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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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2
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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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Fields CR, Dicke SS, Petti MK, Zanni MT, Lomont JP. A Different hIAPP Polymorph Is Observed in Human Serum Than in Aqueous Buffer: Demonstration of a New Method for Studying Amyloid Fibril Structure Using Infrared Spectroscopy. J Phys Chem Lett 2020; 11:6382-6388. [PMID: 32706257 PMCID: PMC7968077 DOI: 10.1021/acs.jpclett.0c01345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There is enormous interest in measuring amyloid fibril structures, but most structural studies measure fibril formation in vitro using aqueous buffer. Ideally, one would like to measure fibril structure and mechanism under more physiological conditions. Toward this end, we have developed a method for studying amyloid fibril structure in human serum. Our approach uses isotope labeling, antibody depletion of the most abundant proteins (albumin and IgG), and infrared spectroscopy to measure aggregation in human serum with reduced protein content. Reducing the nonamyloid protein content enables the measurements by decreasing background signals but retains the full composition of salts, sugars, metal ions, etc. that are naturally present but usually missing from in vitro studies. We demonstrate the method by measuring the two-dimensional infrared (2D IR) spectra of isotopically labeled human islet amyloid polypeptide (hIAPP or amylin). We find that the fibril structure of hIAPP formed in serum differs from that formed via aggregation in aqueous buffer at residues Gly24 and Ala25, which reside in the putative "amyloidogenic core" or FGAIL region of the sequence. The spectra are consistent with extended parallel stacks of strands consistent with β-sheet-like structure, rather than a partially disordered loop that forms in aqueous buffer. These experiments provide a new method for using infrared spectroscopy to monitor the structure of proteins under physiological conditions and reveal the formation of a significantly different polymorph structure in the most important region of hIAPP.
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Affiliation(s)
- Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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4
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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5
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Kumar R, Kumar R, Sharma D, Garg M, Kumar V, Agarwal MC. Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1102-1114. [DOI: 10.1016/j.bbapap.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022]
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6
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Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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Abstract
Abstract
Effects of interfaces on hydrogen-bonded liquids play major roles in nature and technology. Despite their importance, a fundamental understanding of these effects is still lacking. In large parts, this shortcoming is due to the high complexity of these systems, leading to an interference of various interactions and effects. Therefore, it is advisable to take gradual approaches, which start from well designed and defined model systems and systematically increase the level of intricacy towards more complex mimetics. Moreover, it is necessary to combine insights from a multitude of methods, in particular, to link novel preparation strategies and comprehensive experimental characterization with inventive computational and theoretical modeling. Such concerted approach was taken by a group of preparative, experimentally, and theoretically working scientists in the framework of Research Unit FOR 1583 funded by the Deutsche Forschungsgemeinschaft (German Research Foundation). This special issue summarizes the outcome of this collaborative research. In this introductory article, we give an overview of the covered topics and the main results of the whole consortium. The following contributions are review articles or original works of individual research projects.
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Affiliation(s)
- Gerd Buntkowsky
- Institut für Physikalische Chemie , Technische Universität Darmstadt , 64287 Darmstadt , Germany
| | - Michael Vogel
- Institut für Festkörperphysik , Technische Universität Darmstadt , 64295 Darmstadt , Germany
| | - Roland Winter
- Fakultät für Chemie und Chemische Biologie , Technische Universität Dortmund , 44227 Dortmund , Germany
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8
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Effects of Cosolvents and Macromolecular Crowding on the Phase Transitions and Temperature-Pressure Stability of Chiral and Racemic Poly-Lysine. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
FTIR spectroscopy has been used to reveal the effects of different types of cosolvents (TMAO, urea) as well as macromolecular crowding (using the crowding agent Ficoll) on the temperature and pressure dependent structure of poly-L-lysine, poly-D-lysine and their racemic mixture. Compared to the effects of cosolvents on the unfolding transition of proteins, their effects on the α-helix to aggregated β-sheet transition of polylysine are quite small. High hydrostatic pressure has been found to favor the α-helical state over the aggregated β-sheet structure which is reflected in a volume decrease of ΔV=−32 mL mol−1, indicating that the packing mode is more efficient in the α-helical structure. Both, addition of urea and TMAO lead to a decrease in pressure stability of the aggregated β-sheet structure, which is accompanied by a three-fold decrease in ΔV, whereas the macromolecular crowder has little effect on the β-to-α transition. The more than 3 kbar higher β-to-α transition pressure of the racemic mixture compared with PLL confirms the drastic stabilization of β-sheet aggregates if the stereoisomers PLL and PDL are combined. Changes in hydration and packing of the polypeptide occurs upon interaction and fine packing of the polypeptide’s chains of opposed chirality, which are slightly modulated by the properties of cosolute and crowding, only. The underlying solvational and packing mechanisms observed here may be decisive factors responsible for the spontaneous protein aggregation in general and, as such, may shed additional light on the molecular basis of amyloid-associated diseases.
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9
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Schummel PH, Jaworek MW, Rosin C, Högg J, Winter R. Exploring the influence of natural cosolvents on the free energy and conformational landscape of filamentous actin and microtubules. Phys Chem Chem Phys 2018; 20:28400-28411. [DOI: 10.1039/c8cp03041c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural osmolytes have a significant influence on the temperature- and pressure-dependent stability of filamentous actin and microtubules.
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Affiliation(s)
- Paul Hendrik Schummel
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Christopher Rosin
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Jessica Högg
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
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10
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Shimizu S, Smith PE. How Osmolytes Counteract Pressure Denaturation on a Molecular Scale. Chemphyschem 2017; 18:2243-2249. [PMID: 28678423 PMCID: PMC5626881 DOI: 10.1002/cphc.201700503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/30/2017] [Indexed: 11/08/2022]
Abstract
Life in the deep sea exposes enzymes to high hydrostatic pressure, which decreases their stability. For survival, deep sea organisms tend to accumulate various osmolytes, most notably trimethylamine N-oxide used by fish, to counteract pressure denaturation. However, exactly how these osmolytes work remains unclear. Here, a rigorous statistical thermodynamics approach is used to clarify the mechanism of osmoprotection. It is shown that the weak, nonspecific, and dynamic interactions of water and osmolytes with proteins can be characterized only statistically, and that the competition between protein-osmolyte and protein-water interactions is crucial in determining conformational stability. Osmoprotection is driven by a stronger exclusion of osmolytes from the denatured protein than from the native conformation, and water distribution has no significant effect on these changes at low osmolyte concentrations.
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Affiliation(s)
- Seishi Shimizu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas, 66506-0401, USA
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11
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Shah V, Pierre B, Kirtadze T, Shin S, Kim JR. Stabilization of Bacillus circulans xylanase by combinatorial insertional fusion to a thermophilic host protein. Protein Eng Des Sel 2017; 30:281-290. [PMID: 28100651 DOI: 10.1093/protein/gzw081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/21/2016] [Indexed: 11/15/2022] Open
Abstract
High thermostability of an enzyme is critical for its industrial application. While many engineering approaches such as mutagenesis have enhanced enzyme thermostability, they often suffer from reduced enzymatic activity. A thermally stabilized enzyme with unchanged amino acids is preferable for subsequent functional evolution necessary to address other important industrial needs. In the research presented here, we applied insertional fusion to a thermophilic maltodextrin-binding protein from Pyrococcus furiosus (PfMBP) in order to improve the thermal stability of Bacillus circulans xylanase (BCX). Specifically, we used an engineered transposon to construct a combinatorial library of randomly inserted BCX into PfMBP. The library was then subjected to functional screening to identify successful PfMBP-BCX insertion complexes, PfMBP-BCX161 and PfMBP-BCX165, displaying substantially improved kinetic stability at elevated temperatures compared to unfused BCX and other controls. Results from subsequent characterizations were consistent with the view that lowered aggregation of BCX and reduced conformational flexibility at the termini was responsible for increased thermal stability. Our stabilizing approach neither sacrificed xylanase activity nor required changes in the BCX amino acid sequence. Overall, the current study demonstrated the benefit of combinatorial insertional fusion to PfMBP as a systematic tool for the creation of enzymatically active and thermostable BCX variants.
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Affiliation(s)
- Vandan Shah
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Brennal Pierre
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Tamari Kirtadze
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Seung Shin
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
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12
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Low crowding agent concentration destabilizes against pressure unfolding. Biophys Chem 2017; 231:125-134. [PMID: 28502485 DOI: 10.1016/j.bpc.2017.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 02/05/2023]
Abstract
The concentration of macromolecules inside a cell is very high, which can affect the behavior of the enzymes, and consequently influence vital biological processes. This is called macromolecular crowding. Since the most important effect of macromolecular crowding is the excluded volume, we performed pressure experiments, where the volume (as conjugate parameter to the pressure) is the crucial factor. We measured the temperature and pressure stability of bovine serum albumin and lysozyme with various concentrations of crowding agents, dextran, Ficoll™ and lysozyme itself. Our most interesting finding is that low concentration of all the studied crowding agents decreases the pressure stability of the proteins. We explain this by the reduced hydration volume change in the crowded environment. Furthermore, we discuss the volumetric parameters and emphasize the difference between the partial volume of the protein and the volume it influences, and their relation to the excluded volume which is responsible for the macromolecular crowding.
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13
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Osmolyte depletion viewed in terms of the dividing membrane and its work of expansion against osmotic pressure. Biophys Chem 2017; 231:111-115. [PMID: 28283210 DOI: 10.1016/j.bpc.2017.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 01/26/2017] [Indexed: 11/21/2022]
Abstract
How osmolytes enhance the folding, binding, and self-assembly of biological macromolecules at a microscopic scale has long been a matter of debate. Ambiguities persist on the key interpretive concepts, such as the "effective membrane" (which marks the boundary of the volume from which osmolytes are excluded) and the "free energy of exclusion" of osmolytes from biomolecular surfaces. In this paper, we formulate these elusive concepts based upon chemical thermodynamics and rigorous statistical thermodynamics (the Kirkwood-Buff theory). Positioning of the membrane at the osmotic dividing surface is crucial in order not to affect the thermodynamics of solvation. The notion of the free energy (work) of excluding osmolytes is refined to the expansion work against the osmotic pressure, which indeed describes the change of solvation free energy at dilute osmolyte concentrations.
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14
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Parray ZA, Shahid S, Ahmad F, Hassan MI, Islam A. Characterization of intermediate state of myoglobin in the presence of PEG 10 under physiological conditions. Int J Biol Macromol 2017; 99:241-248. [PMID: 28242330 DOI: 10.1016/j.ijbiomac.2017.02.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/24/2017] [Accepted: 02/22/2017] [Indexed: 11/28/2022]
Abstract
The macromolecular crowding progressively has been gaining prominence in recent years as it acts as a sword with double-edge on protein stability and folding, i.e., showing assorted results of having both stabilizing and destabilizing effects. We studied the effects of different concentrations of polyethylene glycol (PEG-10) on structure and stability of myoglobin. The tertiary structure of myoglobin was found to be perturbed in the presence of polyethylene glycol, however there was insignificant change in the secondary structure. It was observed that polyethylene glycol induces molten globule state in myoglobin, where the intermediate state holds hydrophobic patches and larger hydrodynamic volume as compared to the native protein. In addition, isothermal titration calorimetry (ITC) showed strong binding between myoglobin and polyethylene glycol, at the physiological pH. We hypothesize that polyethylene glycol induces molten globule conformation in myoglobin by interacting with heme group of myoglobin. We caution that the binding of protein with crowder and other soft interactions need to be gravely well thought-out when studying macromolecular crowding. In our case, destabilizing protein-crowder interactions could compete and overcome the stabilizing exclusion volume effect.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - 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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15
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Exploring the stability limits of actin and its suprastructures. Biophys J 2016; 107:2982-2992. [PMID: 25517163 DOI: 10.1016/j.bpj.2014.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/28/2014] [Accepted: 11/05/2014] [Indexed: 12/30/2022] Open
Abstract
Actin is the main component of the microfilament system in eukaryotic cells and can be found in distinct morphological states. Global (G)-actin is able to assemble into highly organized, supramolecular cellular structures known as filamentous (F)-actin and bundled (B)-actin. To evaluate the structure and stability of G-, F-, and B-actin over a wide range of temperatures and pressures, we used Fourier transform infrared spectroscopy in combination with differential scanning and pressure perturbation calorimetry, small-angle x-ray scattering, laser confocal scanning microscopy, and transmission electron microscopy. Our analysis was designed to provide new (to our knowledge) insights into the stabilizing forces of actin self-assembly and to reveal the stability of the actin polymorphs, including in conditions encountered in extreme environments. In addition, we sought to explain the limited pressure stability of actin self-assembly observed in vivo. G-actin is not only the least temperature-stable but also the least pressure-stable actin species. Under abyssal conditions, where temperatures as low as 1-4°C and pressures up to 1 kbar are reached, G-actin is hardly stable. However, the supramolecular assemblies of actin are stable enough to withstand the extreme conditions usually encountered on Earth. Beyond ∼3-4 kbar, filamentous structures disassemble, and beyond ∼4 kbar, complete dissociation of F-actin structures is observed. Between ∼1 and 2 kbar, some disordering of actin assemblies commences, in agreement with in vivo observations. The limited pressure stability of the monomeric building block seems to be responsible for the suppression of actin assembly in the kbar pressure range.
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16
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Kumar R, Sharma D, Jain R, Kumar S, Kumar R. Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c. Biophys Chem 2015; 207:61-73. [DOI: 10.1016/j.bpc.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 11/25/2022]
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17
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Analysis of the size dependence of macromolecular crowding shows that smaller is better. Proc Natl Acad Sci U S A 2015; 112:7990-5. [PMID: 26080429 DOI: 10.1073/pnas.1505396112] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aqueous milieu inside cells contains as much as 30-40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations. Consequently crowding, a nonspecific phenomenon believed to arise from the large excluded volume of these macromolecules, has been studied extensively by experimental and theoretical methods. However, the relevant theory has not been applied consistently. When the steric effects of macromolecular crowders and small molecules like water and ions are treated on an equal footing, the effect of the macromolecules is opposite to that commonly believed. Large molecules are less effective at crowding than water and ions. There is also a surprisingly weak dependence on crowder size. Molecules of medium size, ∼5 Å radius, have the same effect as much larger macromolecules like proteins and RNA. These results require a reassessment of observed high-concentration effects and of strategies to mimic in vivo conditions with in vitro experiments.
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18
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Erlkamp M, Grobelny S, Winter R. Crowding effects on the temperature and pressure dependent structure, stability and folding kinetics of Staphylococcal Nuclease. Phys Chem Chem Phys 2015; 16:5965-76. [PMID: 24549181 DOI: 10.1039/c3cp55040k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
FT-IR spectroscopic, small-angle X-ray scattering and calorimetric measurements have been applied to explore the effect of the macromolecular crowder agent Ficoll on the temperature- and pressure-dependent stability diagram and folding reaction of the protein Staphylococcal Nuclease (SNase). Additionally, we compare the experimental data with approximate theoretical predictions. We found that temperature- and pressure-induced equilibrium unfolding of SNase is markedly shifted to higher temperatures and pressures in 30 wt% Ficoll solutions. The structure of the unfolded state ensemble does not seem to be strongly influenced in the presence of the crowder. Self-crowding effects have been found to become important at SNase concentrations above 10 wt% only. Our kinetic results show that the folding rate of SNase decreases markedly in the presence of Ficoll. These results indicate that besides the commonly encountered excluded volume effect, other factors need to be considered when assessing confinement effects on protein folding kinetics. Among those, crowder-induced viscosity changes seem to be prominent.
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Affiliation(s)
- M Erlkamp
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, D-44221 Dortmund, Germany.
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19
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Abstract
Proteins are essential players in the vast majority of molecular level life processes. Since their structure is in most cases substantial for their correct function, study of their structural changes attracted great interest in the past decades. The three dimensional structure of proteins is influenced by several factors including temperature, pH, presence of chaotropic and cosmotropic agents, or presence of denaturants. Although pressure is an equally important thermodynamic parameter as temperature, pressure studies are considerably less frequent in the literature, probably due to the technical difficulties associated to the pressure studies. Although the first steps in the high-pressure protein study have been done 100 years ago with Bridgman's ground breaking work, the field was silent until the modern spectroscopic techniques allowed the characterization of the protein structural changes, while the protein was under pressure. Recently a number of proteins were studied under pressure, and complete pressure-temperature phase diagrams were determined for several of them. This review summarizes the thermodynamic background of the typical elliptic p-T phase diagram, its limitations and the possible reasons for deviations of the experimental diagrams from the theoretical one. Finally we show some examples of experimentally determined pressure-temperature phase diagrams.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary,
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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: 370] [Impact Index Per Article: 37.0] [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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21
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Schuabb C, Berghaus M, Rosin C, Winter R. Exploring the Free Energy and Conformational Landscape of tRNA at High Temperature and Pressure. Chemphyschem 2014; 16:138-46. [DOI: 10.1002/cphc.201402676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Indexed: 11/10/2022]
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22
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Suladze S, Kahse M, Erwin N, Tomazic D, Winter R. Probing volumetric properties of biomolecular systems by pressure perturbation calorimetry (PPC)--the effects of hydration, cosolvents and crowding. Methods 2014; 76:67-77. [PMID: 25168090 DOI: 10.1016/j.ymeth.2014.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 11/16/2022] Open
Abstract
Pressure perturbation calorimetry (PPC) is an efficient technique to study the volumetric properties of biomolecules in solution. In PPC, the coefficient of thermal expansion of the partial volume of the biomolecule is deduced from the heat consumed or produced after small isothermal pressure-jumps. The expansion coefficient strongly depends on the interaction of the biomolecule with the solvent or cosolvent as well as on its packing and internal dynamic properties. This technique, complemented with molecular acoustics and densimetry, provides valuable insights into the basic thermodynamic properties of solvation and volume effects accompanying interactions, reactions and phase transitions of biomolecular systems. After outlining the principles of the technique, we present representative examples on protein folding, including effects of cosolvents and crowding, together with a discussion of the interpretation, and further applications.
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Affiliation(s)
- Saba Suladze
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Marie Kahse
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Nelli Erwin
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Daniel Tomazic
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany.
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23
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Mandal SS, Cristiglio V, Lindner P, Bhattacharyya AJ. Small-angle neutron scattering studies of hemoglobin confined inside silica tubes of varying sizes. Chemphyschem 2013; 15:302-9. [PMID: 24339406 DOI: 10.1002/cphc.201300863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/14/2013] [Indexed: 11/08/2022]
Abstract
In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20-200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small-angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si-tube pore diameter. The high radius of gyration (Rg) and polydispersity of Hb in the 20 nm diameter Si-tube indicates that Hb undergoes a significant amount of aggregation. However, for Si-tube diameters greater or equal to 100 nm, the Rg of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (Rg of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native-like non-aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si-tube size is a key parameter for protein stability and structure.
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Affiliation(s)
- Soumit S Mandal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012 (India), Fax: (+91) 80-23601310
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Bye JW, Falconer RJ. Thermal stability of lysozyme as a function of ion concentration: a reappraisal of the relationship between the Hofmeister series and protein stability. Protein Sci 2013; 22:1563-70. [PMID: 24038575 DOI: 10.1002/pro.2355] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 11/09/2022]
Abstract
Anion and cation effects on the structural stability of lysozyme were investigated using differential scanning calorimetry. At low concentrations (<5 mM) anions and cations alter the stability of lysozyme but they do not follow the Hofmeister (or inverse Hofmeister) series. At higher concentrations protein stabilization follows the well-established Hofmeister series. Our hypothesis is that there are three mechanisms at work. At low concentrations the anions interact with charged side chains where the presence of the ion can alter the structural stability of the protein. At higher concentrations the low charge density anions perchlorate and iodide interact weakly with the protein. Their presence however reduces the Gibbs free energy required to hydrate the core of the protein that is exposed during unfolding therefore destabilizing the structure. At higher concentrations the high charge density anions phosphate and sulfate compete for water with the protein as it unfolds increasing the Gibbs free energy required to hydrate the newly exposed core of the protein therefore stabilizing the structure.
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Affiliation(s)
- Jordan W Bye
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, England, United Kingdom
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