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Some Clues about Enzymes from Psychrophilic Microorganisms. Microorganisms 2022; 10:microorganisms10061161. [PMID: 35744679 PMCID: PMC9227589 DOI: 10.3390/microorganisms10061161] [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: 04/30/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.
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Graziano G. Contrasting the hydration thermodynamics of methane and methanol. Phys Chem Chem Phys 2019; 21:21418-21430. [DOI: 10.1039/c9cp03213d] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydration thermodynamics of methane and methanol depend on the cavity creation work and energy of van der Waals and H-bonding attractions.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio, Via Francesco de Sanctis snc
- 82100 Benevento
- Italy
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Pan A, Mandal B, Rakshit AK, Moulik SP. A Rational Study of the Origin and Generality of Anti-Enthalpy–Entropy Compensation (AEEC) Phenomenon. Z PHYS CHEM 2017. [DOI: 10.1515/zpch-2017-1007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In addition to enthalpy–entropy compensation (EEC), anti-enthalpy–entropy compensation (AEEC) phenomenon is also found in literature. The reports on the latter are limited, and analyses and justifications are so far unclear. Herein we present demonstration on the nature and possibility of the AEEC phenomenon. Although literature reports so far have mostly shown linear AEEC, we have found both linear and non-linear dependences. The non-linearity we consider arises from large “free energy window” (FEW) like EEC, recently presented and discussed. Attempts have been made to rationalize the observations in terms of solvation–desolvation phenomenon of the involved processes anticipated in previous studies. We have found that enthalpy and entropy of formation of gaseous and solid materials may also exhibit AEEC, it can be thus classified as a global phenomenon. In addition to AEEC, the phenomenon of no-enthalpy–entropy compensation (NEEC) is also reported. Thus, the phenomena EEC, AEEC and NEEC are thermodynamic puzzles that require close attention and analysis. With the help of wide range of physical chemical processes, an elaborate general understanding of the linear and non-linear AEEC phenomena has been attempted. The experimental data herein used are collected from literature reports, new measurements were not done. A variety of examples have supported possible generality of AEEC.
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Affiliation(s)
- Animesh Pan
- Centre for Surface Science , Department of Chemistry , Jadavpur University , Kolkata 700032 , India , Tel.: +91-33-2414-6411/+918820454516, Fax: +91-33-2414-6266
- Department of Chemical Engineering , University of Rhode Island , 16 Greenhouse Road , Kingston, RI 02881 , USA
| | - Bithika Mandal
- Centre for Surface Science, Department of Chemistry , Jadavpur University , Kolkata 700032 , India
| | - Animesh K. Rakshit
- Indian Society for Surface Science and Technology , Department of Chemistry , Jadavpur University , Kolkata 700032 , India
| | - Satya P. Moulik
- Centre for Surface Science, Department of Chemistry , Jadavpur University , Kolkata 700032 , India
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Pan A, Kar T, Rakshit AK, Moulik SP. Enthalpy–Entropy Compensation (EEC) Effect: Decisive Role of Free Energy. J Phys Chem B 2016; 120:10531-10539. [DOI: 10.1021/acs.jpcb.6b05890] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Animesh Pan
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Tanmoy Kar
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Animesh K. Rakshit
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Satya P. Moulik
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
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Pan A, Rakshit AK, Moulik SP. Micellization thermodynamics and the nature of enthalpy–entropy compensation. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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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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7
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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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8
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Abstract
There is no fundamental difference in enthalpy–entropy compensation between dispersion and electrostatics or between quantum and molecular mechanics.
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Affiliation(s)
- Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund, Sweden
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9
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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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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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12
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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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Graziano G. Contrasting the denaturing effect of guanidinium chloride with the stabilizing effect of guanidinium sulfate. Phys Chem Chem Phys 2011; 13:12008-14. [PMID: 21617819 DOI: 10.1039/c1cp20843h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanidinium chloride, GdmCl, is a strong denaturing agent of globular proteins, whereas guanidinium sulfate, Gdm(2)SO(4), is a stabilizing agent of globular proteins. The stabilizing activity of Gdm(2)SO(4) is unexpected because the denaturant capability of GdmCl is due to direct interactions of Gdm(+) ions with protein surface groups. It is shown that the statistical thermodynamic approach devised to explain the molecular origin of cold denaturation [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252] can provide a rationalization of the different behaviour of GdmCl and Gdm(2)SO(4) towards globular proteins. The fundamental quantity is the reversible work to create in the aqueous solution a cavity suitable to host the D-state and a cavity suitable to host the N-state. In aqueous GdmCl solutions, this contribution is not large enough to overwhelm the conformational entropy gain upon unfolding and the direct attractions between Gdm(+) ions and protein surface groups; in aqueous Gdm(2)SO(4) solutions, it is so large that it overwhelms the two destabilizing contributions. Sulfate ions, due to their high charge density, interact strongly with water molecules producing a number density increase, that, in turn, renders the cavity creation process very costly, reversing the denaturing power of Gdm(+) ions and stabilizing the N-state of globular proteins.
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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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14
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Riccio A, Graziano G. Cold unfolding of β-hairpins: A molecular-level rationalization. Proteins 2011; 79:1739-46. [DOI: 10.1002/prot.22997] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/03/2010] [Accepted: 01/14/2011] [Indexed: 11/11/2022]
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15
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Graziano G. On the molecular origin of cold denaturation of globular proteins. Phys Chem Chem Phys 2010; 12:14245-52. [PMID: 20882232 DOI: 10.1039/c0cp00945h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A polypeptide chain can adopt very different conformations, a fundamental distinguishing feature of which is the water accessible surface area, WASA, that is a measure of the layer around the polypeptide chain where the center of water molecules cannot physically enter, generating a solvent-excluded volume effect. The large WASA decrease associated with the folding of a globular protein leads to a large decrease in the solvent-excluded volume, and so to a large increase in the configurational/translational freedom of water molecules. The latter is a quantity that depends upon temperature. Simple calculations over the -30 to 150 °C temperature range, where liquid water can exist at 1 atm, show that such a gain decreases significantly on lowering the temperature below 0 °C, paralleling the decrease in liquid water density. There will be a temperature where the destabilizing contribution of the polypeptide chain conformational entropy exactly matches the stabilizing contribution of the water configurational/translational entropy, leading to cold denaturation.
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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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Graziano G. Comment on "Entropy/enthalpy compensation: hydrophobic effect, micelles and protein complexes" by E. Fisicaro, C. Compari and A. Braibanti, Phys. Chem. Chem. Phys., 2004, 6, 4156. Phys Chem Chem Phys 2009; 7:1322-3; discussion 1324-5. [PMID: 19791351 DOI: 10.1039/b419095e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio Via Port'Arsa 11, 82100 Benevento, Italy.
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18
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Graziano G. Salting out of methane by sodium chloride: A scaled particle theory study. J Chem Phys 2008; 129:084506. [DOI: 10.1063/1.2972979] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Starikov EB, Nordén B. Enthalpy−Entropy Compensation: A Phantom or Something Useful? J Phys Chem B 2007; 111:14431-5. [DOI: 10.1021/jp075784i] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Evgeni B. Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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21
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Graziano G. Scaled particle theory study of the length scale dependence of cavity thermodynamics in different liquids. J Phys Chem B 2007; 110:11421-6. [PMID: 16771415 DOI: 10.1021/jp0571269] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been noted that the work of cavity creation in water exhibits a crossover behavior, in that its cavity size dependence changes from volume dependence for small cavities to area dependence for larger cavities [Lum, K.; Chandler, D.; Weeks, J. D. J. Phys. Chem. B 1999, 103, 4570]. It is shown here that this behavior can be reproduced using the scaled particle theory in a straightforward manner for six different liquids (water, methanol, ethanol, benzene, cyclohexane, and carbon tetrachloride). It has also been suggested that the crossover is due to a change in the physical mechanism of the process, from one entropy-dominated to another enthalpy-dominated. However, the crossover behavior can be produced using the scaled particle theory without invoking any change in any physical mechanism. Also, the crossover occurs at a length scale of the size of the liquid molecules, as has been pointed out by others. This is the length regime where the work of cavity creation bears little relation to the bulk liquid surface tension. In addition, it is pointed out that cavity creation can always be considered as a purely entropy-driven process, which is usually accompanied by another process with compensating enthalpy and entropy changes.
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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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23
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Barone V. Theoretical and computational chemistry in Italy: an overview. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Ford DM. Enthalpy-entropy compensation is not a general feature of weak association. J Am Chem Soc 2006; 127:16167-70. [PMID: 16287305 DOI: 10.1021/ja054519c] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Relationships between the enthalpy and entropy changes resulting from perturbations of a system have been discussed in the literature for some time. Both positive correlations (compensation) and negative correlations (anti-compensation) between deltaH and DeltaS have been observed in various experimental contexts, including chemical reaction, physical association, solvation, and protein folding. Many examples have been demonstrated to be statistical artifacts, but some are genuine signatures of the perturbations in molecular characteristics. In particular, recent literature claims that compensation is a general feature of bimolecular associations arising from weak intermolecular interactions. We employ a statistical mechanical framework to predict the magnitude and direction of enthalpy-entropy correlation in bimolecular association. The theory links the macroscale thermodynamic correlation to the relationship between the intermolecular potential parameters. Using a harmonic approximation to the Lennard-Jones model and potential parameters taken from the literature, we show examples of both compensation and anti-compensation for gas-phase self-association among five homologous series. Furthermore, an aggregate presentation of data for 48 different chemical species shows no correlation in either direction, for the case of self-association in a dilute gas phase.
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Affiliation(s)
- David M Ford
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, USA.
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Graziano G. On the hydration heat capacity change of benzene. Biophys Chem 2005; 116:137-44. [PMID: 15950826 DOI: 10.1016/j.bpc.2005.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 03/31/2005] [Accepted: 03/31/2005] [Indexed: 11/28/2022]
Abstract
The heat capacity change associated with the hydration of benzene is a large and positive quantity, but it is significantly smaller than that associated with the hydration of an alkane having the same accessible surface area of benzene, the corresponding alkane. This large difference merits attention and should be rationalized. This task is performed by means of the two-state Muller's model for the reorganization of H-bonds. It results that: (a) the hydration shell of both hydrocarbons consists of H-bonds that are enthalpically stronger but slightly more broken than those in bulk water; (b) the hydration shell of benzene consists, on average, of enthalpically slightly weaker H-bonds with respect to the corresponding alkane. The latter feature, due to the presence of the weak benzene-water H-bonds, is the physical cause of the large difference in the hydration heat capacity change, according to the two-state Muller's model.
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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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Graziano G. Comment on “The hydrophobic effect” by B. Widom, P. Bhimalapuram and K. Koga, Phys. Chem. Chem. Phys., 2003,5, 3085. Phys Chem Chem Phys 2004. [DOI: 10.1039/b405824k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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