1
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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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2
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DeMarino C, Schwab A, Pleet M, Mathiesen A, Friedman J, El-Hage N, Kashanchi F. Biodegradable Nanoparticles for Delivery of Therapeutics in CNS Infection. J Neuroimmune Pharmacol 2016; 12:31-50. [PMID: 27372507 DOI: 10.1007/s11481-016-9692-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/12/2016] [Indexed: 12/18/2022]
Abstract
Despite the significant advances in neurological medicine, it remains difficult to treat ailments directly involving the brain. The blood brain barrier (BBB) is a tightly regulated, selectively permeable barrier that restricts access from the blood into the brain extracellular fluid (BEF). Many conditions such as tumors or infections in the brain are difficult to treat due to the fact that drugs and other therapeutic agents are unable to easily pass through this relatively impermeable barrier. Human Immunodeficiency Virus (HIV) presents a particular problem as it is able to remain dormant in the brain for years protected from antiretroviral drugs by the BBB. The development of nanoscale carriers over the past few decades has made possible the delivery of therapies with the potential to overcome membrane barriers and provide specific, targeted delivery. This review seeks to provide a comprehensive overview of the various aspects of nanoparticle formulation and their applications in improving the delivery efficiency of drugs, specifically antiretroviral therapeutics to the brain to treat HIV.
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Affiliation(s)
- Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Angela Schwab
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Allison Mathiesen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Joel Friedman
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Nazira El-Hage
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA.
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3
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Minute F, Hellmann N, Spinozzi F, Ortore MG, Di Muro P, Bubacco L, Beltramini M. Entrapment and characterization of functional allosteric conformers of hemocyanin in sol–gel matrices. RSC Adv 2016. [DOI: 10.1039/c5ra26377h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Entrapment of hemocyanin in sol–gel stabilizes conformations scarcely populated in solution, allowing for their structural and functional analysis.
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Affiliation(s)
- Fabrizio Minute
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Nadja Hellmann
- Institute for Molecular Biophysics
- University of Mainz
- Mainz
- Germany
| | - Francesco Spinozzi
- Department DISVA
- Marche Polytechnic University and CNISM
- I-60131 Ancona
- Italy
| | | | - Paolo Di Muro
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Luigi Bubacco
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
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4
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Jones EM, Monza E, Balakrishnan G, Blouin GC, Mak PJ, Zhu Q, Kincaid JR, Guallar V, Spiro TG. Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study. J Am Chem Soc 2014; 136:10325-39. [PMID: 24991732 PMCID: PMC4353013 DOI: 10.1021/ja503328a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 12/05/2022]
Abstract
The use of hybrid hemoglobin (Hb), with mesoheme substituted for protoheme, allows separate monitoring of the α or β hemes along the allosteric pathway. Using resonance Raman (rR) spectroscopy in silica gel, which greatly slows protein motions, we have observed that the Fe-histidine stretching frequency, νFeHis, which is a monitor of heme reactivity, evolves between frequencies characteristic of the R and T states, for both α or β chains, prior to the quaternary R-T and T-R shifts. Computation of νFeHis, using QM/MM and the conformational search program PELE, produced remarkable agreement with experiment. Analysis of the PELE structures showed that the νFeHis shifts resulted from heme distortion and, in the α chain, Fe-His bond tilting. These results support the tertiary two-state model of ligand binding (Henry et al., Biophys. Chem. 2002, 98, 149). Experimentally, the νFeHis evolution is faster for β than for α chains, and pump-probe rR spectroscopy in solution reveals an inflection in the νFeHis time course at 3 μs for β but not for α hemes, an interval previously shown to be the first step in the R-T transition. In the α chain νFeHis dropped sharply at 20 μs, the final step in the R-T transition. The time courses are fully consistent with recent computational mapping of the R-T transition via conjugate peak refinement by Karplus and co-workers (Fischer et al., Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 5608). The effector molecule IHP was found to lower νFeHis selectively for α chains within the R state, and a binding site in the α1α2 cleft is suggested.
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Affiliation(s)
- Eric M. Jones
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Emanuele Monza
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Gurusamy Balakrishnan
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - George C. Blouin
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Piotr J. Mak
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Qianhong Zhu
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Victor Guallar
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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5
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Mandal SS, Cristiglio V, Lindner P, Bhattacharyya AJ. Small-angle neutron scattering studies of hemoglobin confined inside silica tubes of varying sizes. Chemphyschem 2013; 15:302-9. [PMID: 24339406 DOI: 10.1002/cphc.201300863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/14/2013] [Indexed: 11/08/2022]
Abstract
In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20-200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small-angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si-tube pore diameter. The high radius of gyration (Rg) and polydispersity of Hb in the 20 nm diameter Si-tube indicates that Hb undergoes a significant amount of aggregation. However, for Si-tube diameters greater or equal to 100 nm, the Rg of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (Rg of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native-like non-aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si-tube size is a key parameter for protein stability and structure.
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Affiliation(s)
- Soumit S Mandal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012 (India), Fax: (+91) 80-23601310
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6
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Holmes-Smith AS, Hollas AC, McLoskey D, Hungerford G. Viability of Saccharomyces cerevisiae incorporated within silica and polysaccharide hosts monitored via time-resolved fluorescence. Photochem Photobiol Sci 2013; 12:2186-94. [PMID: 24145860 DOI: 10.1039/c3pp50202c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The viability of Saccharomyces cerevisiae in biocompatible polymers under different growth conditions and studied using time-resolved fluorescence techniques is presented. Two fluorophores, the viscosity sensitive probe 4-(4-(dimethylamino)styryl)-N-methyl-pyridiniumiodine (DASPMI) and the yeast viability stain 2-chloro-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene)-1-phenylquinolinium iodide (FUN-1) are used to elucidate information on the incorporated yeast cell viability. Variations in cell viscosity, which are indicative of the cell state, were obtained using DASPMI. Prior to observing FUN-1 in yeast cells using fluorescence lifetime imaging, its photophysics in solution and heterogeneous media were investigated. Time-resolved emission spectra were measured and analysed to associate lifetimes to the spectral emission. Preliminary results show that monitoring the fluorescence lifetime of FUN-1 may give a useful insight into cellular metabolism. The results indicate that both fluorophores may be used to monitor the entrapped yeast cell viability, which is important for in vitro studies and applications, such as that in the biofuel industry, where Saccharomyces cerevisiae are required to remain active in high ethanol environments.
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Affiliation(s)
- A Sheila Holmes-Smith
- School of Engineering and Built Environment, Glasgow Caledonian University, Cowcaddens Road, Glasgow, G4 0BA, UK.
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7
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Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin. Chem Phys 2013; 430:88-97. [PMID: 24039330 DOI: 10.1016/j.chemphys.2013.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.
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8
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Roche CJ, Cassera MB, Dantsker D, Hirsch RE, Friedman JM. Generating S-nitrosothiols from hemoglobin: mechanisms, conformational dependence, and physiological relevance. J Biol Chem 2013; 288:22408-25. [PMID: 23775069 DOI: 10.1074/jbc.m113.482679] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In vitro, ferrous deoxy-hemes in hemoglobin (Hb) react with nitrite to generate nitric oxide (NO) through a nitrite reductase reaction. In vivo studies indicate Hb with nitrite can be a source of NO bioactivity. The nitrite reductase reaction does not appear to account fully for this activity because free NO is short lived especially within the red blood cell. Thus, the exporting of NO bioactivity both out of the RBC and over a large distance requires an additional mechanism. A nitrite anhydrase (NA) reaction in which N2O3, a potent S-nitrosating agent, is produced through the reaction of NO with ferric heme-bound nitrite has been proposed (Basu, S., Grubina, R., Huang, J., Conradie, J., Huang, Z., Jeffers, A., Jiang, A., He, X., Azarov, I., Seibert, R., Mehta, A., Patel, R., King, S. B., Hogg, N., Ghosh, A., Gladwin, M. T., and Kim-Shapiro, D. B. (2007) Nat. Chem. Biol. 3, 785-794) as a possible mechanism. Legitimate concerns, including physiological relevance and the nature of the mechanism, have been raised concerning the NA reaction. This study addresses these concerns demonstrating NO and nitrite with ferric hemes under near physiological conditions yield an intermediate having the properties of the purported NA heme-bound N2O3 intermediate. The results indicate that ferric heme sites, traditionally viewed as a source of potential toxicity, can be functionally significant, especially for partially oxygenated/partially met-R state Hb that arises from the NO dioxygenation reaction. In the presence of low levels of nitrite and either NO or a suitable reductant such as L-cysteine, these ferric heme sites can function as a generator for the formation of S-nitrosothiols such as S-nitrosoglutathione and, as such, should be considered as a source of RBC-derived and exportable bioactive NO.
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Affiliation(s)
- Camille J Roche
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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9
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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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10
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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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11
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Jones EM, Balakrishnan G, Spiro TG. Heme reactivity is uncoupled from quaternary structure in gel-encapsulated hemoglobin: a resonance Raman spectroscopic study. J Am Chem Soc 2012; 134:3461-71. [PMID: 22263778 PMCID: PMC3307588 DOI: 10.1021/ja210126j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Encapsulation of hemoglobin (Hb) in silica gel preserves structure and function but greatly slows protein motion, thereby providing access to intermediates along the allosteric pathway that are inaccessible in solution. Resonance Raman (RR) spectroscopy with visible and ultraviolet laser excitation provides probes of heme reactivity and of key tertiary and quaternary contacts. These probes were monitored in gels after deoxygenation of oxyHb and after CO binding to deoxyHb, which initiate conformational change in the R-T and T-R directions, respectively. The spectra establish that quaternary structure change in the gel takes a week or more but that the evolution of heme reactivity, as monitored by the Fe-histidine stretching vibration, ν(FeHis), is completed within two days, and is therefore uncoupled from the quaternary structure. Within each quaternary structure, the evolving ν(FeHis) frequencies span the full range of values between those previously associated with the high- and low-affinity end states, R and T. This result supports the tertiary two-state (TTS) model, in which the Hb subunits can adopt high- and low-affinity tertiary structures, r and t, within each quaternary state. The spectra also reveal different tertiary pathways, involving the breaking and reformation of E and F interhelical contacts in the R-T direction but not the T-R direction. In the latter, tertiary motions are restricted by the T quaternary contacts.
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Affiliation(s)
- Eric M. Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
| | - Gurusamy Balakrishnan
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
| | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
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12
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Roche CJ, Malashkevich V, Balazs TC, Dantsker D, Chen Q, Moreira J, Almo SC, Friedman JM, Hirsch RE. Structural and functional studies indicating altered redox properties of hemoglobin E: implications for production of bioactive nitric oxide. J Biol Chem 2011; 286:23452-66. [PMID: 21531715 PMCID: PMC3123109 DOI: 10.1074/jbc.m110.183186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 04/28/2011] [Indexed: 12/22/2022] Open
Abstract
Hemoglobin (Hb) E (β-Glu26Lys) remains an enigma in terms of its contributions to red blood cell (RBC) pathophysiological mechanisms; for example, EE individuals exhibit a mild chronic anemia, and HbE/β-thalassemia individuals show a range of clinical manifestations, including high morbidity and death, often resulting from cardiac dysfunction. The purpose of this study was to determine and evaluate structural and functional consequences of the HbE mutation that might account for the pathophysiology. Functional studies indicate minimal allosteric consequence to both oxygen and carbon monoxide binding properties of the ferrous derivatives of HbE. In contrast, redox-sensitive reactions are clearly impacted as seen in the following: 1) the ∼2.5 times decrease in the rate at which HbE catalyzes nitrite reduction to nitric oxide (NO) relative to HbA, and 2) the accelerated rate of reduction of aquometHbE by L-cysteine (L-Cys). Sol-gel encapsulation studies imply a shift toward a higher redox potential for both the T and R HbE structures that can explain the origin of the reduced nitrite reductase activity of deoxyHbE and the accelerated rate of reduction of aquometHbE by cysteine. Deoxy- and CO HbE crystal structures (derived from crystals grown at or near physiological pH) show loss of hydrogen bonds in the microenvironment of βLys-26 and no significant tertiary conformational perturbations at the allosteric transition sites in the R and T states. Together, these data suggest a model in which the HbE mutation, as a consequence of a relative change in redox properties, decreases the overall rate of Hb-mediated production of bioactive NO.
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Affiliation(s)
| | | | | | | | | | - Juan Moreira
- From the Departments of Physiology and Biophysics
| | | | | | - Rhoda Elison Hirsch
- Medicine (Division of Hematology), and
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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13
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Bisht NK, Abbruzzetti S, Uppal S, Bruno S, Spyrakis F, Mozzarelli A, Viappiani C, Kundu S. Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1042-53. [PMID: 20940062 DOI: 10.1016/j.bbapap.2010.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/26/2010] [Accepted: 09/28/2010] [Indexed: 10/19/2022]
Abstract
Type 1 non-symbiotic rice hemoglobin (rHb1) shows bis-histidyl heme hexacoordination and is capable of binding diatomic ligands reversibly. The biological function is as yet unclear, but the high oxygen affinity makes it unlikely to be involved in oxygen transport. In order to gain insight into possible physiological roles, we have studied CO rebinding kinetics after laser flash photolysis of rHb1 in solution and encapsulated in silica gel. CO rebinding to wt rHb1 in solution occurs through a fast geminate phase with no sign of rebinding from internal docking sites. Encapsulation in silica gel enhances migration to internal cavities. Site-directed mutagenesis of FB10, a residue known to have a key role in the regulation of hexacoordination and ligand affinity, resulted in substantial effects on the rebinding kinetics, partly inhibiting ligand exit to the solvent, enhancing geminate rebinding and enabling ligand migration within the internal cavities. The mutation of HE7, one of the histidyl residues involved in the hexacoordination, prevents hexacoordination, as expected, but also exposes ligand migration through a complex system of cavities. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Nitin Kumar Bisht
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
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14
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Orzeł Ł, Jańczyk A, Brindell M, Stopa G, Stochel G. New trends in the application of laser flash photolysis – case studies. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.507271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ł. Orzeł
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - A. Jańczyk
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - M. Brindell
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stopa
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stochel
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
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15
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Reátegui E, Aksan A. Effects of water on the structure and low/high temperature stability of confined proteins. Phys Chem Chem Phys 2010; 12:10161-72. [PMID: 20689888 DOI: 10.1039/c003517c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study well-characterized model proteins were confined in silica nanoporous matrices. Confinement of the proteins in silica matrices allowed us to explore the role of water hydrogen bonding on the structures of the proteins in a broad range of temperatures (-120 degrees C to 95 degrees C). At low temperatures confinement suppressed freezing of water, which remained in the liquid state. We obtained direct evidence that the changes in the hydrogen bonding of water induced changes in the structure of confined proteins. At high temperatures, a reduction of hydrogen bonding of water facilitated protein-silica interactions and the confined proteins underwent denaturation. However, the incorporation of the osmolyte, trehalose, reduced protein-silica interactions, and altered the hydrogen bonding of water. As a result, the high temperature thermal stability of the confined proteins was greatly improved.
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Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, USA
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16
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Malsam J, Aksan A. Hydrogen Bonding and Compartmentalization of Water in Supercooled and Frozen Aqueous Acetone Solutions. J Phys Chem B 2010; 114:4238-45. [DOI: 10.1021/jp904381d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason Malsam
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN
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17
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Lepeshkevich SV, Parkhats MV, Stepuro II, Dzhagarov BM. Molecular oxygen binding with α and β subunits within the R quaternary state of human hemoglobin in solutions and porous sol–gel matrices. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1823-30. [DOI: 10.1016/j.bbapap.2009.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 08/18/2009] [Accepted: 08/19/2009] [Indexed: 11/28/2022]
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Friedman A, Friedman J. New biomaterials for the sustained release of nitric oxide: past, present and future. Expert Opin Drug Deliv 2009; 6:1113-22. [PMID: 19663720 DOI: 10.1517/17425240903196743] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitric oxide (NO), the 1992 'Molecule of the Year', is the focus of immense medical and scientific exploration. Interest in NO has grown exponentially since the initial and relatively recent discovery that NO is the long sought after endothelial relaxing factor. There is intense research that is continuing to expose the extensive physiologic impact of NO in virtually all organ and tissue systems under both normal and pathological conditions. Both the rate of delivery and the amount of site-specific generated NO modulate a balance between cytoregulatory and cytotoxic activities. This balancing act and the very short lifetime of NO under physiological conditions pose an extreme challenge with respect to harnessing the exceptional therapeutic potential of this molecule. Over the past two decades, the race to translate the therapeutic potential of NO to the bedside has been overwhelmingly through the development of numerous NO delivery devices/vehicles. So far no one product has emerged as a clearcut winner. This review: discusses and evaluates NO-donating platforms that are available at present; attempts to enhance delivery and efficacy through encapsulation in silane-based hydrogel matrices; and discusses and evaluates the future direction of these advances.
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Affiliation(s)
- Adam Friedman
- Department of Medicine, Albert Einstein of Medicine, Bronx, NY 10467, USA.
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19
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Roche CJ, Friedman JM. NO reactions with sol-gel and solution phase samples of the ferric nitrite derivative of HbA. Nitric Oxide 2009; 22:180-90. [PMID: 19919854 DOI: 10.1016/j.niox.2009.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 11/09/2009] [Accepted: 11/09/2009] [Indexed: 02/07/2023]
Abstract
The reaction of nitric oxide (NO) with the ferric (met) nitrite derivative of human adult hemoglobin Hb is probed for both solution phase and sol-gel encapsulated populations. The evolution of both the Q band absorption spectrum and fitted populations of Hb derivatives are used to show the sequence of events occurring when NO interacts with nitrite bound to a ferric heme in Hb. The sol-gel is used to compare the evolving populations as a function of quaternary state for the starting met-nitrite populations. The redox status of intermediates is probed using the CN(-) anion to trap ferric heme species. The emergent presence of reactive NO species such as N(2)O(3) during the course of the reaction is probed using the fluorescent probe DAF-2 whereas the fluorophore Chemifluor is used as an indirect measure of the ability of the reaction to create S-nitrosothiols on glutathione. The results are consistent with the formation of a stable reactive intermediate capable of generating bioactive forms of NO. The patterns observed are consistent with a proposed mechanism whereby NO reacts with the ferric nitrite derivative to generate N(2)O(3).
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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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20
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Han G, Tar M, Kuppam DSR, Friedman A, Melman A, Friedman J, Davies KP. Nanoparticles as a novel delivery vehicle for therapeutics targeting erectile dysfunction. J Sex Med 2009; 7:224-33. [PMID: 19765204 DOI: 10.1111/j.1743-6109.2009.01507.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Nanoparticles represent a potential novel mechanism for transdermal delivery of erectogenic agents directly to the penis. AIM To determine if nanoparticles encapsulating known erectogenic agents (tadalafil, sialorphin, and nitric oxide [NO]) can improve erectile function in a rat model of erectile dysfunction (ED) as a result of aging (the Sprague-Dawley retired breeder rat). METHODS Nanoparticles encapsulating the erectogenic agents were applied as a gel to the glans and penile shaft of anesthetized Sprague-Dawley rats and the intracorporal pressure/blood pressure (ICP/BP) monitored for up to 2 hours with or without stimulation of the cavernous nerve. Control nanoparticles were made without encapsulating erectogenic agents and applied in a similar manner in separate experiments. RESULTS Nanoparticles encapsulating NO caused spontaneous visible erections in the rat, with an average time of onset of 4.5 minutes, duration of 1.42 minutes, and ICP/BP of 0.67 +/- 0.14. The sialorphin nanoparticles also caused visible spontaneous erections after an average of 4.5 minutes, with a duration of 8 minutes and ICP/BP ratio of 0.72 +/- 0.13. The difference in the erectile response between groups of animals treated with NO or sialorphin nanoparticles was significantly different from the control group treated with empty nanoparticles (P < 0.05) Tadalafil nanoparticles showed a significant increase in the mean ICP/BP (0.737 +/- 0.029) following stimulation of the cavernous nerve (4 mA) 1 hour after application of the nanoparticles with a visibly improved erectile response. CONCLUSIONS Nanoparticles encapsulating three different erectogenic agents resulted in increased erectile function when applied to the penis of a rat model of ED. Nanoparticles represent a potential novel route for topical delivery of erectogenic agents which could improve the safety profile for existing orally administered drugs by avoiding effects of absorption and first-pass metabolism, and would be less hazardous than injection.
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Affiliation(s)
- George Han
- Department of Biophysics and Physiology, Albert Einstein College of Medicine, Bronx, NY, USA
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21
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Reátegui E, Aksan A. Effects of the Low-Temperature Transitions of Confined Water on the Structures of Isolated and Cytoplasmic Proteins. J Phys Chem B 2009; 113:13048-60. [DOI: 10.1021/jp903294q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
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22
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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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23
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24
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Malsam J, Aksan A. Hydrogen Bonding and Kinetic/Thermodynamic Transitions of Aqueous Trehalose Solutions at Cryogenic Temperatures. J Phys Chem B 2009; 113:6792-9. [DOI: 10.1021/jp8099434] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jason Malsam
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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25
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Giordano D, Boechi L, Vergara A, Martí MA, Samuni U, Dantsker D, Grassi L, Estrin DA, Friedman JM, Mazzarella L, di Prisco G, Verde C. The hemoglobins of the sub-Antarctic fishCottoperca gobio, a phyletically basal species - oxygen-binding equilibria, kinetics and molecular dynamics. FEBS J 2009; 276:2266-77. [DOI: 10.1111/j.1742-4658.2009.06954.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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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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27
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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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Abbruzzetti S, Bruno S, Faggiano S, Ronda L, Grandi E, Mozzarelli A, Viappiani C. Characterization of ligand migration mechanisms inside hemoglobins from the analysis of geminate rebinding kinetics. Methods Enzymol 2008; 437:329-45. [PMID: 18433636 DOI: 10.1016/s0076-6879(07)37017-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The presence of internal hydrophobic cavities and packing defects has been demonstrated for several small globular proteins, including hemoglobins. The reduced thermodynamic stability appears to be compensated for by the capability of controlling ligand diffusion through the protein matrix to the active site, possibly by stocking more than one reactant molecule in selected sites. Photolysis of carbon monoxide complexes of hemoglobins encapsulated in silica gels leads to multiphasic geminate rebinding kinetics at room temperature, reflecting rebinding also from different temporary docking sites inside the protein matrix. A careful analysis of the ligand rebinding kinetics allows the determination of the microscopic rates for the underlying reactions, including those governing the migration to and from the docking sites. This chapter describes the experimental approach used to characterize the ligand rebinding kinetics for heme proteins in silica gels after nanosecond laser flash photolysis and the computational methods necessary to retrieve the kinetic parameters.
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29
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Folding myoglobin within a sol-gel glass: protein folding constrained to a small volume. Biophys J 2008; 95:322-32. [PMID: 18339762 DOI: 10.1529/biophysj.106.097428] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unfolding and refolding reaction of myoglobin was examined in solution and within a porous silica sol-gel glass. The sol-gel pores constrain the protein to a volume that is the same size and shape as the folded native state accompanied by a few layers of water solvation. Denaturants such as low pH buffers can be diffused through the gel pores to the protein to initiate unfolding and refolding. Acid-induced unfolding was hindered by the steric constraints imposed by the gel pores such that more denaturing conditions were required within the gel than in solution to create the unfolded state. No new folding intermediates were observed. Refolding of myoglobin was not complete in millimolar pH 7 buffer alone. Addition of 25% glycerol to the pH 7 buffer resulted in nearly complete refolding, and the use of 1 M phosphate buffer resulted in complete refolding. The role of this cosolvent and salt in disrupting the ordered water surrounding the protein within the gel is discussed in light of the Hofmeister series and entropic trapping via a diminished hydrophobic effect within the gel. These results are consistent with the premises of folding models in which secondary and tertiary structures are considered to form within a compact conformation of the protein backbone.
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30
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Oxygen Binding to Heme Proteins in Solution, Encapsulated in Silica Gels, and in the Crystalline State. Methods Enzymol 2008; 437:311-28. [DOI: 10.1016/s0076-6879(07)37016-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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31
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Dunn B, Zink JI. Molecules in glass: probes, ordered assemblies, and functional materials. Acc Chem Res 2007; 40:747-55. [PMID: 17518433 DOI: 10.1021/ar700033b] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Research on the properties and applications of molecules doped into sol-gel-derived silica matrices has expanded rapidly. This Account begins with a brief review of the use of the dopant molecules as probes of the changes that occur as the system evolves from the initial sol to the final xerogel during the formation of monoliths, thin films, and mesostructured films. Methods of deliberately placing desired molecules in specific regions of the mesostructure are discussed, and an application, energy transfer, is presented. Finally, encapsulation of biological molecules is examined, and two important aspects, stabilization of the biomolecules and applications as biosensors, are described.
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Affiliation(s)
- Bruce Dunn
- Department of Materials Science and Engineering, University of California--Los Angeles, California 90095, USA
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32
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Samuni U, Dantsker D, Roche C, Friedman JM. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins. Gene 2007; 398:234-48. [PMID: 17570619 PMCID: PMC1975397 DOI: 10.1016/j.gene.2007.04.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ligand recombination studies play a central role both for characterizing different hemeproteins and their conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent slaved protein dynamics is (are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose-derived glassy matrices.
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Affiliation(s)
- Uri Samuni
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - David Dantsker
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Camille Roche
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Joel M. Friedman
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
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33
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Bruno S, Faggiano S, Spyrakis F, Mozzarelli A, Cacciatori E, Dominici P, Grandi E, Abbruzzetti S, Viappiani C. Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. Gene 2007; 398:224-33. [PMID: 17555890 DOI: 10.1016/j.gene.2007.02.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 02/20/2007] [Accepted: 02/21/2007] [Indexed: 10/23/2022]
Abstract
The ligand rebinding kinetics after photolysis of the CO complexes of Arabidopsis thaliana hemoglobins AHb1 and AHb2 in solution show very different amplitudes in the geminate phase, reflecting different migration pathways of the photodissociated ligand in the system of internal cavities accessible from the heme. The dependence of the geminate phase on CO concentration, temperature, encapsulation in silica gels and presence of glycerol confirms a remarkable difference in the internal structure of the two proteins and a dramatically different role of protein dynamics in regulating the reactivity with CO. This finding strongly supports the idea that they have distinct physiological functions.
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Affiliation(s)
- Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Italy
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34
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Conformational Dynamics of Heme-pocket in Myoglobin Encapsulated in Silica Sol-gel Glasses. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.2.339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Teoli D, Parisi L, Realdon N, Guglielmi M, Rosato A, Morpurgo M. Wet sol–gel derived silica for controlled release of proteins. J Control Release 2006; 116:295-303. [PMID: 17097181 DOI: 10.1016/j.jconrel.2006.09.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 09/12/2006] [Accepted: 09/14/2006] [Indexed: 11/26/2022]
Abstract
The potential of wet sol-gel derived silica gels as new matrices for the entrapment and sustained release of proteins was investigated. Model proteins, BSA, ribonuclease-A and avidin, with differing molecular weights and/or isoelectric points, were entrapped in two silica polymer formulations having different silica contents (4% and 12% wt/v). The conformational stability of the proteins after entrapment and their release after immersion into physiological conditions were measured. Circular dichroism analysis showed that protein conformation is maintained after entrapment and stability is enhanced. Protein-free formulations were injected intramuscularly into BALB/c mice to monitor the in vivo fate of the matrix, and the results showed that the gel is totally reabsorbed, without any apparent surrounding inflammation process. The time required for matrix bioerosion varied between one to three weeks, depending on its SiO(2) content. Erosion was also measured in vitro and the contribution of erosion and diffusion to the release of the embedded proteins was quantified. These data indicate that wet silica polymers obtained by the sol-gel route are promising matrices for the sustained release of protein drugs.
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Affiliation(s)
- Deborah Teoli
- University of Padova, Department of Pharmaceutical Sciences, Via Marzolo 5, 35131-Padova, Italy
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36
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Roche CJ, Guo F, Friedman JM. Molecular level probing of preferential hydration and its modulation by osmolytes through the use of pyranine complexed to hemoglobin. J Biol Chem 2006; 281:38757-68. [PMID: 17057250 DOI: 10.1074/jbc.m608835200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two spectroscopic probes are used to expose molecular level changes in hydration shell water interactions that directly relate to such issues as preferential hydration and protein stability. The major focus of the present study is on the use of pyranine (HPT) fluorescence to probe as a function of added osmolytes (PEG, urea, trehalose, and magnesium), the extent to which glycerol is preferentially excluded from the hydration shell of free HPT and HPT localized in the diphosphoglycerate (DPG) binding site of hemoglobin in both solution and in Sol-Gel matrices. The pyranine study is complemented by the use of vibronic side band luminescence from the gadolinium cation that directly exposes the changes in hydrogen bonding between first and second shell waters as a function of added osmolytes. Together the results form the basis for a water partitioning model that can account for both preferential hydration and water/osmolyte-mediated conformational changes in protein structure.
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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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37
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Roche CJ, Dantsker D, Samuni U, Friedman JM. Nitrite reductase activity of sol-gel-encapsulated deoxyhemoglobin. Influence of quaternary and tertiary structure. J Biol Chem 2006; 281:36874-82. [PMID: 16984908 DOI: 10.1074/jbc.m603914200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrite reductase activity of deoxyhemoglobin (HbA) in the red blood cell has been proposed as a non-nitric-oxide synthase source of deliverable nitric oxide (NO) within the vasculature. An essential element in this scheme is the dependence of this reaction on the quaternary/tertiary structure of HbA. In the present work sol-gel encapsulation is used to trap and stabilize deoxy-HbA in either the T or R quaternary state, thus allowing for the clear-cut monitoring of nitrite reductase activity as a function of quaternary state with and without effectors. The results indicate that reaction is not only R-T-dependent but also heterotropic effector-dependent within a given quaternary state. The use of the maximum entropy method to analyze carbon monoxide (CO) recombination kinetics from fully and partially liganded sol-gel-encapsulated T-state species provides a framework for understanding effector modulation of T-state reactivity by influencing the distribution of high and low reactivity T-state conformations.
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Affiliation(s)
- Camille J Roche
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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38
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Ronda L, Bruno S, Viappiani C, Abbruzzetti S, Mozzarelli A, Lowe KC, Bettati S. Circular dichroism spectroscopy of tertiary and quaternary conformations of human hemoglobin entrapped in wet silica gels. Protein Sci 2006; 15:1961-7. [PMID: 16823042 PMCID: PMC2242581 DOI: 10.1110/ps.062272306] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The relative contributions to changes in visible and near UV circular dichroism spectra of hemoglobin of heme ligation and tertiary and quaternary conformational transitions were separated by exploiting the slowing down of structural relaxations for proteins encapsulated in wet, nanoporous silica gels. Spectral signatures, previously assumed to be characteristic of T and R quaternary states, were demonstrated to be specific to different tertiary conformations. The results support the view that ligation and allosteric effectors can modulate the structural and functional properties of hemoglobin by regulating the equilibrium between the same tertiary species within both quaternary states.
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Affiliation(s)
- Luca Ronda
- Department of Biochemistry and Molecular Biology, University of Parma, Italy
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39
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Massari AM, Finkelstein IJ, Fayer MD. Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy. J Am Chem Soc 2006; 128:3990-7. [PMID: 16551107 PMCID: PMC2532503 DOI: 10.1021/ja058745y] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.
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Samuni U, Roche CJ, Dantsker D, Juszczak LJ, Friedman JM. Modulation of reactivity and conformation within the T-quaternary state of human hemoglobin: the combined use of mutagenesis and sol-gel encapsulation. Biochemistry 2006; 45:2820-35. [PMID: 16503637 PMCID: PMC3558951 DOI: 10.1021/bi050010i] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A range of conformationally distinct functional states within the T quaternary state of hemoglobin are accessed and probed using a combination of mutagenesis and sol-gel encapsulation that greatly slow or eliminate the T --> R transition. Visible and UV resonance Raman spectroscopy are used to probe the proximal strain at the heme and the status of the alpha(1)beta(2) interface, respectively, whereas CO geminate and bimolecular recombination traces in conjunction with MEM (maximum entropy method) analysis of kinetic populations are used to identify functionally distinct T-state populations. The mutants used in this study are Hb(Nbeta102A) and the alpha99-alpha99 cross-linked derivative of Hb(Wbeta37E). The former mutant, which binds oxygen noncooperatively with very low affinity, is used to access low-affinity ligated T-state conformations, whereas the latter mutant is used to access the high-affinity end of the distribution of T-state conformations. A pattern emerges within the T state in which ligand reactivity increases as both the proximal strain and the alpha(1)beta(2) interface interactions are progressively lessened after ligand binding to the deoxy T-state species. The ligation and effector-dependent interplay between the heme environment and the stability of the Trp beta37 cluster in the hinge region of the alpha(1)beta(2) interface appears to determine the distribution of the ligated T-state species generated upon ligand binding. A qualitative model is presented, suggesting that different T quaternary structures modulate the stability of different alphabeta dimer conformations within the tetramer.
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41
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Avnir D, Coradin T, Lev O, Livage J. Recent bio-applications of sol–gel materials. ACTA ACUST UNITED AC 2006. [DOI: 10.1039/b512706h] [Citation(s) in RCA: 629] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Schirò G, Cammarata M, Levantino M, Cupane A. Spectroscopic markers of the T<-->R quaternary transition in human hemoglobin. Biophys Chem 2005; 114:27-33. [PMID: 15792858 DOI: 10.1016/j.bpc.2004.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 11/04/2004] [Accepted: 11/04/2004] [Indexed: 11/21/2022]
Abstract
In this work, we use a sol-gel protocol to trap and compare the R and T quaternary states of both the deoxygenated (deoxyHb) and carbonmonoxide (HbCO) derivatives of human hemoglobin. The near infrared optical absorption band III and the infrared CO stretching band are used to detect the effect of quaternary structure on the spectral properties of deoxyHb and HbCO; comparison with myoglobin allows for an assessment of tertiary and quaternary contributions to the measured band shifts. The R<-->T transition is shown to cause a blue shift of the band III by approximately 35 cm(-1) for deoxyHb and a red shift of the CO stretching band by only approximately 0.3 cm(-1) for HbCO. This clearly shows that quaternary structure changes are transmitted to the heme pocket and that effects on deoxyHb are much larger than on HbCO, at least as far as the band energies are concerned. Experiments performed in the ample temperature interval of 300-10K show that the above quaternary structure effects are "static" and do not influence the dynamic properties of the heme pocket, at least as probed by the temperature dependence of band III and of the CO stretching band. The availability of quaternary structure sensitive spectroscopic markers and the quantitative measurement of the quaternary structure contribution to band shifts will be of considerable help in the analysis of flash-photolysis experiments on hemoglobin. Moreover, it will enable one to characterize the dynamic properties of functionally relevant hemoglobin intermediates and to study the kinetics of both the T-->R and R-->T quaternary transitions through time-resolved spectroscopy.
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Affiliation(s)
- Giorgio Schirò
- National Institute for the Physics of Matter (INFM) and Department of Physical and Astronomical Sciences, University of Palermo, via Archirafi 36, I-90123, Palermo, Italy
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43
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Sui J, Tleugabulova D, Brennan JD. Direct and indirect monitoring of peptide-silica interactions using time-resolved fluorescence anisotropy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:4996-5001. [PMID: 15896042 DOI: 10.1021/la0473963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The present work extends the application of time-resolved fluorescence anisotropy (TRFA) of a cationic probe rhodamine 6G (R6G) in aqueous Ludox to in situ monitoring of peptide adsorption onto the silica particles. Steady-state anisotropy and TRFA of R6G in Ludox sols were measured to characterize the extent of the ionic binding of the probe to silica particles in the presence of varying levels of tripeptides of varying charge, including Lys-Trp-Lys (KWK), N-acetylated Lys-Trp-Lys (Ac-KWK), Glu-Trp-Glu (EWE), and N-acetylated Glu-Trp-Glu (Ac-EWE). The results were compared to those obtained by direct observation of peptide adsorption using the steady-state anisotropy of the intrinsic tryptophan residue. Ionic binding of the peptides to Ludox particles produced an increase in the steady-state Trp anisotropy that was dependent on the number of cationic groups present, but the limiting anisotropy values were relatively low, indicating significant rotational freedom of the indole residue in the adsorbed peptides. On the other hand, R6G showed significant decreases in anisotropy in the presence of cationic peptides, consistent with the cationic peptides blocking the adsorption of the dye to the silica surface. Thus, R6G is able to indirectly report on the binding of peptides to Ludox particles. It was noteworthy that, while there were similar trends in the data obtained from steady-state anisotropy and TRFA studies of R6G, the use of steady-state anisotropy to assess binding of peptides overestimated the degree of peptide adsorption relative to the value obtained by TRFA. The study shows that the competitive binding method can be used to assess the binding of various biologically relevant compounds onto silica surfaces and demonstrates the potential of TRFA for probing peptide-silica and protein-silica interactions.
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Affiliation(s)
- Jie Sui
- Department of Chemistry, McMaster University, Hamilton, ON, L8S 4M1, Canada
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44
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Pioselli B, Bettati S, Mozzarelli A. Confinement and crowding effects on tryptophan synthase alpha2beta2 complex. FEBS Lett 2005; 579:2197-202. [PMID: 15811341 DOI: 10.1016/j.febslet.2005.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Revised: 02/07/2005] [Accepted: 03/04/2005] [Indexed: 11/25/2022]
Abstract
Biological molecules experience in vivo a highly crowded environment. The investigation of the functional properties of the tryptophan synthase alpha(2)beta(2) complex either entrapped in wet nanoporous silica gels or in the presence of the crowding agents dextran 70 and ficoll 70 indicates that the rates of the conformational transitions associated to catalysis and regulation are reduced, and an open and less catalytically active conformation is stabilized.
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Affiliation(s)
- Barbara Pioselli
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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45
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Fuentes L, Oyola J, Fernández M, Quiñones E. Conformational changes in azurin from Pseudomona aeruginosa induced through chemical and physical protocols. Biophys J 2005; 87:1873-80. [PMID: 15345565 PMCID: PMC1304591 DOI: 10.1529/biophysj.104.042580] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Azurin from Pseudomona aeruginosa is a small copper protein with a single tryptophan (Trp) buried in the structure. The Gibbs free energies associated with the folding of holo azurin, calculated monitoring Trp fluorescence and changes in absorbance on the ligand-to-metal band, are different because these techniques probe their local environments, thereby being able to probe different conformational changes. The presence of an intermediate state was observed during the chemical denaturation of the protein. Upon denaturation, a 30-fold increase is observed in the magnitude of the quenching constant of the tryptophan fluorescence by acrylamide, because this residue becomes more accessible to the quencher. Entrapping the protein in sol-gel materials lowers its stability possibly because the solvation properties of the macromolecule are changed. The thermal denaturation of azurin immobilized in a sol-gel monolith is irreversible, which tends to rule out an aggregation mechanism to account for the irreversibility of the denaturation of the protein free in solution. Unlike the Cu(II) ion, the Gd(III) ion accommodates in site B of azurin with high affinity and the folding free energy of Gd-azurin is larger than that of apo azurin.
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Affiliation(s)
- Lymari Fuentes
- Department of Chemistry, University of Puerto Rico, San Juan, Puerto Rico 00931-3346
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46
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Compared esterification kinetics of the lipase from Burkholderia cepacia either free or encapsulated in a silica aerogel. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.molcatb.2004.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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Lepeshkevich SV, Konovalova NV, Stepuro II, Dzhagarov BM. Kinetic studies of oxygenation of α- and β-subunits within pyridoxal 5′-phosphate derivatives of human hemoglobin. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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48
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Pioselli B, Bettati S, Demidkina TV, Zakomirdina LN, Phillips RS, Mozzarelli A. Tyrosine phenol-lyase and tryptophan indole-lyase encapsulated in wet nanoporous silica gels: Selective stabilization of tertiary conformations. Protein Sci 2004; 13:913-24. [PMID: 15044726 PMCID: PMC2280055 DOI: 10.1110/ps.03492904] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The pyridoxal 5'-phosphate-dependent enzymes tyrosine phenol-lyase and tryptophan indole-lyase were encapsulated in wet nanoporous silica gels, a powerful method to selectively stabilize tertiary and quaternary protein conformations and to develop bioreactors and biosensors. A comparison of the enzyme reactivity in silica gels and in solution was carried out by determining equilibrium and kinetic parameters, exploiting the distinct spectral properties of catalytic intermediates and reaction products. The encapsulated enzymes exhibit altered distributions of ketoenamine and enolimine tautomers, increased values of inhibitors dissociation constants, slow attaining of steady-state in the presence of substrate and substrate analogs, modified steady-state distribution of catalytic intermediates, and a sixfold-eightfold decrease of specific activities. This behavior can be rationalized by a reduced conformational flexibility for the encapsulated enzymes and a selective stabilization of either the open (inactive) or the closed (active) form of the enzymes. Despite very similar structures and catalytic mechanisms, the influence of encapsulation is more pronounced for tyrosine phenol-lyase than tryptophan indole-lyase. This finding indicates that subtle structural and dynamic differences can lead to distinct interactions of the protein with the gel matrix.
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Affiliation(s)
- Barbara Pioselli
- Department of Biochemistry and Molecular Biology, University of Parma, Via Parco delle Scienze 23/A, 43100 Parma, Italy
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Viappiani C, Bettati S, Bruno S, Ronda L, Abbruzzetti S, Mozzarelli A, Eaton WA. New insights into allosteric mechanisms from trapping unstable protein conformations in silica gels. Proc Natl Acad Sci U S A 2004; 101:14414-9. [PMID: 15385676 PMCID: PMC521967 DOI: 10.1073/pnas.0405987101] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Indexed: 11/18/2022] Open
Abstract
To understand why the classical two-state allosteric model of Monod, Wyman, and Changeux explains cooperative oxygen binding by hemoglobin but does not explain changes in oxygen affinity by allosteric inhibitors, we have investigated the kinetic properties of unstable conformations transiently trapped by encapsulation in silica gels. Conformational trapping reveals that after nanosecond photodissociation of carbon monoxide a large fraction of the subunits of the T quaternary structure has kinetic properties almost identical to those of subunits of the R quaternary structure. Addition of allosteric inhibitors reduces both the fraction of R-like subunits and the oxygen affinity of the T quaternary structure. These kinetic and equilibrium results are readily explained by a recently proposed generalization of the Monod-Wyman-Changeux model in which a pre-equilibrium between two functionally different tertiary, rather than quaternary, conformations plays the central role.
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50
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Dantsker D, Samuni U, Ouellet Y, Wittenberg BA, Wittenberg JB, Milani M, Bolognesi M, Guertin M, Friedman JM. Viscosity-dependent Relaxation Significantly Modulates the Kinetics of CO Recombination in the Truncated Hemoglobin TrHbN from Mycobacterium tuberculosis. J Biol Chem 2004; 279:38844-53. [PMID: 15234986 DOI: 10.1074/jbc.m401513200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic traces were generated for the nanosecond and slower rebinding of photodissociated CO to trHbN in solution and in porous sol-gel matrices as a function of viscosity, conformation, and mutation. TrHbN is one of the two truncated hemoglobins from Mycobacterium tuberculosis. The kinetic traces were analyzed in terms of three distinct phases. These three phases are ascribed to rebinding: (i) from the distal heme pocket, (ii) from the adjacent apolar tunnel prior to conformational relaxation, and (iii) from the apolar tunnel subsequent to conformational relaxation. The fractional content of each of these phases was shown to be a function of the viscosity and, in the case of the sol-gel-encapsulated samples, sample preparation history. The observed kinetic patterns support a model consisting of the following elements: (i) the viscosity and conformation-sensitive dynamics of the Tyr(B10) side chain facilitate diffusion of the dissociated ligand from the distal heme pocket into the adjacent tunnel; (ii) the distal heme pocket architecture determines ligand access from the tunnel back to the heme iron; (iii) the distal heme pocket architecture is governed by a ligand-dependent hydrogen bonding network that limits the range of accessible side chain positions; and (iv) the apolar tunnel linking the heme site to the solvent biases the competition between water and ligand for occupancy of the vacated polar distal heme pocket greatly toward the nonpolar ligand. Implications of these finding with respect to biological function are discussed.
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Affiliation(s)
- David Dantsker
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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