1
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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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2
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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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3
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Fossum CJ, Johnson BOV, Golde ST, Kielman AJ, Finke B, Smith MA, Lowater HR, Laatsch BF, Bhattacharyya S, Hati S. Insights into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study. ACS OMEGA 2023; 8:44820-44830. [PMID: 38046287 PMCID: PMC10688029 DOI: 10.1021/acsomega.3c06006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Intrinsic tryptophan fluorescence spectroscopy is an important tool for examining the effects of molecular crowding and confinement on the structure, dynamics, and function of proteins. Synthetic crowders such as dextran, ficoll, polyethylene glycols, polyvinylpyrrolidone, and their respective monomers are used to mimic crowded intracellular environments. Interactions of these synthetic crowders with tryptophan and the subsequent impact on its fluorescence properties are therefore critically important for understanding the possible interference created by these crowders. In the present study, the effects of polymer and monomer crowders on tryptophan fluorescence were assessed by using experimental and computational approaches. The results of this study demonstrated that both polymer and monomer crowders have an impact on the tryptophan fluorescence intensity; however, the molecular mechanisms of quenching were different. Using Stern-Volmer plots and a temperature variation study, a physical basis for the quenching mechanism of commonly used synthetic crowders was established. The quenching of free tryptophan was found to involve static, dynamic, and sphere-of-action mechanisms. In parallel, computational studies employing Kohn-Sham density functional theory provided a deeper insight into the effects of intermolecular interactions and solvation, resulting in differing quenching modes for these crowders. Taken together, the study offers new physical insights into the quenching mechanisms of some commonly used monomer and polymer synthetic crowders.
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Affiliation(s)
| | - Benjamin O. V. Johnson
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Spencer T. Golde
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Alexis J. Kielman
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Brianna Finke
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Macey A. Smith
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Harrison R. Lowater
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Bethany F. Laatsch
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
| | - Sanchita Hati
- Department of Chemistry and
Biochemistry, University of Wisconsin-Eau
Claire, Eau Claire, Wisconsin 54701, United States
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4
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Garnica-Galvez S, Skoufos I, Tzora A, Diakakis N, Prassinos N, Zeugolis DI. Macromolecular crowding in equine bone marrow mesenchymal stromal cell cultures using single and double hyaluronic acid macromolecules. Acta Biomater 2023; 170:111-123. [PMID: 37634833 DOI: 10.1016/j.actbio.2023.08.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023]
Abstract
Macromolecular crowding (MMC) enhances and accelerates extracellular matrix (ECM) deposition in eukaryotic cell culture. Single hyaluronic acid (HA) molecules have not induced a notable increase in the amount and rate of deposited ECM. Thus, herein we assessed the physicochemical properties and biological consequences in equine bone marrow mesenchymal stromal cell cultures of single and mixed HA molecules and correlated them to the most widely used MMC agents, the FicollⓇ cocktail (FC) and carrageenan (CR). Dynamic light scattering analysis revealed that all HA cocktails had significantly higher hydrodynamic radius than the FC and CR; the FC and the 0.5 mg/ml 100 kDa and 500 kDa single HA molecules had the highest charge; and, in general, all molecules had high polydispersity index. Biological analyses revealed that none of the MMC agents affected cell morphology and basic cell functions; in general, CR outperformed all other macromolecules in collagen type I and V deposition; FC, the individual HA molecules and the HA cocktails outperformed CR in collagen type III deposition; FC outperformed CR and the individual HA molecules and the HA cocktails outperformed their constituent HA molecules in collagen type IV deposition; FC and certain HA cocktails outperformed CR and constituent HA molecules in collagen type VI deposition; and all individual HA molecules outperformed FC and CR and the HA cocktails outperformed their constituent HA molecules in laminin deposition. With respect to tri-lineage analysis, CR and HA enhanced chondrogenesis and osteogenesis, whilst FC enhanced adipogenesis. This work opens new avenues in mixed MMC in eukaryotic cell culture. STATEMENT OF SIGNIFICANCE: Mixed macromolecular crowding (MMC) in eukaryotic cell culture is still under-investigated. Herein, single and double hyaluronic acid (HA) macromolecules, along with the traditional MMC agents FicollⓇ cocktail (FC) and carrageenan (CR), were used as MMC agents in equine mesenchymal stromal cell cultures. Biological analysis showed that none of the MMC agents affected cell morphology and basic cell functions. Protein deposition analysis made apparent that CR outperformed all other macromolecules in collagen type I and collagen type V deposition, whilst FC, the individual HA macromolecules and the HA cocktails outperformed CR in collagen type III deposition. Tri-lineage analysis revealed that CR and HA enhanced chondrogenesis and osteogenesis, whilst FC enhanced adipogenesis. These data illustrate that MMC agents are not inert macromolecules.
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Affiliation(s)
- Sergio Garnica-Galvez
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece; School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland.
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5
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Connecting the Dots: Macromolecular Crowding and Protein Aggregation. J Fluoresc 2023; 33:1-11. [PMID: 36417150 DOI: 10.1007/s10895-022-03082-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
Proteins are one of the dynamic macromolecules that play a significant role in many physiologically important processes to sustain life on the earth. Proteins need to be properly folded into their active conformation to perform their function. Alteration in the protein folding process may lead to the formation of misfolded conformers. Accumulation of these misfolded conformers can result in the formation of protein aggregates which are attributed to many human pathological conditions including neurodegeneration, cataract, neuromuscular disorders, and diabetes. Living cells naturally have heterogeneous crowding environments with different concentrations of various biomolecules. Macromolecular crowding condition has been found to alter the protein conformation. Here in this review, we tried to show the relation between macromolecular crowding, protein aggregation, and its consequences.
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6
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Raina N, Hassan MI, Ahmad F, Islam A, Singh AK. PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect. J Biomol Struct Dyn 2022; 40:13265-13277. [PMID: 34726117 DOI: 10.1080/07391102.2021.1987990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of Tm (midpoint of denaturation) and ΔGD0 (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
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7
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Bai Q, Chen X, Chen J, Liu Z, Lin YN, Yang S, Liang D. Morphology and Dynamics of Coexisting Phases in Coacervate Solely Controlled by Crowded Environment. ACS Macro Lett 2022; 11:1107-1111. [PMID: 36006377 DOI: 10.1021/acsmacrolett.2c00409] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The membraneless organelles (MLOs) play a key role in the cell, yet it is unclear what controls the morphology and dynamics of MLOs in crowded cell medium. Using a biphasic coacervate droplet as a model of MLO, we online monitored the liquid-liquid phase separation process in crowded medium provided by poly(ethylene oxide) (PEO) or dextran. In PEO solution, which has an affinity with the inner phase, the spherical droplets evolve into clusters, networks, and completely phase inverted spheres in sequence with increasing PEO concentration, while in dextran solution, which has an affinity with the outer phase, the coacervates maintain the morphology but vary in phase ratio. Flower-like and even Janus structures are formed in the mixed PEO/dextran medium. Our work demonstrates that MLOs could be controlled solely by the crowded cell medium.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ya-Nan Lin
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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8
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Parray ZA, Ahmad F, Chaudhary AA, Rudayni HA, Al-Zharani M, Hassan MI, Islam A. Size-Dependent Interplay of Volume Exclusion Versus Soft Interactions: Cytochrome c in Macromolecular Crowded Environment. Front Mol Biosci 2022; 9:849683. [PMID: 35693552 PMCID: PMC9174945 DOI: 10.3389/fmolb.2022.849683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Even though there are a great number of possible conformational states, how a protein generated as a linear unfolded polypeptide efficiently folds into its physiologically active form remained a fascinating and unanswered enigma inside crowded conditions of cells. In this study, various spectroscopic techniques have been exploited to know and understand the effect and mechanism of action of two different sizes of polyethylene glycols, or PEGs (molecular mass ∼10 and ∼20 kilo Daltons, kDa), on cytochrome c (cyt c). The outcomes showed that small size of the PEG leads to perturbation of the protein structure, and conversely, large size of the PEG has stabilizing effect on cyt c. Moreover, binding measurements showed that small size of PEG interacts strongly via soft interactions compared to the larger size of PEG, the latter being governed more by excluded volume effect or preferential exclusion from the protein. Overall, this finding suggests that conformations of protein may be influenced in cellular crowded conditions via interactions which depend upon the size of molecule in the environment. This study proposes that both volume exclusion and soft (chemical) interactions governs the protein’s conformation and functional activities. The cellular environment’s internal architecture as evident from crowder size and shape in this study has a significant role.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Hassan Ahmad Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Asimul Islam,
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9
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Gupta M, Chowdhury PK. Protein dynamics as a sensor for macromolecular crowding: Insights into mixed crowding. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Parray ZA, Naqvi AAT, Ahmad F, Hassan MI, Islam A. Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Siddiqui GA, Naeem A. Refolding of Hemoglobin Under Macromolecular Confinement: Impersonating In Vivo Volume Exclusion. J Fluoresc 2021; 31:1371-1377. [PMID: 34156613 DOI: 10.1007/s10895-021-02751-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of macromolecular crowding and confinement on nature and interactions of biomacromolecules cannot be ruled out. This study demonstrates the effect of volume exclusion due to macromolecular crowding on refolding rate of Gn-HCl induced unfolded hemoglobin. The in vivo like crowding milieu was created using dextran 70. Unfolding of Hb was followed by the absorbance at 280 nm and intrinsic fluorescence intensity along with a bathochromic shift that shows the destabilization of Hb in the presence of the denaturing agent. This was supported by a decrease in soret absorbance, increased hydrodynamic radii and loss in secondary structure, evidenced from dynamic light scattering and circular dichroism experiments respectively. Refolding process of Hb was followed by an increase in soret absorbance, decrease in intrinsic fluorescence intensity with a hypsochromic shift, decreased hydrodynamic radii and gain in secondary structural content. The results revealed that the effect of confinement and volume exclusion is insignificant on the process of Hb refolding.
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Affiliation(s)
- Gufran Ahmed Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India.
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12
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It is time to crowd your cell culture media - Physicochemical considerations with biological consequences. Biomaterials 2021; 275:120943. [PMID: 34139505 DOI: 10.1016/j.biomaterials.2021.120943] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
In vivo, the interior and exterior of cells is populated by various macromolecules that create an extremely crowded milieu. Yet again, in vitro eukaryotic cell culture is conducted in dilute culture media that hardly imitate the native tissue density. Herein, the concept of macromolecular crowding is discussed in both intracellular and extracellular context. Particular emphasis is given on how the physicochemical properties of the crowding molecules govern and determine kinetics, equilibria and mechanism of action of biochemical and biological reactions, processes and functions. It is evidenced that we are still at the beginning of appreciating, let alone effectively implementing, the potential of macromolecular crowding in permanently differentiated and stem cell culture systems.
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13
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Goyal D, Ahmad S, Mahmood A, Chander Sharma S. Interactions of dextransucrase purified from Streptococcus mutans 890 with plant polyphenols. Biochem Biophys Rep 2021; 26:100980. [PMID: 33748439 PMCID: PMC7967010 DOI: 10.1016/j.bbrep.2021.100980] [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] [Received: 01/19/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/02/2022] Open
Abstract
Plant polyphenols have been extensively studied for their chemopreventive properties for human health. Dextransucrase plays an essential role in synthesizing exopolysaccharides from its exclusive substrate sucrose in Streptococcus mutans. In the present study, the effect of polyphenols gallic acid and tannic acid was investigated on the dextransucrase activity. The enzyme was purified by ethanol precipitation followed by column chromatography by Sephadex G-200 gel chromatography, followed by PEG-400 treatment. The purified enzyme exhibited 52 fold enrichment with 17.5% yield and specific activity of 3.54 Units/mg protein. On SDS-PAGE enzyme protein gave a single band with a molecular weight of 160 kDa. Dextransucrase activity was inhibited 80–90% by 0.04 mM tannic acid (TA) or 0.4 mM gallic acid (GA) suggesting that tannic acid has 10- fold more inhibitory potential than gallic acid on the activity of dextransucrase. CD/ORD studies revealed modifications in the tertiary structure of enzyme protein in presence of tannic acid and gallic acid, which were further confirmed by fluorescence spectra of the protein in presence of tannic acid. These results suggest that inhibition of dextransucrase activity in S. mutans by polyphenols may have potential applications in the prevention and control of dental caries. Dextransuccrase an important enzyme of S. mutans is involved in the metabolism of sucrose. Purified enzyme is inhibited (80-90%) by plant polyphenols. Observed inhibition is due to change in teritary structure. S. mutans is an important cariogenic agent. Plant polyphenols are good anticariogenic agents.
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Affiliation(s)
- Dimple Goyal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Shabeer Ahmad
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Akhtar Mahmood
- Department of Biochemistry, Panjab University, Chandigarh, India
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14
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Wilcox XE, Chung CB, Slade KM. Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase. Biochem Biophys Rep 2021; 26:100956. [PMID: 33665382 PMCID: PMC7905371 DOI: 10.1016/j.bbrep.2021.100956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/03/2021] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease Vmax and Km for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in Vmax is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD+ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding. Yeast alcohol dehydrogenase reduction of acetaldehyde is enhanced by crowding. Crowding effects on YADH kinetics depend on the direction of the reaction. Crowders like dextran can be used as a tool to elucidate enzyme mechanism. Excluded volume optimizes YADH hydride transfer; viscosity hinders product release. The presence of a depletion layer with large crowders mitigates their effects.
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Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California at Davis, CA, 95616, USA
| | - Charmaine B Chung
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
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15
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Abstract
Multiple therapeutic proteins can be combined into a single dose for synergistic targeting to multiple sites of action. Such proteins would be mixed in dose-specific ratios to provide the correct potency for each component, and yet the formulations must also preserve their activity and keep degradation to a minimum. Mixing different therapeutic proteins could adversely affect their stability, and reduce the shelf life of each individual component, making the control of such products very challenging. In this study, a therapeutic monoclonal antibody and a related Fab fragment, were combined to investigate the impact of coformulation on their degradation kinetics. Under mildly destabilizing conditions, these proteins were found to protect each other from degradation. The protective effect appeared to originate from the interaction of Fab and IgG1 in small soluble oligomers, or through the rapid coalescence of pre-existing monomeric IgG1 nuclei into a dead-end aggregate, rather than through macromolecular crowding or diffusion-limitations.
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Ross ML, Kunkel J, Long S, Asuri P. Combined Effects of Confinement and Macromolecular Crowding on Protein Stability. Int J Mol Sci 2020; 21:ijms21228516. [PMID: 33198190 PMCID: PMC7697604 DOI: 10.3390/ijms21228516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/18/2023] Open
Abstract
Confinement and crowding have been shown to affect protein fates, including folding, functional stability, and their interactions with self and other proteins. Using both theoretical and experimental studies, researchers have established the independent effects of confinement or crowding, but only a few studies have explored their effects in combination; therefore, their combined impact on protein fates is still relatively unknown. Here, we investigated the combined effects of confinement and crowding on protein stability using the pores of agarose hydrogels as a confining agent and the biopolymer, dextran, as a crowding agent. The addition of dextran further stabilized the enzymes encapsulated in agarose; moreover, the observed increases in enhancements (due to the addition of dextran) exceeded the sum of the individual enhancements due to confinement and crowding. These results suggest that even though confinement and crowding may behave differently in how they influence protein fates, these conditions may be combined to provide synergistic benefits for protein stabilization. In summary, our study demonstrated the successful use of polymer-based platforms to advance our understanding of how in vivo like environments impact protein function and structure.
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Effects of macromolecular crowding on the folding and aggregation of glycosylated MUC5AC. Biochem Biophys Res Commun 2020; 529:984-990. [PMID: 32819609 DOI: 10.1016/j.bbrc.2020.06.156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To investigate the effects of macromolecular crowding on the folding and aggregation of MUC5AC with different levels of glycosylation during refolding. METHODS Part 1:An in vitro catalytic reaction comprising the ppGalNAc T2 enzyme, uridine-5'-diphospho-N-galactosamine (UDP-GalNAc) and an 11-amino acid peptide substrate, was used to assess the enzyme activity of the ppGalNAc T2 enzyme in macromolecular crowding environment respectively with bovine serum albumin (BSA), polyethylene glycol (PEG2000), Dextran70 and Ficoll70 at different concentration and temperature. Part 2: The recombinant MUC5AC was expressed in HEK293 cells and purified by nickel column chromatography. The purified protein was treated with PNGase F, and the degree of glycosylation was analyzed by SDS-PAGE. Macromolecular crowding was simulated using PEG2000 at the concentrations of 50, 100, and 200 g/L. Deglycosylated-MUC5AC (d-MUC5AC) and glycosylated MUC5AC (g-MUC5AC) were denatured by GdnHCl and renatured by dilution in a refolding buffer. Protein aggregation was monitored continuously by absorbance reading at 488 nm using a UV spectrophotometer at 25 °C. The refolded proteins were centrifuged, the protein concentration of the supernatant was measured, and refolding yield in different refolding buffers was determined. RESULTS Enzyme activityof ppGalNAc T2 was observed to increase with increasing crowding agent concentration, with highest enzyme activity at 200 g/L. Compared with the group in the absence of crowding reagent, the refolding yield of g-MUC5AC and d-MUC5AC were reduced significantly in the presence of different concentrations of PEG2000 (200, 100, and 50 g/L). Compared with the dilute solution, aggregation increased significantly in the presence of PEG2000, especially at 200 g/L. Moreover, in the crowded reagent with the same concentration, the refolding yield of d-MUC5AC was higher than that of g-MUC5AC, whereas the degree of aggregation of d-MUC5AC was lower than that of g-MUC5AC. CONCLUSION The crowded intracellular environment reduces the refolding rate of MUC5AC and strongly induces the misfolding and aggregation of glycosylated MUC5AC.
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Molecular and macromolecular crowding-induced stabilization of proteins: Effect of dextran and its building block alone and their mixtures on stability and structure of lysozyme. Int J Biol Macromol 2020; 150:1238-1248. [DOI: 10.1016/j.ijbiomac.2019.10.135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022]
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Wilcox XE, Ariola A, Jackson JR, Slade KM. Overlap Concentration and the Effect of Macromolecular Crowding on Citrate Synthase Activity. Biochemistry 2020; 59:1737-1746. [DOI: 10.1021/acs.biochem.0c00073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xander E. Wilcox
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Ashton Ariola
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, New York 14456, United States
| | - Jasmine R. Jackson
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, New York 14456, United States
| | - Kristin M. Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, New York 14456, United States
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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Polydispersity and negative charge are key modulators of extracellular matrix deposition under macromolecular crowding conditions. Acta Biomater 2019; 88:197-210. [PMID: 30831324 DOI: 10.1016/j.actbio.2019.02.050] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/15/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Macromolecular crowding is a biophysical phenomenon that stems from the volume excluded by macromolecules, as they undergo steric repulsion and electrostatic interactions. The excluded volume depends on the shape, size, charge and polydispersity of the molecules. Although theoretical/computational models have been used to assess the influence of macromolecular crowding in biological media, real-time experiments are scarce. Herein, we evaluated the influence of hydrodynamic radius, charge and polydispersity of (a) various concentrations of different crowders (carrageenan, Ficoll™ and dextran sulphate); (b) various molecular weights of different crowders (70, 400 and 100 kDa of Ficoll™ and 10, 100 and 500 kDa of dextran sulphate) and (c) various cocktails of the same crowders (cocktails of various concentrations of different molecular weights Ficoll™ and dextran sulphate) on extracellular matrix deposition in human dermal fibroblast culture. The use of crowding cocktails with different molecular weight/concentrations of Ficoll™ or dextran sulphate molecules led to increased polydispersity and enhanced collagen type I deposition in comparison to their mono-domain counterparts. Carrageenan, however, induced the highest deposition of collagen type I due to its negative charge and inherent polydispersity. Our data contribute to a better understanding of the influence of the biophysical properties of the crowders on extracellular matrix deposition in vitro. STATEMENT OF SIGNIFICANCE: Macromolecular crowding is a biophysical phenomenon that accelerates and enhances extracellular matrix deposition in cell culture systems. Herein, we demonstrate that negatively charged and polydispersed macromolecules or cocktails of macromolecules, as opposed to neutral and monodomain macromolecules, induce highest extracellular matrix deposition in human dermal fibroblast cultures.
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Mixture of Macromolecular Crowding Agents Has a Non-additive Effect on the Stability of Proteins. Appl Biochem Biotechnol 2019; 188:927-941. [PMID: 30737628 DOI: 10.1007/s12010-019-02972-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
The folding and unfolding of proteins inside a cell take place in the presence of macromolecules of various shapes and sizes. Such crowded conditions can significantly affect folding, stability, and biophysical properties of proteins. Thus, to logically mimic the intracellular environment, the thermodynamic stability of two different proteins (lysozyme and α-lactalbumin) was investigated in the presence of mixtures of three crowding agents (ficoll 70, dextran 70, and dextran 40) at different pH values. These crowders possess different shapes and sizes. It was observed that the stabilizing effect of mixtures of crowders is more than the sum effects of the individual crowder, i.e., the stabilizing effect is non-additive in nature. Moreover, dextran 40 (in the mixture) has been found to exhibit the greatest stabilization when compared with other crowders in the mixture. In other words, the small size of the crowder has been observed to be a dominant factor in stabilization of the proteins. Graphical Abstract.
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Ji X, Su Z, Ma G, Zhang S. Sandwiching multiple dehydrogenases and shared cofactor between double polyelectrolytes for enhanced communication of cofactor and enzymes. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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Biswas S, Kundu J, Mukherjee SK, Chowdhury PK. Mixed Macromolecular Crowding: A Protein and Solvent Perspective. ACS OMEGA 2018; 3:4316-4330. [PMID: 30023892 PMCID: PMC6044960 DOI: 10.1021/acsomega.7b01864] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
In the living cell, biomolecules perform their respective functions in the presence of not only one type of macromolecules but rather in the presence of various macromolecules with different shapes and sizes. In this study, we have investigated the effects of five single macromolecular crowding agents, Dextran 6, Dextran 40, Dextran 70, Ficoll 70, and PEG 8000 and their binary mixtures on the modulation in the domain separation of human serum albumin using a Förster resonance energy transfer-based approach and the translational mobility of a small fluorescent probe fluorescein isothiocyanate (FITC) using fluorescence correlation spectroscopy (FCS). Our observations suggest that mixed crowding induces greater cooperativity in the domain movement as compared to the components of the mixtures. Thermodynamic analyses of the same provide evidence of crossovers from enthalpy-based interactions to effects dominated by hard-sphere potential. When compared with those obtained for individual crowders, both domain movements and FITC diffusion studies show significant deviations from ideality, with an ideal solution being considered to be that arising from the sum of the contributions of those obtained in the presence of individual crowding agents. Considering the fact that domain movements are local (on the order of a few angstroms) in nature while translational movements span much larger lengthscales, our results imply that the observed deviation from simple additivity exists at several possible levels or lengthscales in such mixtures. Moreover, the nature and the type of deviation not only depend on the identities of the components of the crowder mixtures but are also influenced by the particular face of the serum protein (either the domain I-II or the domain II-III face) that the crowders interact with, thus providing further insights into the possible existence of microheterogeneities in such solutions.
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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Barhoum S, Palit S, Yethiraj A. Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 94-95:1-10. [PMID: 27247282 DOI: 10.1016/j.pnmrs.2016.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.
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Affiliation(s)
- Suliman Barhoum
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
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Ishrat M, Imtaiyaz Hassan M, Ahmad F, Moosavi-Movahedi AA, Islam A. Effect of dextran on the thermodynamic stability and structure of ribonuclease A. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0726-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Mittal S, Chowhan RK, Singh LR. Macromolecular crowding: Macromolecules friend or foe. Biochim Biophys Acta Gen Subj 2015; 1850:1822-31. [DOI: 10.1016/j.bbagen.2015.05.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/27/2015] [Accepted: 05/04/2015] [Indexed: 12/11/2022]
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30
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Shahid S, Ahmad F, Hassan MI, Islam A. Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture: An insight into stability-activity trade-off. Arch Biochem Biophys 2015; 584:42-50. [PMID: 26325080 DOI: 10.1016/j.abb.2015.08.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/19/2015] [Accepted: 08/23/2015] [Indexed: 12/25/2022]
Abstract
The cellular environment is crowded with different kinds of molecules with varying sizes, shapes and compositions. Most of the experiments studying the nature and behaviour of a protein have been done on the isolated protein in dilute buffer solutions which actually do not imitate the in vivo situation. To understand the consequences of such crowded environment, we investigated the effect of macromolecular crowding on the stability and activity of hen egg white lysozyme. Two crowding agents, dextran 70 and ficoll 70 which have different shapes and composition, have been employed in this study. To mimic the cellular condition from physiological point of view, the effect of mixtures of both the crowding agents has been also studied. The results indicate that owing to volume exclusion, lysozyme is stabilized while its activity decays with the increasing concentration of both the crowders elucidating the hypothesis of stability-activity trade-off. Mixed macromolecular crowding exerts greater effect than the sum of constituent crowding agents (dextran 70 and ficoll 70).
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Affiliation(s)
- Sumra Shahid
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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31
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Ferreira LA, Madeira PP, Breydo L, Reichardt C, Uversky VN, Zaslavsky BY. Role of solvent properties of aqueous media in macromolecular crowding effects. J Biomol Struct Dyn 2015; 34:92-103. [PMID: 25616385 DOI: 10.1080/07391102.2015.1011235] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.
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Affiliation(s)
- Luisa A Ferreira
- a Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
| | - Pedro P Madeira
- b Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering , University of Porto , Dr. Roberto Frias St., 4200 465 Porto , Portugal
| | - Leonid Breydo
- c Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
| | | | - Vladimir N Uversky
- b Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering , University of Porto , Dr. Roberto Frias St., 4200 465 Porto , Portugal.,e Institute for Biological Instrumentation , Russian Academy of Sciences , 142290 Pushchino , Moscow Region , Russia.,f Faculty of Science, Biology Department , King Abdulaziz University , P.O. Box 80203, Jeddah 21589 , Kingdom of Saudi Arabia.,g Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Boris Y Zaslavsky
- a Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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Poggi CG, Slade KM. Macromolecular Crowding and the Steady-State Kinetics of Malate Dehydrogenase. Biochemistry 2014; 54:260-7. [DOI: 10.1021/bi5011255] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher G. Poggi
- Department
of Chemistry, Hobart and William Smith College, Geneva, New York 14456, United States
| | - Kristin M. Slade
- Department
of Chemistry, Hobart and William Smith College, Geneva, New York 14456, United States
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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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Satyam A, Kumar P, Fan X, Gorelov A, Rochev Y, Joshi L, Peinado H, Lyden D, Thomas B, Rodriguez B, Raghunath M, Pandit A, Zeugolis D. Macromolecular crowding meets tissue engineering by self-assembly: a paradigm shift in regenerative medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:3024-3034. [PMID: 24505025 DOI: 10.1002/adma.201304428] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/07/2013] [Indexed: 06/03/2023]
Abstract
MMC, the addition of inert polydispersed macromolecules in the culture media, effectively emulates the dense in vivo extracellular space, resulting in amplified deposition of ECM in vitro and subsequent production of cohesive, ECM-rich living substitutes.
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Affiliation(s)
- Abhigyan Satyam
- Network of Excellence for Functional Biomaterials (NFB), National University of Ireland Galway, (NUI Galway), Galway, Ireland
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Suthar MK, Doharey PK, Verma A, Saxena JK. Behavior of Plasmodium falciparum purine nucleoside phosphorylase in macromolecular crowded environment. Int J Biol Macromol 2013; 62:657-62. [DOI: 10.1016/j.ijbiomac.2013.09.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
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Ma Q, Hu JY, Chen J, Liang Y. The role of crowded physiological environments in prion and prion-like protein aggregation. Int J Mol Sci 2013; 14:21339-52. [PMID: 24284393 PMCID: PMC3856008 DOI: 10.3390/ijms141121339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023] Open
Abstract
Prion diseases and prion- like protein misfolding diseases are related to the accumulation of abnormal aggregates of the normal host proteins including prion proteins and Tau protein. These proteins possess self-templating and transmissible characteristics. The crowded physiological environments where the aggregation of these amyloidogenic proteins takes place can be imitated in vitro by the addition of macromolecular crowding agents such as inert polysaccharides. In this review, we summarize the aggregation of prion proteins in crowded physiological environments and discuss the role of macromolecular crowding in prion protein aggregation. We also summarize the aggregation of prion- like proteins including human Tau protein, human α-synuclein, and human copper, zinc superoxide dismutase under macromolecular crowding environments and discuss the role of macromolecular crowding in prion- like protein aggregation. The excluded-volume effects caused by macromolecular crowding could accelerate the aggregation of neurodegenerative disease-associated proteins while inhibiting the aggregation of the proteins that are not neurodegenerative disease-associated.
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Affiliation(s)
- Qian Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Aghera N, Udgaonkar JB. The Utilization of Competing Unfolding Pathways of Monellin Is Dictated by Enthalpic Barriers. Biochemistry 2013; 52:5770-9. [DOI: 10.1021/bi400688w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nilesh Aghera
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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Li C, Xu WC, Xie ZS, Pan K, Hu J, Chen J, Pang DW, Yang FQ, Liang Y. Cupric ions induce the oxidation and trigger the aggregation of human superoxide dismutase 1. PLoS One 2013; 8:e65287. [PMID: 23755211 PMCID: PMC3670862 DOI: 10.1371/journal.pone.0065287] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 04/23/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS), partly caused by the mutations and aggregation of human copper, zinc superoxide dismutase (SOD1), is a fatal degenerative disease of motor neurons. Because SOD1 is a major copper-binding protein present at relatively high concentration in motor neurons and copper can be a harmful pro-oxidant, we want to know whether aberrant copper biochemistry could underlie ALS pathogenesis. In this study, we have investigated and compared the effects of cupric ions on the aggregation of ALS-associated SOD1 mutant A4V and oxidized wild-type SOD1. METHODOLOGY/PRINCIPAL FINDINGS As revealed by 90° light scattering, dynamic light scattering, SDS-PAGE, and atomic force microscopy, free cupric ions in solution not only induce the oxidation of either apo A4V or Zn2-A4V and trigger the oligomerization and aggregation of oxidized A4V under copper-mediated oxidative conditions, but also trigger the aggregation of non-oxidized form of such a pathogenic mutant. As evidenced by mass spectrometry and SDS-PAGE, Cys-111 is a primary target for oxidative modification of pathological human SOD1 mutant A4V by either excess Cu(2+) or hydrogen peroxide. The results from isothermal titration calorimetry show that A4V possesses two sets of independent binding sites for Cu(2+): a moderate-affinity site (10(6) M(-1)) and a high-affinity site (10(8) M(-1)). Furthermore, Cu(2+) binds to wild-type SOD1 oxidized by hydrogen peroxide in a way similar to A4V, triggering the aggregation of such an oxidized form. CONCLUSIONS/SIGNIFICANCE We demonstrate that excess cupric ions induce the oxidation and trigger the aggregation of A4V SOD1, and suggest that Cu(2+) plays a key role in the mechanism of aggregation of both A4V and oxidized wild-type SOD1. A plausible model for how pathological SOD1 mutants aggregate in ALS-affected motor neurons with the disruption of copper homeostasis has been provided.
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Affiliation(s)
- Cheng Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen-Chang Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen-Sheng Xie
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kai Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiao Hu
- College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Jie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Fu-Quan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Phillip Y, Schreiber G. Formation of protein complexes in crowded environments--from in vitro to in vivo. FEBS Lett 2013; 587:1046-52. [PMID: 23337873 PMCID: PMC7094571 DOI: 10.1016/j.febslet.2013.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/24/2012] [Accepted: 01/06/2013] [Indexed: 01/17/2023]
Abstract
Traditionally, biochemical studies are performed in dilute homogenous solutions, which are very different from the dense mixture of molecules found in cells. Thus, the physiological relevance of these studies is in question. This recognition motivated scientists to formulate the effect of crowded solutions in general, and excluded volume in particular, on biochemical processes. Using polymers or proteins as crowders, it was shown that while crowding tends to significantly enhance the formation of complexes containing many subunits, dimerizations are only mildly affected. Computer simulations, together with experimental evidence, indicate soft interactions and diffusion as critical factors that operate in a concerted manner with excluded volume to modulate protein binding. Yet, these approaches do not truly mimic the cellular environment. In vivo studies may overcome this shortfall. The few studies conducted thus far suggest that in cells, binding and folding occur at rates close to those determined in dilute solutions. Obtaining quantitative biochemical information on reactions inside living cells is currently a main challenge of the field, as the complexity of the intracellular milieu was what motivated crowding research to begin with.
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Affiliation(s)
- Yael Phillip
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Chen Z, Chen XJ, Xia M, He HW, Wang S, Liu H, Gong H, Yan YB. Chaperone-like effect of the linker on the isolated C-terminal domain of rabbit muscle creatine kinase. Biophys J 2013; 103:558-566. [PMID: 22947872 DOI: 10.1016/j.bpj.2012.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 11/25/2022] Open
Abstract
Intramolecular chaperones (IMCs), which are specific domains/segments encoded in the primary structure of proteins, exhibit chaperone-like activity against the aggregation of the other domains in the same molecule. In this research, we found that the truncation of the linker greatly promoted the thermal aggregation of the isolated C-terminal domain (CTD) of rabbit muscle creatine kinase (RMCK). Either the existence of the linker covalently linked to CTD or the supply of the synthetic linker peptide additionally could successfully protect the CTD of RMCK against aggregation in a concentration-dependent manner. Truncated fragments of the linker also behaved as a chaperone-like effect with lower efficiency, revealing the importance of its C-terminal half in the IMC function of the linker. The aggregation sites in the CTD of RMCK were identified by molecular dynamics simulations. Mutational analysis of the three key hydrophobic residues resulted in opposing effects on the thermal aggregation between the CTD with intact or partial linker, confirming the role of linker as a lid to protect the hydrophobic residues against exposure to solvent. These observations suggested that the linkers in multidomain proteins could act as IMCs to facilitate the correct folding of the aggregation-prone domains. Furthermore, the intactness of the IMC linker after proteolysis modulates the production of off-pathway aggregates, which may be important to the onset of some diseases caused by the toxic effects of aggregated proteolytic fragments.
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Affiliation(s)
- Zhe Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Xiang-Jun Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China; Key Laboratory of Bio-Resources and Eco-Environment of MOE, College of Life Science, Sichuan University, Chengdu, China
| | - Mengdie Xia
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hua-Wei He
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Sha Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Huihui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yong-Bin Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China.
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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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43
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Fan YQ, Liu HJ, Li C, Luan YS, Yang JM, Wang YL. Effects of macromolecular crowding on refolding of recombinant human brain-type creatine kinase. Int J Biol Macromol 2012; 51:113-8. [DOI: 10.1016/j.ijbiomac.2012.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/07/2012] [Accepted: 04/12/2012] [Indexed: 12/29/2022]
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Finn TE, Nunez AC, Sunde M, Easterbrook-Smith SB. Serum albumin prevents protein aggregation and amyloid formation and retains chaperone-like activity in the presence of physiological ligands. J Biol Chem 2012; 287:21530-40. [PMID: 22549788 DOI: 10.1074/jbc.m112.372961] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although serum albumin has an established function as a transport protein, evidence is emerging that serum albumin may also have a role as a molecular chaperone. Using established techniques to characterize chaperone interactions, this study demonstrates that bovine serum albumin: 1) preferentially binds stressed over unstressed client proteins; 2) forms stable, soluble, high molecular weight complexes with stressed client proteins; 3) reduces the aggregation of client proteins when it is present at physiological levels; and 4) inhibits amyloid formation by both WT and L55P transthyretin. Although the antiaggregatory effect of serum albumin is maintained in the presence of physiological levels of Ca(2+) and Cu(2+), the presence of free fatty acids significantly alters this activity: stabilizing serum albumin at normal levels but diminishing chaperone-like activity at high concentrations. Moreover, here it is shown that depletion of albumin from human plasma leads to a significant increase in aggregation under physiologically relevant heat and shear stresses. This study demonstrates that serum albumin possesses chaperone-like properties and that this activity is maintained under a number of physiologically relevant conditions.
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Affiliation(s)
- Thomas E Finn
- School of Molecular Bioscience and Discipline of Pharmacology, The University of Sydney, Sydney, New South Wales 2006, Australia
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45
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Ma Q, Fan JB, Zhou Z, Zhou BR, Meng SR, Hu JY, Chen J, Liang Y. The contrasting effect of macromolecular crowding on amyloid fibril formation. PLoS One 2012; 7:e36288. [PMID: 22558423 PMCID: PMC3340346 DOI: 10.1371/journal.pone.0036288] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/29/2012] [Indexed: 12/05/2022] Open
Abstract
Background Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1) have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins. Methodology/Principal Findings As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l. Conclusions/Significance We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins) has been proposed.
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Affiliation(s)
- Qian Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun-Bao Fan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zheng Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bing-Rui Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Sheng-Rong Meng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ji-Ying Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Lim VI, Curran JF, Garber MB. Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition. J Theor Biol 2012; 301:42-8. [PMID: 22365908 DOI: 10.1016/j.jtbi.2012.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/24/2012] [Accepted: 02/08/2012] [Indexed: 10/28/2022]
Abstract
It has become clear that water should not be treated as an inert environment, but rather as an integral and active component of molecules. Here, we consider molecules and their hydration shells together as single entities. We show that: (1) the rate of association of molecules should be determined by the energetic barriers arising from interactions between their hydration shells; (2) replacing non-polar atoms of molecular surfaces with polar atoms increases these barriers; (3) reduction of the hydration shells during molecular association is the driving force for association not only of non-polar, but of polar molecules as well; (4) in most cases the dehydration of polar atoms during molecular association thermodynamically counteracts association; (5) on balance the thermodynamic stability of associated complexes is basically determined by the action of these two opposing factors: reduction of the hydration shells and dehydration of polar atoms; (6) molecular crowding reduces the energetic barriers counteracting association and changes the thermodynamic stability of associated complexes. These results lead to a mechanism for biomolecular recognition in the context of which the formation of unique structures is provided by rapidly forming kinetic traps with a biologically necessary lifetime but with a marginal thermodynamic stability. The mechanism gives definitive answers to questions concerning the heart of specific interactions between biomolecules, their folding and intracellular organization. Predictions are given that can be subjected to direct experimental tests.
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Affiliation(s)
- Valery I Lim
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
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48
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HARVE KARTHIKS, RAGHUNATH MICHAEL, LAREU RICKYR, RAJAGOPALAN RAJ. MACROMOLECULAR CROWDING IN BIOLOGICAL SYSTEMS: DYNAMIC LIGHT SCATTERING (DLS) TO QUANTIFY THE EXCLUDED VOLUME EFFECT (EVE). ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048006000215] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Macromolecules crowd defined spaces, thereby excluding other like-sized molecules from the volume they occupy. These excluded-volume effect(s) (EVE) are well characterized for intracellular and partially for extracellular compartments such as blood plasma. We showed that EVE in fibroblast culture leads to faster enzymatic procollagen conversion and matrix deposition. Apparently, EVE can be applied to emulate in vivo conditions in an in vitro setting. Thus, we attempted to quantitatively capture the crowding potential of various macromolecules using dynamic light scattering under physiological conditions. We found that charged macromolecules like dextran sulfate (negative, 500 kDa) have a hydrodynamic radii of 46.4 ± 0.3 nm i.e. ~4 fold larger than that of neutral macromolecules like Ficoll (neutral, 400 kDa) and thus show greater EVE potential. At biologically effective concentrations viscosity was not increased. Unexpectedly, we observed a dramatic drop of hydrodynamic radii of all macromolecules tested above a threshold concentration. This suggested a hyper-crowding state in which the crowders compacted themselves mutually. We will use this hyper-crowding threshold to determine retrogradely rules that allow to predict the conditions for optimum crowding effects (such as the half-hyper-crowding concentration) in biological systems. We propose Dynamic Light Scattering (DLS) as a potential tool to estimate EVE in biotechnical applications.
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Affiliation(s)
- KARTHIK S. HARVE
- Tissue Modulation Laboratory, Division of Bioengineering, National University of Singapore, Singapore
| | - MICHAEL RAGHUNATH
- Tissue Modulation Laboratory, Division of Bioengineering, National University of Singapore, Singapore
| | - RICKY R. LAREU
- Tissue Modulation Laboratory, NUS Tissue Engineering Program, National University of Singapore, Singapore
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - RAJ RAJAGOPALAN
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
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Zhou Z, Yan X, Pan K, Chen J, Xie ZS, Xiao GF, Yang FQ, Liang Y. Fibril formation of the rabbit/human/bovine prion proteins. Biophys J 2011; 101:1483-92. [PMID: 21943430 DOI: 10.1016/j.bpj.2011.08.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/26/2011] [Accepted: 08/11/2011] [Indexed: 01/07/2023] Open
Abstract
Prion diseases are infectious fatal neurodegenerative diseases including Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle. The misfolding and conversion of cellular PrP in such mammals into pathogenic PrP is believed to be the key procedure. Rabbits are among the few mammalian species that exhibit resistance to prion diseases, but little is known about the molecular mechanism underlying such resistance. Here, we report that the crowding agents Ficoll 70 and dextran 70 have different effects on fibrillization of the recombinant full-length PrPs from different species: although these agents dramatically promote fibril formation of the proteins from human and cow, they significantly inhibit fibrillization of the rabbit protein by stabilizing its native state. We also find that fibrils formed by the rabbit protein contain less β-sheet structure and more α-helix structure than those formed by the proteins from human and cow. In addition, amyloid fibrils formed by the rabbit protein do not generate a proteinase K-resistant fragment of 15-16-kDa, but those formed by the proteins from human and cow generate such proteinase K-resistant fragments. Together, these results suggest that the strong inhibition of fibrillization of the rabbit PrP by the crowded physiological environment and the absence of such a protease-resistant fragment for the rabbit protein could be two of the reasons why rabbits are resistant to prion diseases.
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Affiliation(s)
- Zheng Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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Kumar K, Bhargava P, Roy U. In vitro refolding of triosephosphate isomerase from L. donovani. Appl Biochem Biotechnol 2011; 164:1207-14. [PMID: 21365180 DOI: 10.1007/s12010-011-9206-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/14/2011] [Indexed: 11/30/2022]
Abstract
The triosephosphate isomerase of Leishmania donovani (LdTIM) was expressed at high level in Escherichia coli. The TIM gene was cloned in expression vector pET-23(a) with C-terminal 6× His tag fused in frame, and expressed as a 27.6-kDa protein in E. coli as inclusion bodies. The recombinant LdTIM from E. coli lysate was solubilized in 6 M guanidine hydrochloride and purified by Ni-NTA chromatography. In the present study, the effect of bovine serum albumin on the reactivation of TIM was investigated. Furthermore, 8-anilino-1-naphthalene sulfonic acid was used to detect the structural changes induced by bovine serum albumin (BSA). Here, we conclude that BSA assists in the refolding and regain of LdTIM enzyme activity by providing framework for structure formation. This study indicates that numerous protein-protein contacts are constantly occurring inside the cell that leads to the formation of native protein.
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Affiliation(s)
- Kishore Kumar
- Division of Biochemistry, Central Drug Research Institute, Lucknow 226001, UP, India
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