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Jia J, Peng X, Qi W, Su R, He Z. Effects of macromolecular crowding on alkaline phosphatase unfolding, conformation and stability. Int J Biol Macromol 2017; 101:373-382. [PMID: 28344089 DOI: 10.1016/j.ijbiomac.2017.03.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/27/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
The interior of the cell is tightly packed with various biological macromolecules, which affects physiological processes, especially protein folding process. To explore how macromolecular crowding may influence protein folding process, alkaline phosphatase (ALP) was chosen as a model protein, and the unfolding process of ALP induced by GdnHCl was studied in the presence of crowding agents such as PEG 4000, Dextran 70 and Ficoll 70. The effect of macromolecular crowding on the denatured state of ALP was directly probed by measuring enzyme activities, fluorescence spectroscopy and circular dichroism. From the results of circular dichroism, GdnHCl induced a biphasic change, suggesting that a three-state unfolding mechanism was involved in the denaturation process irrespective of the absence or presence of crowding agents. It was also found that crowding agents had a little impact on the unfolding process of ALP. The results of phase diagrams also demonstrated that the unfolding process of ALP induced by GdnHCl was three-state mechanism. Moreover, the results of fluorescence spectra demonstrated that with the increase of GdnHCl concentration, the structure of protein had changed, but existence of crowding agents can make protein structure more stable. Our results can provide valuable information for understanding the protein folding in vivo.
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Affiliation(s)
- Jiajia Jia
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China.
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China
| | - Zhimin He
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China
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13
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Gtari W, Bey H, Aschi A, Bitri L, Othman T. Impact of macromolecular crowding on structure and properties of pepsin and trypsin. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 72:98-105. [DOI: 10.1016/j.msec.2016.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/24/2016] [Accepted: 11/13/2016] [Indexed: 11/25/2022]
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14
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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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15
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Yarawsky AE, English LR, Whitten ST, Herr AB. The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. J Mol Biol 2017; 429:261-279. [PMID: 27890783 PMCID: PMC5363081 DOI: 10.1016/j.jmb.2016.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022]
Abstract
Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a 135-aa-long, proline/glycine-rich region (PGR) that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the PGR using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide with unusually high polyproline type II helix propensity. In contrast to many intrinsically disordered polypeptides, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon the addition of the osmolyte trimethylamine N-oxide or the cosolvent 2,2,2-trifluoroethanol. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B Herr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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16
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Kadumuri RV, Gullipalli J, Subramanian S, Jaipuria G, Atreya HS, Vadrevu R. Crowding interactions perturb structure and stability by destabilizing the stable core of the α-subunit of tryptophan synthase. FEBS Lett 2016; 590:2096-105. [PMID: 27311646 DOI: 10.1002/1873-3468.12259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/06/2016] [Accepted: 06/13/2016] [Indexed: 11/12/2022]
Abstract
The consequences of crowding derived from relatively small and intrinsically disordered proteins are not clear yet. We report the effect of ficoll-70 on the structure and stability of native and partially folded states of the 29 kDa alpha subunit of tryptophan synthase (αTS). Overall, combining the changes in the circular dichroism and fluorescence spectra, in conjunction with the gradual loss of cooperativity under urea denaturation in the presence of increasing amounts of ficoll, it may be concluded that the crowding agent perturbs not only the native state but also the partially folded state of αTS. Importantly, NMR data indicate that ficoll interacts with the residues that constitute the stable core of the protein thus shedding light on the origin of the observed perturbation.
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Affiliation(s)
- Rajashekar Varma Kadumuri
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Jagadeesh Gullipalli
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - SriVidya Subramanian
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, India
| | | | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
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17
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Paul SS, Sil P, Chakraborty R, Haldar S, Chattopadhyay K. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c. Biochemistry 2016; 55:2332-43. [DOI: 10.1021/acs.biochem.6b00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simanta Sarani Paul
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Ritobrita Chakraborty
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Shubhasis Haldar
- Department
of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz
18, 82152 Martinsried, Germany
| | - Krishnananda Chattopadhyay
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
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18
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Stojanovski B, Breydo L, Uversky VN, Ferreira GC. Macromolecular crowders and osmolytes modulate the structural and catalytic properties of alkaline molten globular 5-aminolevulinate synthase. RSC Adv 2016. [DOI: 10.1039/c6ra22533k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Tertiary structure, solvation and kinetic properties of the catalytically active aminolevulinate synthase molten globule are modulated by crowders or osmolytes.
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Affiliation(s)
- Bosko M. Stojanovski
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Leonid Breydo
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Gloria C. Ferreira
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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19
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Sales AE, Breydo L, Porto TS, Porto ALF, Uversky VN. Hydrophobicity-dependent effects of polymers on different protein conformations. RSC Adv 2016. [DOI: 10.1039/c6ra07910e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polymers can either induce or disrupt secondary and tertiary structure in partially disordered protein conformations. The balance of the forces driving these structural changes depends on the polymer hydrophobicity and protein sequence and structure.
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Affiliation(s)
- Amanda E. Sales
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Leonid Breydo
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Tatiana S. Porto
- Academic Unit of Garanhuns
- Federal Rural University of Pernambuco
- Garanhuns
- Brazil
| | - Ana L. F. Porto
- Department of Morphology and Animal Physiology
- Federal Rural University of Pernambuco
- 52171-900 Recife
- Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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Spier MR, Behsnilian D, Zielinski A, Konietzny U, Greiner R. Studies Towards the Stabilisation of a Mushroom Phytase Produced by Submerged Cultivation. Protein J 2015; 34:367-79. [DOI: 10.1007/s10930-015-9631-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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21
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Zhu L, Pan W, Lu X, Li D, Zhao J, Liang D. The growth of filaments under macromolecular confinement using scaling theory. Chem Commun (Camb) 2015; 51:15928-31. [DOI: 10.1039/c5cc06748k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular confinement regulates the growth rate, structure, and length of the filaments, which can be quantitatively described using scaling theory.
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Affiliation(s)
- Lin Zhu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Wei Pan
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Xi Lu
- Beijing National Laboratory for Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P.R. China
| | - Desheng Li
- Beijing National Laboratory for Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P.R. China
| | - Jiang Zhao
- Beijing National Laboratory for Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P.R. China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
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22
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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23
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Denatured state structural property determines protein stabilization by macromolecular crowding: a thermodynamic and structural approach. PLoS One 2013; 8:e78936. [PMID: 24265729 PMCID: PMC3827121 DOI: 10.1371/journal.pone.0078936] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of protein structure and stability gained to date has been acquired through investigations made under dilute conditions where total macromolecular concentration never surpasses 10 g l−1. However, biological macromolecules are known to evolve and function under crowded intracellular environments that comprises of proteins, nucleic acids, ribosomes and carbohydrates etc. Crowded environment is known to result in altered biological properties including thermodynamic, structural and functional aspect of macromolecules as compared to the macromolecules present in our commonly used experimental dilute buffers (for example, Tris HCl or phosphate buffer). In this study, we have investigated the thermodynamic and structural consequences of synthetic crowding agent (Ficoll 70) on three different proteins (Ribonuclease-A, lysozyme and holo α-lactalbumin) at different pH values. We report here that the effect of crowding is protein dependent in terms of protein thermal stability and structure. We also observed that the structural characteristics of the denatured state determines if crowding will have an effect or not on the protein stability.
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24
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Fan YQ, Lee J, Oh S, Liu HJ, Li C, Luan YS, Yang JM, Zhou HM, Lü ZR, Wang YL. Effects of osmolytes on human brain-type creatine kinase folding in dilute solutions and crowding systems. Int J Biol Macromol 2012; 51:845-58. [DOI: 10.1016/j.ijbiomac.2012.07.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 01/06/2023]
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25
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Zhang DL, Wu LJ, Chen J, Liang Y. Effects of macromolecular crowding on the structural stability of human α-lactalbumin. Acta Biochim Biophys Sin (Shanghai) 2012; 44:703-11. [PMID: 22735492 DOI: 10.1093/abbs/gms052] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The folding of protein, an important process for protein to fulfill normal functions, takes place in crowded physiological environments. α-Lactalbumin, as a model system for protein-folding studies, has been used extensively because it can form stable molten globule states under a range of conditions. Here we report that the crowding agents Ficoll 70, dextran 70, and polyethylene glycol (PEG) 2000 have different effects on the structural stability of human α-lactalbumin (HLA) represented by the transition to a molten globule state: dextran 70 dramatically enhances the thermal stability of Ca(2+)-depleted HLA (apo-HLA) and Ficoll 70 enhances the thermal stability of apo-HLA to some extent, while PEG 2000 significantly decreases the thermal stability of apo-HLA. Ficoll 70 and dextran 70 have no obvious effects on trypsin degradation of apo-HLA but PEG 2000 accelerates apo-HLA degradation by trypsin and destabilizes the native conformation of apo-HLA. Furthermore, no interaction is observed between apo-HLA and Ficoll 70 or dextran 70, but a weak, non-specific interaction between the apo form of the protein and PEG 2000 is detected, and such a weak, non-specific interaction could overcome the excluded-volume effect of PEG 2000. Our data are consistent with the results of protein stability studies in cells and suggest that stabilizing excluded-volume effects of crowding agents can be ameliorated by non-specific interactions between proteins and crowders.
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Affiliation(s)
- De-Lin Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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26
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Kudlay A, Cheung MS, Thirumalai D. Influence of the shape of crowding particles on the structural transitions in a polymer. J Phys Chem B 2012; 116:8513-22. [PMID: 22616622 DOI: 10.1021/jp212535n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the structural transitions in a polymer induced by spherical and nonspherical crowding particles over a wide range of conditions. The polymer conformations are specified by the radius of gyration and the quality of the solvent in the absence of crowding particles. In the presence of crowding particles, the structures are altered by the volume fraction, size, shape, and polydispersity of the crowders. We show that crowding induces an array of structural changes, ranging from helix, helical hairpin (HH), and multiple helix bundles (HBs), depending on the interplay of multiple length and energy scales including the solvent quality, length of the polymer, temperature, and the characteristics of the crowding agents. In nearly good solvents, the polymer undergoes coil-helix transition in accord with the predictions based on the entropic stabilization mechanism. Higher-order (HH and HB) structures are obtained in poor or moderately poor solvents. In a binary mixture of spherical crowders, the effect of the two components is largely additive with the polymer undergoing greater compaction at higher volume fraction. In contrast to spherical crowders, spherocylinder-like crowders have a dramatically different effect on the diagram of states of the polymer. In the presence of spherocylinders, the polymer prefers to form a nearly ideal helix, especially at low temperatures and high aspect ratios of the crowders, at volume fractions that are not large enough for nematic order. Surprisingly, there is a complete absence of HH and HB in the range of conditions explored here. The dominant formation of spherocylinder-induced helix formation is due to the tendency of the spherocylinders and the polymer to align along the director formed by an increase in nematic order only in the vicinity of the polymer. Our study, which has produced several testable predictions, shows that only by probing the effects of crowding on a polymer (or a protein and RNA) over a wide range of conditions can the diagram of states be quantitatively described.
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Affiliation(s)
- Alexander Kudlay
- Biophysics Program, Institute for Physical Sciences and Technology, University of Houston, Houston, Texas 77204, United States
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27
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Samiotakis A, Cheung MS. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. J Chem Phys 2012; 135:175101. [PMID: 22070323 DOI: 10.1063/1.3656691] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.
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28
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Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments. PLoS One 2012; 7:e30131. [PMID: 22272286 PMCID: PMC3260218 DOI: 10.1371/journal.pone.0030131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/14/2011] [Indexed: 01/01/2023] Open
Abstract
Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined.
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29
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Gilman-Politi R, Harries D. Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes. J Chem Theory Comput 2011; 7:3816-28. [PMID: 26598272 DOI: 10.1021/ct200455n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many polyols and carbohydrates serve in different organisms as protective osmolytes that help to stabilize proteins in their native, functional state, even under a variety of environmental stresses. However, despite their important role, much of the molecular mechanism by which these osmolytes exert their action remains elusive. We have recently shown experimentally that, although polyols and carbohydrates are excluded from protein and peptide interfaces, as also expected for the known entropic "crowding" mechanism, the osmolyte folding action can in fact primarily be enthalpic in nature. To follow this newly resolved enthalpically driven stabilization mechanism, we report here on molecular dynamics simulations of a model peptide that can fold in solution into a β-hairpin. In agreement with experiments, our simulations indicate that sorbitol, a representative polyol, promotes peptide folding by preferential exclusion. At the molecular level, simulations further show that peptide stabilization can be explained by sorbitol's perturbation of the solution hydrogen bonding network in the peptide first hydration shells. Consequently, fewer hydrogen bonds between peptide and solvating water are lost upon folding, and additional internal peptide hydrogen bonds are formed in the presence of sorbitol, while internal peptide and water-associated hydrogen bonds are strengthened, resulting in stabilization of the peptide folded state. We further find that changes in water orientational entropy are reduced upon folding in sorbitol solution, reflecting the struggle of water molecules to maintain optimal hydrogen bonding in the presence of competing polyols. By providing first molecular underpinnings for enthalpically driven osmolyte stabilization of peptides and proteins, this mechanism should allow a better understanding of the variety of physical forces by which protective osmolytes act in biologically realistic solutions.
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Affiliation(s)
- Regina Gilman-Politi
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
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30
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Interactions of formulation excipients with proteins in solution and in the dried state. Adv Drug Deliv Rev 2011; 63:1053-73. [PMID: 21756953 DOI: 10.1016/j.addr.2011.06.011] [Citation(s) in RCA: 257] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/18/2011] [Accepted: 06/23/2011] [Indexed: 12/12/2022]
Abstract
A variety of excipients are used to stabilize proteins, suppress protein aggregation, reduce surface adsorption, or to simply provide physiological osmolality. The stabilizers encompass a wide variety of molecules including sugars, salts, polymers, surfactants, and amino acids, in particular arginine. The effects of these excipients on protein stability in solution are mainly caused by their interaction with the protein and the container surface, and most importantly with water. Some excipients stabilize proteins in solution by direct binding, while others use a number of fundamentally different mechanisms that involve indirect interactions. In the dry state, any effects that the excipients confer to proteins through their interactions with water are irrelevant, as water is no longer present. Rather, the excipients stabilize proteins through direct binding and their effects on the physical properties of the dried powder. This review will describe a number of mechanisms by which the excipients interact with proteins in solution and with various interfaces, and their effects on the physical properties of the dried protein structure, and explain how the various interaction forces are related to their observed effects on protein stability.
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31
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Szasz CS, Alexa A, Toth K, Rakacs M, Langowski J, Tompa P. Protein disorder prevails under crowded conditions. Biochemistry 2011; 50:5834-44. [PMID: 21634433 DOI: 10.1021/bi200365j] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crowding caused by the high concentrations of macromolecules in the living cell changes chemical equilibria, thus promoting aggregation and folding reactions of proteins. The possible magnitude of this effect is particularly important with respect to the physiological structure of intrinsically disordered proteins (IDPs), which are devoid of well-defined three-dimensional structures in vitro. To probe this effect, we have studied the structural state of three IDPs, α-casein, MAP2c, and p21(Cip1), in the presence of the crowding agents Dextran and Ficoll 70 at concentrations up to 40%, and also the small-molecule osmolyte, trimethylamine N-oxide (TMAO), at concentrations up to 3.6 M. The structures of IDPs under highly diluted and crowded conditions were compared by a variety of techniques, fluorescence spectroscopy, acrylamide quenching, 1-anilino-8-naphthalenesulfonic acid (ANS) binding, fluorescence correlation spectroscopy (FCS), and far-UV and near-UV circular dichroism (CD) spectroscopy, which allow us to visualize various levels of structural organization within these proteins. We observed that crowding causes limited structural changes, which seem to reflect the functional requirements of these IDPs. α-Casein, a protein of nutrient function in milk, changes least under crowded conditions. On the other hand, MAP2c and, to a lesser degree, p21(Cip1), which carry out their functions by partner binding and accompanying partially induced folding, show signs of local structuring and also some global compaction upon crowded conditions, in particular in the presence of TMAO. The observations are compatible with the possible preformation of binding-competent conformations in these proteins. The magnitude of these changes, however, is far from that of the cooperative folding transitions elicited by crowding in denatured globular proteins; i.e., these IDPs do remain in a state of rapidly interconverting structural ensemble. Altogether, our results underline that structural disorder is the physiological state of these proteins.
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Affiliation(s)
- C S Szasz
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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32
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Rosen J, Kim YC, Mittal J. Modest Protein−Crowder Attractive Interactions Can Counteract Enhancement of Protein Association by Intermolecular Excluded Volume Interactions. J Phys Chem B 2011; 115:2683-9. [DOI: 10.1021/jp200625k] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonathan Rosen
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Young C. Kim
- Center for Computational Materials Science, Naval Research Laboratory, Washington, DC 20375, United States
| | - Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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33
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Kim YC, Best RB, Mittal J. Macromolecular crowding effects on protein–protein binding affinity and specificity. J Chem Phys 2010; 133:205101. [DOI: 10.1063/1.3516589] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Hong J, Gierasch LM. Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state. J Am Chem Soc 2010; 132:10445-52. [PMID: 20662522 DOI: 10.1021/ja103166y] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interior of cells is highly crowded with macromolecules, which impacts all physiological processes. To explore how macromolecular crowding may influence cellular protein folding, we interrogated the folding landscape of a model beta-rich protein, cellular retinoic acid-binding protein I (CRABP I), in the presence of an inert crowding agent (Ficoll 70). Urea titrations revealed a crowding-induced change in the water-accessible polar amide surface of its denatured state, based on an observed ca. 15% decrease in the change in unfolding free energy with respect to urea concentration (the m-value), and the effect of crowding on the equilibrium stability of CRABP I was less than our experimental error (i.e., < or = 1.2 kcal/mol). Consequently, we directly probed the effect of crowding on the denatured state of CRABP I by measuring side-chain accessibility using iodide quenching of tryptophan fluorescence and chemical modification of cysteines. We observed that the urea-denatured state is more compact under crowded conditions, and the observed extent of reduction of the m-value by crowding agent is fully consistent with the extent of reduction of the accessibility of the Trp and Cys probes, suggesting a random and nonspecific compaction of the unfolded state. The thermodynamic consequences of crowding-induced compaction are discussed. In addition, over a wide range of Ficoll concentration, crowding significantly retarded the unfolding kinetics of CRABP I without influencing the urea dependence of the unfolding rate, arguing for no appreciable change in the nature of the transition state. Our results demonstrate how macromolecular crowding may influence protein folding by effects on both the unfolded state ensemble and unfolding kinetics.
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Affiliation(s)
- Jiang Hong
- Department of Biochemistry & Molecular Biology, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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35
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Le Coeur C, Teixeira J, Busch P, Longeville S. Compression of random coils due to macromolecular crowding: scaling effects. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061914. [PMID: 20866447 DOI: 10.1103/physreve.81.061914] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 05/05/2010] [Indexed: 05/29/2023]
Abstract
The addition of a macromolecular crowding agent to a dilute solution of polymer exerts a compressive force that tends to reduce the size of the chain. We study here the effect of changing the size ratio between the random coil and the crowding agent. The compression occurs at lower crowding agent concentration, Φ when polymer molecular weight increases. The Flory exponent ν(Φ) decreases from ν(0)≃0.48 in water down to 0.3 with macromolecular crowding. The effective polymer-polymer interactions change from repulsive to strongly attractive inducing aggregation of the chains. This effect changes drastically for larger polymer sizes, being much more pronounced at high molecular weights.
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Affiliation(s)
- C Le Coeur
- Laboratoire Léon Brillouin, CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France
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36
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Domach MM, Walker LM. Stabilizing Biomacromolecules in Nontoxic Nano-Structured Materials. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.jala.2010.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Increases in the use of protein-based pharmaceuticals require the development of cost-effective methods of storage and transport of sensitive biomolecules. In this article, we review the general problems of protein stabilization, aspects specific to antibodies, and a proposed method for protecting proteins based on nanostructured hydrogels. This review is not intended to be comprehensive, but instead to provide the reader with specific examples that capture some of the key challenges and opportunities of the field.
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Affiliation(s)
- Michael M. Domach
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA
| | - Lynn M. Walker
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA
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37
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Lee B, LeDuc PR, Schwartz R. Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:041918. [PMID: 19905353 PMCID: PMC2879169 DOI: 10.1103/physreve.80.041918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/07/2009] [Indexed: 05/28/2023]
Abstract
The intracellular environment imposes a variety of constraints on biochemical reaction systems that can substantially change reaction rates and equilibria relative to an ideal solution-based environment. One of the most notable features of the intracellular environment is its dense macromolecular crowding, which, among many other effects, tends to strongly enhance binding and assembly reactions. Despite extensive study of biochemistry in crowded media, it remains extremely difficult to predict how crowding will quantitatively affect any given reaction system due to the dependence of the crowding effect on numerous assumptions about the reactants and crowding agents involved. We previously developed a two dimensional stochastic off-lattice model of binding reactions based on the Green's function reaction dynamics method in order to create a versatile simulation environment in which one can explore interactions among many parameters of a crowded assembly system. In the present work, we examine interactions among several critical parameters for a model dimerization system: the total concentration of reactants and inert particles, the binding probability upon a collision between two reactant monomers, the mean time of dissociation reactions, and the diffusion coefficient of the system. Applying regression models to equilibrium constants across parameter ranges shows that the effect of the total concentration is approximately captured by a low-order nonlinear polynomial model, while the other three parameter effects are each accurately captured by a linear model. Furthermore, validation on tests with multi-parameter variations reveals that the effects of these parameters are separable from one another over a broad range of variation in all four parameters. The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved.
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Affiliation(s)
- Byoungkoo Lee
- 654 Mellon Institute, Carnegie Mellon/University of Pittsburgh Joint Program in Computational Biology, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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38
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Hazy E, Tompa P. Limitations of Induced Folding in Molecular Recognition by Intrinsically Disordered Proteins. Chemphyschem 2009; 10:1415-9. [DOI: 10.1002/cphc.200900205] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Le Coeur C, Demé B, Longeville S. Compression of random coils due to macromolecular crowding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:031910. [PMID: 19391974 DOI: 10.1103/physreve.79.031910] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Indexed: 05/27/2023]
Abstract
The conformation of a linear polymer chain is studied as a function of the concentration of a macromolecular crowding agent by neutron scattering. Excluded volume to random coil due to macromolecular crowding in cells is predicted to exert a compressive force that will tend to reduce its size. It is shown that when reducing free volume due to macromolecular crowding, we observe a compression of the polymer chain with a reduction in its radius of gyration of up to approximately 30% and that the effective chain-chain interactions are strongly modified.
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Affiliation(s)
- C Le Coeur
- Laboratoire Léon Brillouin, CEA-CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France
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40
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Engel R, Westphal AH, Huberts DH, Nabuurs SM, Lindhoud S, Visser AJ, van Mierlo CP. Macromolecular Crowding Compacts Unfolded Apoflavodoxin and Causes Severe Aggregation of the Off-pathway Intermediate during Apoflavodoxin Folding. J Biol Chem 2008; 283:27383-27394. [DOI: 10.1074/jbc.m802393200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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41
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Zhou HX, Rivas G, Minton AP. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 2008; 37:375-97. [PMID: 18573087 DOI: 10.1146/annurev.biophys.37.032807.125817] [Citation(s) in RCA: 1531] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion, are discussed. Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
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Free energy of sickle hemoglobin polymerization: a scaled-particle treatment for use with dextran as a crowding agent. Biophys J 2008; 94:3629-34. [PMID: 18212015 DOI: 10.1529/biophysj.107.117465] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fundamental to the analysis of protein polymerization is the free energy of association, typically determined from solubility. It has been previously shown that concentrated 70 kDa dextran lowers the solubility of sickle hemoglobin, due to molecular crowding, and provides a useful ranking tool for the effects of inhibitors and molecular modifications. Because hemoglobin occupies a substantial volume as well, crowding effects of both hemoglobin and dextran contribute to the nonideality of the solution. We show how scaled-particle theory can be used to account for both types of crowding, thus allowing the determination of solubility in the absence of dextran, given data measured in its presence. The approach adopted approximates dextran as a sphere with a volume that decreases as the concentration of dextran increases. We use an asymptotic relation to describe the volume, which decreases nearly linearly by a factor of two over the range studied, from 60 to 230 mg/ml. This compression is similar to previously observed compression of sephadex beads and ficoll solutions. In the limit of low hemoglobin concentrations, the theory reduces to the previously-used approach of Ogston. Our method therefore provides a means of measuring the free energy of association of molecules that occupy significant volume fractions, even when assisted by the crowding of dextran and we present a tabulation of all known free energies of polymerization of sickle hemoglobin measured in the presence of dextran.
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Zhou BR, Zhou Z, Hu QL, Chen J, Liang Y. Mixed macromolecular crowding inhibits amyloid formation of hen egg white lysozyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:472-80. [PMID: 18252208 DOI: 10.1016/j.bbapap.2008.01.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 12/20/2007] [Accepted: 01/08/2008] [Indexed: 11/17/2022]
Abstract
The effects of two single macromolecular crowding agents, Ficoll 70 and bovine serum albumin (BSA), and one mixed macromolecular crowding agent containing both BSA and Ficoll 70, on amyloid formation of hen egg white lysozyme have been examined by thioflavin T binding, Congo red binding, transmission electron microscopy, and activity assay, as a function of crowder concentration and composition. Both the mixed crowding agent and the protein crowding agent BSA at 100 g/l almost completely inhibit amyloid formation of lysozyme and stabilize lysozyme activity on the investigated time scale, but Ficoll 70 at the same concentration neither impedes amyloid formation of lysozyme effectively nor stabilizes lysozyme activity. Further kinetic and isothermal titration calorimetry analyses indicate that a mixture of 5 g/l BSA and 95 g/l Ficoll 70 inhibits amyloid formation of lysozyme and maintains lysozyme activity via mixed macromolecular crowding as well as weak, nonspecific interactions between BSA and nonnative lysozyme. Our data demonstrate that BSA and Ficoll 70 cooperatively contribute to both the inhibitory effect and the stabilization effect of the mixed crowding agent, suggesting that mixed macromolecular crowding inside the cell may play a role in posttranslational quality control mechanism.
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Affiliation(s)
- Bing-Rui Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Chen Y, Ding F, Nie H, Serohijos AW, Sharma S, Wilcox KC, Yin S, Dokholyan NV. Protein folding: then and now. Arch Biochem Biophys 2008; 469:4-19. [PMID: 17585870 PMCID: PMC2173875 DOI: 10.1016/j.abb.2007.05.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/11/2007] [Accepted: 05/21/2007] [Indexed: 01/19/2023]
Abstract
Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Nikolay V. Dokholyan
- † To whom correspondence should be addressed: Nikolay V. Dokholyan, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599. Fax: 919-966-2852.
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Zhou HX. Protein folding in confined and crowded environments. Arch Biochem Biophys 2007; 469:76-82. [PMID: 17719556 PMCID: PMC2223181 DOI: 10.1016/j.abb.2007.07.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/12/2007] [Accepted: 07/12/2007] [Indexed: 11/17/2022]
Abstract
Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k(B)T but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.
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Ohashi T, Galiacy SD, Briscoe G, Erickson HP. An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins. Protein Sci 2007; 16:1429-38. [PMID: 17586775 PMCID: PMC2206698 DOI: 10.1110/ps.072845607] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We have experimentally studied the fluorescence resonance energy transfer (FRET) between green fluorescent protein (GFP) molecules by inserting folded or intrinsically unstructured proteins between CyPet and Ypet. We discovered that most of the enhanced FRET signal previously reported for this pair was due to enhanced dimerization, so we engineered a monomerizing mutation into each. An insert containing a single fibronectin type III domain (3.7 nm end-to-end) gave a moderate FRET signal while a two-domain insert (7.0 nm) gave no FRET. We then tested unstructured proteins of various lengths, including the charged-plus-PQ domain of ZipA, the tail domain of alpha-adducin, and the C-terminal tail domain of FtsZ. The structures of these FRET constructs were also studied by electron microscopy and sedimentation. A 12 amino acid linker and the N-terminal 33 amino acids of the charged domain of the ZipA gave strong FRET signals. The C-terminal 33 amino acids of the PQ domain of the ZipA and several unstructured proteins with 66-68 amino acids gave moderate FRET signals. The 150 amino acid charged-plus-PQ construct gave a barely detectable FRET signal. FRET efficiency was calculated from the decreased donor emission to estimate the distance between donor and acceptor. The donor-acceptor distance varied for unstructured inserts of the same length, suggesting that they had variable stiffness (persistence length). We conclude that GFP-based FRET can be useful for studying intrinsically unstructured proteins, and we present a range of calibrated protein inserts to experimentally determine the distances that can be studied.
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Affiliation(s)
- Tomoo Ohashi
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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