1
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Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
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Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
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2
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A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion. BIOLOGY 2022; 11:biology11121764. [PMID: 36552273 PMCID: PMC9775367 DOI: 10.3390/biology11121764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.
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3
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Hanke M, Hansen N, Tomm E, Grundmeier G, Keller A. Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate. Int J Mol Sci 2022; 23:ijms23158547. [PMID: 35955680 PMCID: PMC9368935 DOI: 10.3390/ijms23158547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.
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4
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Paladino A, Balasco N, Graziano G, Vitagliano L. A Protein Data Bank survey of multimodal binding of thiocyanate to proteins: Evidence for thiocyanate promiscuity. Int J Biol Macromol 2022; 208:29-36. [PMID: 35259436 DOI: 10.1016/j.ijbiomac.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
Over the last one and half century, a myriad of studies has demonstrated that Hofmeister ions have a major impact on protein stability and solubility. Nevertheless, the definition of the physico-chemical basis of their activity has proved to be highly challenging and controversial. Here, by exploiting the enormous information content of the Protein Data Bank, we explored the binding to proteins of thiocyanate, the anion of the series exerting the highest solubilization/destabilization effects. The survey, which led to the identification and characterization of 712 thiocyanate binding sites, provides a comprehensive and atomic-level view of the varied interactions that the ion forms with proteins. The inspection of these sites highlights a limited tendency of thiocyanate to interact with structured water molecules, in line with the reported poor hydration of the ion. On the other hand, the thiocyanate makes interactions with protein nonpolar moieties, especially with the backbone Cα atom. In as many as 104 cases, the ion exclusively makes nonpolar contacts. In conclusion, these findings suggest that the ability of thiocyanate to bind all types of protein exposed patches may lead to the formation of a negatively charged electrostatic barrier that could prevent protein-protein aggregation and promote protein solubility. Moreover, the denaturing action of thiocyanate may be ascribed to its ability to establish multiple attractive interactions with protein surfaces.
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Affiliation(s)
- Antonella Paladino
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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5
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Pica A, Graziano G. A Rationalization of the Effect That TMAO, Glycine, and Betaine Exert on the Collapse of Elastin-like Polypeptides. Life (Basel) 2022; 12:life12020140. [PMID: 35207427 PMCID: PMC8876568 DOI: 10.3390/life12020140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/16/2022] Open
Abstract
Elastin-like polypeptides (ELPs) are soluble in water at low temperature, but, on increasing the temperature, they undergo a reversible and cooperative, coil-to-globule collapse transition. It has been shown that the addition to water of either trimethylamine N-oxide (TMAO), glycine, or betaine causes a significant decrease of T(collapse) in the case of a specific ELP. Traditional rationalizations of these phenomena do not work in the present case. We show that an alternative approach, grounded in the magnitude of the solvent-excluded volume effect and its temperature dependence (strictly linked to the translational entropy of solvent and co-solute molecules), is able to rationalize the occurrence of ELP collapse in water on raising the temperature, as well as the T(collapse) lowering caused by the addition to water of either TMAO, glycine, or betaine.
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Affiliation(s)
- Andrea Pica
- ALPX, 71 Avenue des Martyrs, 38000 Grenoble, France;
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
- Correspondence:
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6
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Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
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7
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Hiller S. Molecular chaperones and their denaturing effect on client proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:1-8. [PMID: 33136251 PMCID: PMC7897196 DOI: 10.1007/s10858-020-00353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
Advanced NMR methods combined with biophysical techniques have recently provided unprecedented insight into structure and dynamics of molecular chaperones and their interaction with client proteins. These studies showed that several molecular chaperones are able to dissolve aggregation-prone polypeptides in aqueous solution. Furthermore, chaperone-bound clients often feature fluid-like backbone dynamics and chaperones have a denaturing effect on clients. Interestingly, these effects that chaperones have on client proteins resemble the effects of known chaotropic substances. Following this analogy, chaotropicity could be a fruitful concept to describe, quantify and rationalize molecular chaperone function. In addition, the observations raise the possibility that at least some molecular chaperones might share functional similarities with chaotropes. We discuss these concepts and outline future research in this direction.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
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8
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Cozzolino S, Graziano G. The magnitude of macromolecular crowding caused by Dextran and Ficoll for the conformational stability of globular proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Guanidinium binding to proteins: The intriguing effects on the D1 and D2 domains of Thermotoga maritima Arginine Binding Protein and a comprehensive analysis of the Protein Data Bank. Int J Biol Macromol 2020; 163:375-385. [PMID: 32629051 DOI: 10.1016/j.ijbiomac.2020.06.290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
Abstract
Thermotoga maritima Arginine Binding Protein has been extensively characterized because of its peculiar features and its possible use as a biosensor. In this characterization, deletion of the C-terminal helix to obtain the monomeric protein TmArgBP20-233 and dissection of the monomer in its two domains, D1 and D2, have been performed. In the present study the stability of these three forms against guanidinium chloride is investigated by means of circular dichroism and differential scanning calorimetry measurements. All three proteins show a high conformational stability; moreover, D1 shows an unusual behavior in the presence of low concentrations of guanidinium chloride. This finding has led us to investigate a possible binding interaction by means of isothermal titration calorimetry and X-ray crystallography; the results indicate that D1 is able to bind the guanidinium ion (GuH+), due to its similarity with the arginine terminal moiety. The analysis of the structural and dynamic properties of the D1-GuH+ complex indicates that the protein binds the ligand through multiple and diversified interactions. An exhaustive survey of the binding modes of GuH+ to proteins indicates that this is a rather common feature. These observations provide interesting insights into the effects that GuH+ is able to induce in protein structures.
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10
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Francisco OA, Glor HM, Khajehpour M. Salt Effects on Hydrophobic Solvation: Is the Observed Salt Specificity the Result of Excluded Volume Effects or Water Mediated Ion-Hydrophobe Association? Chemphyschem 2020; 21:484-493. [PMID: 31944529 DOI: 10.1002/cphc.201901000] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/14/2020] [Indexed: 12/30/2022]
Abstract
The solubility of hydrophobic molecules in water is sensitive to salt addition in an ion-specific manner. Such "salting-out" and "salting-in" properties have been shown to be a major contributor to the measured ion-specific Hofmeister effects that are observed in many biophysical phenomena. Various theoretical models have suggested a number of disparate mechanisms for salting-out (salting-in) of hydrophobic moieties, the most popular of which include preferential interaction, water-mediated association, and electrostriction models. However, a complete molecular level description of this ion-specificity is not yet available. This work investigates the ion-specific nature of hydrophobic solvation by studying how sodium and chloride salts affect the thermodynamics of 1,2-hexanediol micellization. The results of this study are analyzed in terms of scaled-particle theory and we show that salt addition can affect hydrophobic solvation in two modalities: salt addition changes the cavitation free energy; salt addition also influences the solvent-solute interaction energy by changing the hydration of the hydrophobic solute. These two effects are salt specific in nature and we suggest that for small hydrophobic solutes these effects are the main cause of salt-specific Hofmeister effects on their solubility.
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Affiliation(s)
| | - Hayden M Glor
- Department of Chemistry, University of Manitoba, Canada
| | - Mazdak Khajehpour
- University of Manitoba, 468 Parker Bldg., Winnipeg, Manitoba, R3T2 N2, Canada.,Department of Chemistry, University of Manitoba, Canada
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11
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Pica A, Graziano G. Effect of sodium thiocyanate and sodium perchlorate on poly(N-isopropylacrylamide) collapse. Phys Chem Chem Phys 2019; 22:189-195. [PMID: 31799525 DOI: 10.1039/c9cp05706d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The T(collapse) of poly(N-isopropylacrylamide), PNIPAM, shows a nonlinear dependence on the concentration of NaSCN or NaClO4; in the case of NaClO4, for example, at very low concentrations of the salt, T(collapse) increases with the concentration, while it has an opposite trend at higher NaClO4 concentrations [J. Am. Chem. Soc., 2005, 127, 14505]. These puzzling experimental data can be rationalized by considering that low charge density and poorly hydrated ions, such as thiocyanate and perchlorate, interact preferentially with the surface of the polymer, and cause an increase of the magnitude of the energetic term that stabilizes swollen conformations at low salt concentrations. However, as both swollen and collapsed PNIPAM conformations are accessible to such ions in view of their large conformational freedom, the difference in the number of ions bound to PNIPAM surface upon collapse changes little on increasing the salt concentration. Thus, the energetic term that favors swollen conformations increases with salt concentration to a lesser extent than the solvent-excluded volume term (linked to the density increase caused by salt addition to water), that favors collapsed conformations, leading to a nonlinear trend of T(collapse).
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Affiliation(s)
- Andrea Pica
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, Grenoble, France
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12
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Pica A, Graziano G. Why does urea have a different effect on the collapse temperature of PDEAM and PNIPAM? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Amsdr A, Noudeh ND, Liu L, Chalikian TV. On urea and temperature dependences of m-values. J Chem Phys 2019; 150:215103. [DOI: 10.1063/1.5097936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alah Amsdr
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Negar Dehghan Noudeh
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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14
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Reid JESJ, Aquino PHG, Walker AJ, Karadakov PB, Shimizu S. Statistical Thermodynamics Unveils How Ions Influence an Aqueous Diels‐Alder Reaction. Chemphyschem 2019; 20:1538-1544. [DOI: 10.1002/cphc.201900024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/15/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Joshua E. S. J. Reid
- York Structural Biology Laboratory Department of ChemistryUniversity of York Heslington York YO10 5DD United Kingdom
- Bioniqs Ltd., BioCity Nottingham Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Pedro H. G. Aquino
- York Structural Biology Laboratory Department of ChemistryUniversity of York Heslington York YO10 5DD United Kingdom
| | - Adam J. Walker
- Bioniqs Ltd., BioCity Nottingham Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Peter B. Karadakov
- Department of ChemistryUniversity of York Heslington York YO10 5DD United Kingdom
| | - Seishi Shimizu
- York Structural Biology Laboratory Department of ChemistryUniversity of York Heslington York YO10 5DD United Kingdom
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15
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Balamurugan K, Prakash M, Subramanian V. Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids. J Phys Chem B 2019; 123:2191-2202. [PMID: 30672268 DOI: 10.1021/acs.jpcb.8b08968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions between the guanidinium cation (Gdm+) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm+ and AAs with and without water molecules. It is observed that nonhydrated Gdm+ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm+ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm+ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm+ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm+. Moreover, the interaction of AAs with Gdm+ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm+ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm+ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm+ cation.
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Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Muthuramalingam Prakash
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Venkatesan Subramanian
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-CLRI Campus , Chennai 600 020 , India
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16
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Graziano G. On the opposite effect of guanidinium chloride and guanidinium sulphate on the kinetics of the Diels-Alder reaction. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents. Phys Chem Chem Phys 2018; 20:29389-29398. [PMID: 30451257 DOI: 10.1039/c8cp04421j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia - 80126 Napoli, Italy.
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18
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Ekholm V, Vazdar M, Mason PE, Bialik E, Walz MM, Öhrwall G, Werner J, Rubensson JE, Jungwirth P, Björneholm O. Anomalous surface behavior of hydrated guanidinium ions due to ion pairing. J Chem Phys 2018; 148:144508. [PMID: 29655316 DOI: 10.1063/1.5024348] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Surface affinity of aqueous guanidinium chloride (GdmCl) is compared to that of aqueous tetrapropylammonium chloride (TPACl) upon addition of sodium chloride (NaCl) or disodium sulfate (Na2SO4). The experimental results have been acquired using the surface sensitive technique X-ray photoelectron spectroscopy on a liquid jet. Molecular dynamics simulations have been used to produce radial distribution functions and surface density plots. The surface affinities of both TPA+ and Gdm+ increase upon adding NaCl to the solution. With the addition of Na2SO4, the surface affinity of TPA+ increases, while that of Gdm+ decreases. From the results of MD simulations it is seen that Gdm+ and SO42- ions form pairs. This finding can be used to explain the decreased surface affinity of Gdm+ when co-dissolved with SO42- ions. Since SO42- ions avoid the surface due to the double charge and strong water interaction, the Gdm+-SO42- ion pair resides deeper in the solutions' bulk than the Gdm+ ions. Since TPA+ does not form ion pairs with SO42-, the TPA+ ions are instead enriched at the surface.
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Affiliation(s)
- Victor Ekholm
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Mario Vazdar
- Rudjer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Philip E Mason
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Erik Bialik
- Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Marie-Madeleine Walz
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden
| | - Gunnar Öhrwall
- MAX IV Laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
| | - Josephina Werner
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Jan-Erik Rubensson
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Olle Björneholm
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
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19
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The unusual visible fluorescence violating the Kasha's rule suggests the aggregation of guanidinium carbonate in its aqueous medium. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Vigorita M, Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction ability of TMAO toward different denaturing agents. Biopolymers 2018; 109:e23104. [DOI: 10.1002/bip.23104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/22/2017] [Accepted: 01/16/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Marilisa Vigorita
- Dipartimento di Scienze e Tecnologie; Università degli Studi del Sannio, Via Port'Arsa 11; Benevento 82100 Italy
| | - Serena Cozzolino
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
| | - Rosario Oliva
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie; Università degli Studi del Sannio, Via Port'Arsa 11; Benevento 82100 Italy
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
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21
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Merlino A, Pontillo N, Graziano G. A driving force for polypeptide and protein collapse. Phys Chem Chem Phys 2017; 19:751-756. [DOI: 10.1039/c6cp07397b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polypeptide collapse is driven by the solvent-excluded volume decrease, the presence of nonpolar side chains is not so important.
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Affiliation(s)
- Antonello Merlino
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- 80126 Napoli
- Italy
| | - Nicola Pontillo
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- 80126 Napoli
- Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio
- 82100 Benevento
- Italy
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22
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Abstract
AbstractA general theory of hydrophobic hydration and pairwise hydrophobic interaction has been developed in the last years. The main ingredient is the recognition that: (a) cavity creation (necessary to insert a solute molecule into water) causes a solvent-excluded volume effect that leads to a loss in the translational entropy of water molecules; (b) the merging of two cavities (necessary to form the contact minimum configuration of two nonpolar molecules) causes a decrease in the solvent-excluded volume effect and so an increase in the translational entropy of water molecules. The performance of the theoretical approach is tested by reproducing both the hydration thermodynamics of xenon and the thermodynamics associated with the formation of the contact minimum configuration of two xenon atoms, over a large temperature range.
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Affiliation(s)
- Giuseppe Graziano
- 1Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port’Arsa 11 – 82100 Benevento, Italy
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23
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Excluded volume contribution to cosolvent-mediated modulation of macromolecular folding and binding reactions. Biophys Chem 2016; 209:1-8. [DOI: 10.1016/j.bpc.2015.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/31/2015] [Accepted: 11/01/2015] [Indexed: 11/19/2022]
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24
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Pica A, Graziano G. On urea's ability to stabilize the globule state of poly(N-isopropylacrylamide). Phys Chem Chem Phys 2016; 18:14426-33. [DOI: 10.1039/c5cp07507f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urea stabilizes the PNIPAM globule state because the increase in the solvent-excluded volume effect overwhelms the direct energetic interactions with the PNIPAM surface.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II Complesso Universitario di Monte Sant'Angelo
- Via Cintia – 80126 Napoli
- Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio
- Via Port'Arsa 11 – 82100 Benevento
- Italy
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25
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Pica A, Graziano G. An alternative explanation of the cononsolvency of poly(N-isopropylacrylamide) in water–methanol solutions. Phys Chem Chem Phys 2016; 18:25601-25608. [DOI: 10.1039/c6cp04753j] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Water/methanol competition in the interaction with PNIPAM causes a decrease in the magnitude of attractive energy, leading to cononsolvency.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- 80126 Napoli
- Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio
- 82100 Benevento
- Italy
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26
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On the effect of hydrostatic pressure on the conformational stability of globular proteins. Biopolymers 2015; 103:711-8. [DOI: 10.1002/bip.22736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 11/07/2022]
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27
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Chalikian TV. Effect of cosolvent on protein stability: a theoretical investigation. J Chem Phys 2015; 141:22D504. [PMID: 25494775 DOI: 10.1063/1.4895530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a statistical thermodynamic algorithm for analyzing solvent-induced folding/unfolding transitions of proteins. The energetics of protein transitions is governed by the interplay between the cavity formation contribution and the term reflecting direct solute-cosolvent interactions. The latter is viewed as an exchange reaction in which the binding of a cosolvent to a solute is accompanied by release of waters of hydration to the bulk. Our model clearly differentiates between the stoichiometric and non-stoichiometric interactions of solvent or co-solvent molecules with a solute. We analyzed the urea- and glycine betaine (GB)-induced conformational transitions of model proteins of varying size which are geometrically approximated by a sphere in their native state and a spherocylinder in their unfolded state. The free energy of cavity formation and its changes accompanying protein transitions were computed based on the concepts of scaled particle theory. The free energy of direct solute-cosolvent interactions were analyzed using empirical parameters previously determined for urea and GB interactions with low molecular weight model compounds. Our computations correctly capture the mode of action of urea and GB and yield realistic numbers for (∂ΔG°/∂a3)T,P which are related to the m-values of protein denaturation. Urea is characterized by negative values of (∂ΔG°/∂a3)T,P within the entire range of urea concentrations analyzed. At concentrations below ∼1 M, GB exhibits positive values of (∂ΔG°/∂a3)T,P which turn positive at higher GB concentrations. The balance between the thermodynamic contributions of cavity formation and direct solute-cosolvent interactions that, ultimately, defines the mode of cosolvent action is extremely subtle. A 20% increase or decrease in the equilibrium constant for solute-cosolvent binding may change the sign of (∂ΔG°/∂a3)T,P thereby altering the mode of cosolvent action (stabilizing to destabilizing or vice versa).
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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28
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Pica A, Graziano G. On the Effect of Sodium Chloride and Sodium Sulfate on Cold Denaturation. PLoS One 2015; 10:e0133550. [PMID: 26197394 PMCID: PMC4511003 DOI: 10.1371/journal.pone.0133550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 11/28/2022] Open
Abstract
Both sodium chloride and sodium sulfate are able to stabilize yeast frataxin, causing an overall increase of its thermodynamic stability curve, with a decrease in the cold denaturation temperature and an increase in the hot denaturation one. The influence of low concentrations of these two salts on yeast frataxin stability can be assessed by the application of a theoretical model based on scaled particle theory. First developed to figure out the mechanism underlying cold denaturation in water, this model is able to predict the stabilization of globular proteins provided by these two salts. The densities of the salt solutions and their temperature dependence play a fundamental role.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia – 80126 Napoli, Italy
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port’Arsa 11–82100 Benevento, Italy
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29
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Heiles S, Cooper RJ, DiTucci MJ, Williams ER. Hydration of guanidinium depends on its local environment. Chem Sci 2015; 6:3420-3429. [PMID: 28706704 PMCID: PMC5490459 DOI: 10.1039/c5sc00618j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/14/2015] [Indexed: 01/10/2023] Open
Abstract
Hydration of gaseous guanidinium (Gdm+) with up to 100 water molecules attached was investigated using infrared photodissociation spectroscopy in the hydrogen stretch region between 2900 and 3800 cm-1. Comparisons to IR spectra of low-energy computed structures indicate that at small cluster size, water interacts strongly with Gdm+ with three inner shell water molecules each accepting two hydrogen bonds from adjacent NH2 groups in Gdm+. Comparisons to results for tetramethylammonium (TMA+) and Na+ enable structural information for larger clusters to be obtained. The similarity in the bonded OH region for Gdm(H2O)20+vs. Gdm(H2O)100+ and the similarity in the bonded OH regions between Gdm+ and TMA+ but not Na+ for clusters with <50 water molecules indicate that Gdm+ does not significantly affect the hydrogen-bonding network of water molecules at large size. These results indicate that the hydration around Gdm+ changes for clusters with more than about eight water molecules to one in which inner shell water molecules only accept a single H-bond from Gdm+. More effective H-bonding drives this change in inner-shell water molecule binding to other water molecules. These results show that hydration of Gdm+ depends on its local environment, and that Gdm+ will interact with water even more strongly in an environment where water is partially excluded, such as the surface of a protein. This enhanced hydration in a limited solvation environment may provide new insights into the effectiveness of Gdm+ as a protein denaturant.
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Affiliation(s)
- Sven Heiles
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Richard J Cooper
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Matthew J DiTucci
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Evan R Williams
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
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30
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Pica A, Graziano G. On the effect of sodium salts on the coil-to-globule transition of poly(N-isopropylacrylamide). Phys Chem Chem Phys 2015; 17:27750-7. [DOI: 10.1039/c5cp04094a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Addition of sodium salts to water increases the density, thereby increasing the magnitude of the solvent-excluded volume effect and stabilizing the globule state of PNIPAM.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- Naples
- Italy
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31
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Macdonald RD, Khajehpour M. Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions. Biophys Chem 2014; 196:25-32. [PMID: 25268875 DOI: 10.1016/j.bpc.2014.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022]
Abstract
Guanidinium chloride (GdmCl) is one of the most common protein denaturants. Although GdmCl is well known in the field of protein folding, the mechanism by which it denatures proteins is not well understood. In fact, there are few studies looking at its effects on hydrophobic interactions. In this work the effect of GdmCl on hydrophobic interactions has been studied by observing how the denaturant influences model systems of phenyl and alkyl hydrophobic contact pairs. Contact pair formation is monitored through the use of fluorescence spectroscopy, i.e., measuring the intrinsic phenol fluorescence being quenched by carboxylate ions. Hydrophobic interactions are isolated from other interactions through a previously developed methodology. The results show that GdmCl does not significantly affect hydrophobic interactions between small moieties such as methyl groups and phenol; while on the other hand, the interaction of larger hydrophobes such as hexyl and heptyl groups with phenol is significantly destabilized.
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Affiliation(s)
- Ryan D Macdonald
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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32
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Abstract
A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy.
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33
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An alternative explanation for the collapse of unfolded proteins in an aqueous mixture of urea and guanidinium chloride. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Cooper RJ, Heiles S, DiTucci MJ, Williams ER. Hydration of Guanidinium: Second Shell Formation at Small Cluster Size. J Phys Chem A 2014; 118:5657-66. [DOI: 10.1021/jp506429a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Richard J. Cooper
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Sven Heiles
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew J. DiTucci
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
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35
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Molecular bases of protein halotolerance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:850-8. [DOI: 10.1016/j.bbapap.2014.02.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 02/04/2023]
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36
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Graziano G. Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane. J Chem Phys 2014; 140:094503. [DOI: 10.1063/1.4866972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Why Do Tetrapropylammonium Chloride and Sulphate Salts Destabilize the Native State of Globular Proteins? ScientificWorldJournal 2014; 2014:870106. [PMID: 24616650 PMCID: PMC3925590 DOI: 10.1155/2014/870106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/04/2013] [Indexed: 11/25/2022] Open
Abstract
It has recently been shown that aqueous solutions of tetrapropylammonium chloride and sulphate salts destabilize the folded conformation of Trp-peptides (Dempsey et al., 2011). This result is rationalized by the application of a statistical thermodynamic approach (Graziano, 2010). It is shown that the magnitude of the solvent-excluded volume effect, the main contribution for the native state stability, decreases in both aqueous 2 M TPACl solution and aqueous 1 M TPA2SO4 solution. This happens because TPA+ ions are so large in size and interact so weakly with water molecules, due to their very low charge density, to be able to counteract the electrostrictive effect of chloride and sulphate ions on the water structure, so that the density of their aqueous solutions is smaller or only slightly larger than that of water.
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38
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Graziano G. A view on the dogma of hydrophobic imperialism in protein folding. J Biomol Struct Dyn 2013; 31:1016-9. [DOI: 10.1080/07391102.2012.748545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Binding, unfolding and refolding dynamics of serum albumins. Biochim Biophys Acta Gen Subj 2013; 1830:5394-404. [PMID: 23707713 DOI: 10.1016/j.bbagen.2013.05.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND The serum albumins (human and bovine serum albumin) occupy a seminal position among all proteins investigated until today as they are the most abundant circulatory proteins. They play the major role of a transporter of many bio-active substances which include various fatty acids, drug molecules, and amino acids to the target cells. Hence, studying the interaction of these serum albumins with different binding agents has attracted enormous research interests from decades. The nature and magnitude of these bindings have direct consequence on drug delivery, pharmacokinetics, therapeutic efficacy and drug design and control. SCOPE OF THE REVIEW In the present review, we summarize the binding characteristics of both the serum albumins with surfactants, lipids and vesicles, polymers and dendrimers, nanomaterials and drugs. Finally we have reviewed the effect of various chemical and physical denaturants on these albumins with a special emphasis on protein unfolding and refolding dynamics. MAJOR CONCLUSIONS The topic of binding and dynamics of protein unfolding and refolding spans across all areas of inter-disciplinary sciences and will benefit clinical toxicology and medicines. The extensive data from several contemporary research based on albumins will help us to understand protein dynamics in a more illustrious manner. GENERAL SIGNIFICANCE These data have immense significance in understanding and unravelling the mechanisms of protein unfolding/refolding and thus can pave the way to prevent protein mis-folding/aggregation which sometimes leads to severe consequences like Parkinson's and Alzheimer's diseases. This article is a part of a Special Issue entitled Serum Albumin. This article is part of a Special Issue entitled Serum Albumin.
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Hunger J, Neueder R, Buchner R, Apelblat A. A Conductance Study of Guanidinium Chloride, Thiocyanate, Sulfate, and Carbonate in Dilute Aqueous Solutions: Ion-Association and Carbonate Hydrolysis Effects. J Phys Chem B 2013; 117:615-22. [DOI: 10.1021/jp311425v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Johannes Hunger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Roland Neueder
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Alexander Apelblat
- Department of Chemical
Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
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41
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Graziano G. On the signature of the hydrophobic effect at a single molecule level. Phys Chem Chem Phys 2013; 15:7389-95. [DOI: 10.1039/c3cp50616a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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43
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Pica A, Russo Krauss I, Castellano I, La Cara F, Graziano G, Sica F, Merlino A. Effect of NaCl on the conformational stability of the thermophilic γ-glutamyltranspeptidase from Geobacillus thermodenitrificans: Implication for globular protein halotolerance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:149-57. [DOI: 10.1016/j.bbapap.2012.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/10/2012] [Accepted: 09/27/2012] [Indexed: 12/28/2022]
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44
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Shao Q, Fan Y, Yang L, Gao YQ. Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein. J Chem Theory Comput 2012; 8:4364-73. [DOI: 10.1021/ct3002267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Qiang Shao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Yubo Fan
- Bioinformatics and
Bioengineering
Program, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, Texas 77030, United
States
| | - Lijiang Yang
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
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45
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Graziano G. On the effect of trimethylamine N-oxide on the conformational equilibrium of the chaperone Hsp90. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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46
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Pica A, Russo Krauss I, Castellano I, Rossi M, La Cara F, Graziano G, Sica F, Merlino A. Exploring the unfolding mechanism of γ-glutamyltranspeptidases: the case of the thermophilic enzyme from Geobacillus thermodenitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:571-7. [PMID: 22322192 DOI: 10.1016/j.bbapap.2012.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/19/2012] [Accepted: 01/23/2012] [Indexed: 10/14/2022]
Abstract
γ-glutamyltranspeptidases (γ-GTs) are ubiquitous enzymes that catalyze the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. These enzymes are generally synthesized as precursor proteins, which undergo an intra-molecular autocatalytic cleavage yielding a large and a small subunit. In this study, circular dichroism and intrinsic fluorescence measurements have been used to investigate the structural features and the temperature- and guanidinium hydrochloride (GdnHCl)-induced unfolding of the mature form of the γ-GT from Geobacillus thermodenitrificans (GthGT) and that of its T353A mutant, which represents a mimic of the precursor protein. Data indicate that a) the mutant and the mature GthGT have a different secondary structure content and a slightly different exposure of hydrophobic regions, b) the thermal unfolding processes of both GthGT forms occur through a three-state model, characterized by a stable intermediate species, whereas chemical denaturations proceed through a single transition, c) both GthGT forms exhibit remarkable stability against temperature, but they do not display a strong resistance to the denaturing action of GdnHCl. These findings suggest that electrostatic interactions significantly contribute to the protein stability and that both the precursor and the mature form of GthGT assume compact and stable conformations to resist to the extreme temperatures where G. thermodenidrificans lives. Owing to its thermostability and unique catalytic properties, GthGT is an excellent candidate to be used as a glutaminase in food industry.
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Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples, Naples, Italy
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47
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Graziano G. On the effect of low concentrations of alcohols on the conformational stability of globular proteins. Phys Chem Chem Phys 2012; 14:2769-73. [DOI: 10.1039/c2cp23463g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Graziano G. A rationale for the contrasting activity (towards globular proteins) of tert-butyl alcohol and trimethylamine N-oxide. Phys Chem Chem Phys 2012; 14:13088-94. [DOI: 10.1039/c2cp41363a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Graziano G. How does sucrose stabilize the native state of globular proteins? Int J Biol Macromol 2011; 50:230-5. [PMID: 22085755 DOI: 10.1016/j.ijbiomac.2011.10.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/17/2022]
Abstract
It is well known that sucrose stabilizes the native state of globular proteins against both chemical denaturants and temperature. A largely accepted explanation of sucrose-induced stabilization is not yet emerged. It is shown that the same theoretical approach able to rationalize the occurrence of cold denaturation, the contrasting role of GdmCl and Gdm(2)SO(4), and the TMAO counteraction of urea denaturing activity [PCCP 12 (2010) 14245; PCCP 13 (2011) 12008; PCCP 13 (2011) 17689] works well also in the case of sucrose. The solvent-excluded volume effect plays the fundamental role because sucrose addition to water causes a marked increase in volume packing density due to the large size of sucrose molecules, that act as crowding agents.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Benevento, Italy.
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Graziano G. How does trimethylamine N-oxide counteract the denaturing activity of urea? Phys Chem Chem Phys 2011; 13:17689-95. [PMID: 21894338 DOI: 10.1039/c1cp22176k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trimethylamine N-oxide, TMAO, stabilizes globular proteins and is able to counteract the denaturing activity of urea. The mechanism of this counteraction has remained elusive up to now. A rationalization is proposed grounded on the same theoretical model used to clarify the origin of cold denaturation, and the denaturing activity of GdmCl versus the stabilizing one of Gdm(2)SO(4) [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252; G. Graziano, Phys. Chem. Chem. Phys., 2011, 13, 12008-12014]. The fundamental quantities are: (a) the difference in the solvent-excluded volume on passing from the N-state to the D-state, calculated in water and in aqueous osmolyte solution; (b) the difference in energetic attractions of the N-state and the D-state with the surrounding solvent molecules, calculated in water and in aqueous osmolyte solution. In aqueous 8 M urea + 4 M TMAO solution, the first quantity is so large and positive to counteract the second one that is large and negative due to preferential binding of urea molecules to the protein surface. This happens because aqueous 8 M urea + 4 M TMAO solution has a volume packing density markedly larger than that of water, rendering the cavity creation process much more costly. The volume packing density increase reflects the strength of the attractions of water molecules with both urea and TMAO molecules. This mechanism readily explains why TMAO counteraction is operative even though urea molecules are preferentially located on the protein surface.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.
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