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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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Faggiano S, Ronda L, Bruno S, Abbruzzetti S, Viappiani C, Bettati S, Mozzarelli A. From hemoglobin allostery to hemoglobin-based oxygen carriers. Mol Aspects Med 2021; 84:101050. [PMID: 34776270 DOI: 10.1016/j.mam.2021.101050] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022]
Abstract
Hemoglobin (Hb) plays its vital role through structural and functional properties evolutionarily optimized to work within red blood cells, i.e., the tetrameric assembly, well-defined oxygen affinity, positive cooperativity, and heterotropic allosteric regulation by protons, chloride and 2,3-diphosphoglycerate. Outside red blood cells, the Hb tetramer dissociates into dimers, which exhibit high oxygen affinity and neither cooperativity nor allosteric regulation. They are prone to extravasate, thus scavenging endothelial NO and causing hypertension, and cause nephrotoxicity. In addition, they are more prone to autoxidation, generating radicals. The need to overcome the adverse effects associated with cell-free Hb has always been a major hurdle in the development of substitutes of allogeneic blood transfusions for all clinical situations where blood is unavailable or cannot be used due to, for example, religious objections. This class of therapeutics, indicated as hemoglobin-based oxygen carriers (HBOCs), is formed by genetically and/or chemically modified Hbs. Many efforts were devoted to the exploitation of the wealth of biochemical and biophysical information available on Hb structure, function, and dynamics to design safe HBOCs, overcoming the negative effects of free plasma Hb. Unfortunately, so far, no HBOC has been approved by FDA and EMA, except for compassionate use. However, the unmet clinical needs that triggered intensive investigations more than fifty years ago are still awaiting an answer. Recently, HBOCs "repositioning" has led to their successful application in organ perfusion fluids.
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Affiliation(s)
- Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Luca Ronda
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy.
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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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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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Roche CJ, Dantsker D, Alayash AI, Friedman JM. Enhanced nitrite reductase activity associated with the haptoglobin complexed hemoglobin dimer: functional and antioxidative implications. Nitric Oxide 2012; 27:32-9. [PMID: 22521791 DOI: 10.1016/j.niox.2012.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/29/2012] [Accepted: 04/11/2012] [Indexed: 10/28/2022]
Abstract
The presence of acellular hemoglobin (Hb) within the circulation is generally viewed as a pathological state that can result in toxic consequences. Haptoglobin (Hp), a globular protein found in the plasma, binds with high avidity the αβ dimers derived from the dissociation of Hb tetramer and thus helps clear free Hb. More recently there have been compelling indications that the redox properties of the Hp bound dimer (Hb-Hp) may play a more active role in controlling toxicity by limiting the potential tissue damage caused by propagation of the free-radicals generated within the heme containing globin chains. The present study further examines the potential protective effect of Hp through its impact on the production of nitric oxide (NO) from nitrite through nitrite reductase activity of the Hp bound αβ Hb dimer. The presented results show that the Hb dimer in the Hb-Hp complex has oxygen binding, CO recombination and spectroscopic properties consistent with an Hb species having properties similar to but not exactly the same as the R quaternary state of the Hb tetramer. Consistent with these observations is the finding that the initial nitrite reductase rate for Hb-Hp is approximately ten times that of HbA under the same conditions. These results in conjunction with the earlier redox properties of the Hb-Hp are discussed in terms of limiting the pathophysiological consequences of acellular Hb in the circulation.
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Affiliation(s)
- Camille J Roche
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Hemoglobin loaded polymeric nanoparticles: Preparation and characterizations. Eur J Pharm Sci 2011; 43:57-64. [DOI: 10.1016/j.ejps.2011.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/08/2011] [Accepted: 03/23/2011] [Indexed: 11/19/2022]
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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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Bettati S, Viappiani C, Mozzarelli A. Hemoglobin, an “evergreen” red protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1317-24. [DOI: 10.1016/j.bbapap.2009.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 03/23/2009] [Indexed: 10/20/2022]
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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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Ronda L, Bruno S, Abbruzzetti S, Viappiani C, Bettati S. Ligand reactivity and allosteric regulation of hemoglobin-based oxygen carriers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1365-77. [DOI: 10.1016/j.bbapap.2008.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/21/2008] [Accepted: 04/24/2008] [Indexed: 01/05/2023]
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Ronda L, Abbruzzetti S, Bruno S, Bettati S, Mozzarelli A, Viappiani C. Ligand-Induced Tertiary Relaxations During the T-to-R Quaternary Transition in Hemoglobin. J Phys Chem B 2008; 112:12790-4. [DOI: 10.1021/jp803040j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Ronda
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefania Abbruzzetti
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bettati
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Cristiano Viappiani
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
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Shibayama N. Circular dichroism study on the early folding events of β-lactoglobulin entrapped in wet silica gels. FEBS Lett 2008; 582:2668-72. [DOI: 10.1016/j.febslet.2008.06.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 06/17/2008] [Accepted: 06/20/2008] [Indexed: 11/27/2022]
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Hydration dependent dynamics in sol–gel encapsulated myoglobin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:543-9. [DOI: 10.1007/s00249-007-0249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 11/15/2007] [Accepted: 11/20/2007] [Indexed: 10/22/2022]
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