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A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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Wohlfromm T, Vogel M. On the coupling of protein and water dynamics in confinement: Spatially resolved molecular dynamics simulation studies. J Chem Phys 2019; 150:245101. [DOI: 10.1063/1.5097777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Timothy Wohlfromm
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Fomina M, Schirò G, Cupane A. Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectroscopy. Biophys Chem 2013; 185:25-31. [PMID: 24309207 DOI: 10.1016/j.bpc.2013.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022]
Abstract
In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein+hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin+hydration water system and, thermodynamically, to decrease the glass transition temperature; these effects tend to saturate at h values greater than ~0.3. Moreover, the calorimetric scans put in evidence the occurrence of an endothermic peak whose onset temperature is located at ~230K independent of hydration. From the point of view of the protein equilibrium fluctuations, while the amplitude of anharmonic mean square displacements is found to increase with hydration, their onset temperature (i.e. the onset temperature of the well known "protein dynamical transition") is hydration independent. On the basis of the above results, the relevance of protein+hydration water relaxations and of the thermodynamic state of hydration water to the onset of the protein dynamical transition is discussed.
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Affiliation(s)
- Margarita Fomina
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy
| | - Giorgio Schirò
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy
| | - Antonio Cupane
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy.
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Thörn C, Gustafsson H, Olsson L. Immobilization of feruloyl esterases in mesoporous materials leads to improved transesterification yield. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bellavia G, Giuffrida S, Cottone G, Cupane A, Cordone L. Protein thermal denaturation and matrix glass transition in different protein-trehalose-water systems. J Phys Chem B 2011; 115:6340-6. [PMID: 21488647 DOI: 10.1021/jp201378y] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biopreservation by saccharides is a widely studied issue due to its scientific and technological importance; in particular, ternary amorphous protein-saccharide-water systems are extensively exploited to model the characteristics of the in vivo biopreservation process. We present here a differential scanning calorimetry (DSC) study on amorphous trehalose-water systems with embedded different proteins (myoglobin, lysozyme, BSA, hemoglobin), which differ for charge, surface, and volume properties. In our study, the protein/trehalose molar ratio is kept constant at 1/40, while the water/sugar molar ratio is varied between 2 and 300; results are compared with those obtained for binary trehalose-water systems. DSC upscans offer the possibility of investigating, in the same measurement, the thermodynamic properties of the matrix (glass transition, T(g)) and the functional properties of the encapsulated protein (thermal denaturation, T(den)). At high-to-intermediate hydration, the presence of the proteins increases the glass transition temperature of the encapsulating matrix. The effect mainly depends on size properties, and it can be ascribed to confinement exerted by the protein on the trehalose-water solvent. Conversely, at low hydration, lower T(g) values are measured in the presence of proteins: the lack of water promotes sugar-protein interactions, thus weakening the confinement effect and softening the matrix with respect to the binary system. A parallel T(den) increase is also observed; remarkably, this stabilization can reach ∼70 K at low hydration, a finding potentially of high biotechnological relevance. A linear relationship between T(g) and T(den) is also observed, in line with previous results; this finding suggests that collective water-trehalose interactions, responsible for the glass transition, also influence the protein denaturation.
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Affiliation(s)
- Giuseppe Bellavia
- Dipartimento di Fisica, Università di Palermo and CNISM,Via Archirafi 36, I-90123 Palermo, Italy
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Natali F, Marasini C, Ferrando R, Gliozzi A. Study of Protein Dynamics vs. Amyloid Formation. ACTA ACUST UNITED AC 2010. [DOI: 10.1524/zpch.2010.6100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Protein fibril formation has been often associated to manifestation of serious and devastating amyloyd diseases, including Alzheimer and BSA. The main mechanism for the formation of amyloid fibrils is the accumulation of protein aggregates in body´s organs.In this paper, we try to compare the dynamical behaviour of two amyloidogenic proteins, the Insulin and the Myoglobin. Insulin has been chosen for its pharmacological extensive use in diabete´s therapy, while Myoglobin is used as control, since its dynamics is now largely known. The investigation has been performed through incoherent elastic neutron scattering over a wide temperature range. Our results suggest an enhanced stiffness of Insulin with respect to Myoglobin.
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Schiró G, Caronna C, Natali F, Cupane A. Molecular origin and hydration dependence of protein anharmonicity: an elastic neutron scattering study. Phys Chem Chem Phys 2010; 12:10215-20. [DOI: 10.1039/c003482g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bellavia G, Cottone G, Giuffrida S, Cupane A, Cordone L. Thermal denaturation of myoglobin in water--disaccharide matrixes: relation with the glass transition of the system. J Phys Chem B 2009; 113:11543-9. [PMID: 19719261 DOI: 10.1021/jp9041342] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins embedded in glassy saccharide systems are protected against adverse environmental conditions [Crowe et al. Annu. Rev. Physiol. 1998, 60, 73-103]. To further characterize this process, we studied the relationship between the glass transition temperature of the protein-containing saccharide system (T(g)) and the temperature of thermal denaturation of the embedded protein (T(den)). To this end, we studied by differential scanning calorimetry the thermal denaturation of ferric myoglobin in water/disaccharide mixtures containing nonreducing (trehalose, sucrose) or reducing (maltose, lactose) disaccharides. All the samples studied are, at room temperature, liquid systems whose viscosity varies from very low to very large values, depending on the water content. At a high water/saccharide mole ratio, homogeneous glass formation does not occur; regions of glass form, whose T(g) does not vary by varying the saccharide content, and the disaccharide barely affects the myoglobin denaturation temperature. At a suitably low water/saccharide mole ratio, by lowering the temperature, the systems undergo transition to the glassy state whose T(g) is determined by the water content; the Gordon-Taylor relationship between T(g) and the water/disaccharide mole ratio is obeyed; and T(den) increases by decreasing the hydration regardless of the disaccharide, such effect being entropy-driven. The presence of the protein was found to lower the T(g). Furthermore, for nonreducing disaccharides, plots of T(den) vs T(g) give linear correlations, whereas for reducing disaccharides, data exhibit an erratic behavior below a critical water/disaccharide ratio. We ascribe this behavior to the likelihood that in the latter samples, proteins have undergone Maillard reaction before thermal denaturation.
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Affiliation(s)
- Giuseppe Bellavia
- Dipartimento di Scienze Fisiche ed Astronomiche, Universita di Palermo and CNISM, Via Archirafi 36, Palermo, Italy I-90123
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Schirò G, Cupane A, Vitrano E, Bruni F. Dielectric Relaxations in Confined Hydrated Myoglobin. J Phys Chem B 2009; 113:9606-13. [DOI: 10.1021/jp901420r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giorgio Schirò
- CNISM and Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Palermo, Italy, and CNISM and Dipartimento di Fisica “E. Amaldi”, Università di Roma Tre, Rome, Italy
| | - Antonio Cupane
- CNISM and Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Palermo, Italy, and CNISM and Dipartimento di Fisica “E. Amaldi”, Università di Roma Tre, Rome, Italy
| | - Eugenio Vitrano
- CNISM and Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Palermo, Italy, and CNISM and Dipartimento di Fisica “E. Amaldi”, Università di Roma Tre, Rome, Italy
| | - Fabio Bruni
- CNISM and Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Palermo, Italy, and CNISM and Dipartimento di Fisica “E. Amaldi”, Università di Roma Tre, Rome, Italy
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Francesca N, Peters J, Russo D, Barbieri S, Chiapponi C, Cupane A, Deriu A, Di Bari MT, Farhi E, Gerelli Y, Mariani P, Paciaroni A, Rivasseau C, Schirò G, Sonvico F. IN13 Backscattering Spectrometer at ILL: Looking for Motions in Biological Macromolecules and Organisms. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10448630802474083] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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