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de Armiño DJA, Di Lella S, Montepietra D, Delcanale P, Bruno S, Giordano D, Verde C, Estrin DA, Viappiani C, Abbruzzetti S. Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Protein Sci 2024; 33:e5064. [PMID: 38864722 PMCID: PMC11168075 DOI: 10.1002/pro.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) genome is one of the few examples of coexistence of multiple hemoglobin genes encoding, among others, two constitutively transcribed 2/2 hemoglobins (2/2Hbs), also named truncated Hbs (TrHbs), belonging to the Group II (or O), annotated as PSHAa0030 and PSHAa2217. In this work, we describe the ligand binding kinetics and their interrelationship with the dynamical properties of globin Ph-2/2HbO-2217 by combining experimental and computational approaches and implementing a new computational method to retrieve information from molecular dynamic trajectories. We show that our approach allows us to identify docking sites within the protein matrix that are potentially able to transiently accommodate ligands and migration pathways connecting them. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy barrier, while inner cavities play only a minor role in modulating rebinding kinetics.
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Affiliation(s)
- Diego Javier Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Santiago Di Lella
- Departamento de Química Biológica and IQUIBICEN‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Daniele Montepietra
- Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Nanoscience Institute—CNR‐NANOModenaItaly
| | - Pietro Delcanale
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefano Bruno
- Department of Food and Drug SciencesUniversity of ParmaParmaItaly
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Dario A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
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Lepeshkevich SV, Sazanovich IV, Parkhats MV, Gilevich SN, Dzhagarov BM. Towards understanding non-equivalence of α and β subunits within human hemoglobin in conformational relaxation and molecular oxygen rebinding. Chem Sci 2021; 12:7033-7047. [PMID: 34123331 PMCID: PMC8153241 DOI: 10.1039/d1sc00712b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Picosecond to millisecond laser time-resolved transient absorption spectroscopy was used to study molecular oxygen (O2) rebinding and conformational relaxation following O2 photodissociation in the α and β subunits within human hemoglobin in the quaternary R-like structure. Oxy-cyanomet valency hybrids, α2(Fe2+-O2)β2(Fe3+-CN) and α2(Fe3+-CN)β2(Fe2+-O2), were used as models for oxygenated R-state hemoglobin. An extended kinetic model for geminate O2 rebinding in the ferrous hemoglobin subunits, ligand migration between the primary and secondary docking site(s), and nonexponential tertiary relaxation within the R quaternary structure, was introduced and discussed. Significant functional non-equivalence of the α and β subunits in both the geminate O2 rebinding and concomitant structural relaxation was revealed. For the β subunits, the rate constant for the geminate O2 rebinding to the unrelaxed tertiary structure and the tertiary transition rate were found to be greater than the corresponding values for the α subunits. The conformational relaxation following the O2 photodissociation in the α and β subunits was found to decrease the rate constant for the geminate O2 rebinding, this effect being more than one order of magnitude greater for the β subunits than for the α subunits. Evidence was provided for the modulation of the O2 rebinding to the individual α and β subunits within human hemoglobin in the R-state structure by the intrinsic heme reactivity through a change in proximal constraints upon the relaxation of the tertiary structure on a picosecond to microsecond time scale. Our results demonstrate that, for native R-state oxyhemoglobin, O2 rebinding properties and spectral changes following the O2 photodissociation can be adequately described as the sum of those for the α and β subunits within the valency hybrids. The isolated β chains (hemoglobin H) show similar behavior to the β subunits within the valency hybrids and can be used as a model for the β subunits within the R-state oxyhemoglobin. At the same time, the isolated α chains behave differently to the α subunits within the valency hybrids.
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Affiliation(s)
- Sergei V Lepeshkevich
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Harwell Campus OX11 0QX UK
| | - Marina V Parkhats
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Syargey N Gilevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus 5 Academician V. F. Kuprevich Street Minsk 220141 Belarus
| | - Boris M Dzhagarov
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
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Abstract
Human hemoglobin is the textbook example of the stereochemistry of an allosteric protein and of the exquisite control that a protein can exert over ligand binding. However, the fundamental basis by which the protein facilitates the ligand movement remains unknown. In this study, we used cryogenic X-ray crystallography and a high-repetition pulsed laser irradiation technique to elucidate the atomic details of ligand migration processes in hemoglobin after photolysis of the bound CO. Our data clarify the distinct CO migration pathways in the individual subunits of hemoglobin and unravel the functional roles of the internal cavities and neighboring amino acid residues in ligand exit and entry. Our results also demonstrate the high gas permeability and porosity of hemoglobin, facilitating O2 delivery. Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.
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Lepeshkevich SV, Gilevich SN, Parkhats MV, Dzhagarov BM. Molecular oxygen migration through the xenon docking sites of human hemoglobin in the R-state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1110-1121. [DOI: 10.1016/j.bbapap.2016.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022]
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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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6
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Spyrakis F, Lucas F, Bidon-Chanal A, Viappiani C, Guallar V, Luque FJ. Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1957-67. [PMID: 23583621 DOI: 10.1016/j.bbapap.2013.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
Abstract
This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1)→Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy.
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7
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Abbruzzetti S, Tilleman L, Bruno S, Viappiani C, Desmet F, Van Doorslaer S, Coletta M, Ciaccio C, Ascenzi P, Nardini M, Bolognesi M, Moens L, Dewilde S. Ligation tunes protein reactivity in an ancient haemoglobin: kinetic evidence for an allosteric mechanism in Methanosarcina acetivorans protoglobin. PLoS One 2012; 7:e33614. [PMID: 22479420 PMCID: PMC3313925 DOI: 10.1371/journal.pone.0033614] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | | | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Paolo Ascenzi
- Dipartimento di Biologia, Università Roma Tre, Roma, Italy
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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8
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Lucas MF, Guallar V. An atomistic view on human hemoglobin carbon monoxide migration processes. Biophys J 2012; 102:887-96. [PMID: 22385860 DOI: 10.1016/j.bpj.2012.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 01/02/2012] [Accepted: 01/11/2012] [Indexed: 10/28/2022] Open
Abstract
A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed.
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Affiliation(s)
- M Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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9
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Abbruzzetti S, Faggiano S, Spyrakis F, Bruno S, Mozzarelli A, Astegno A, Dominici P, Viappiani C. Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana. IUBMB Life 2011; 63:1094-100. [PMID: 22034287 DOI: 10.1002/iub.546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 07/02/2011] [Indexed: 01/26/2023]
Abstract
Type 1 nonsymbiotic hemoglobin from Arabidopsis thaliana (AHb1) shows a partial bis-histidyl hexacoordination but can reversibly bind diatomic ligands. The physiological function is still unclear, but the high oxygen affinity rules out a function related to O2 sensing, carrying, or storing. To gain insight into its possible functional roles, we have investigated its O2 and NO rebinding kinetics after laser flash photolysis. The rate constants of the rebinding from the primary docking site for both O2 and NO are higher than CO, with lower photolysis yields. Moreover, the amplitude of the geminate phase increases and, as for CO, the numerical analysis of the experimental curves suggests the existence of an internal pathway leading, with high rate, to an additional docking site. However, the accessibility to this site seems to be strongly ligand-dependent, being lower for O2 and higher for NO.
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10
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Lepeshkevich SV, Biziuk SA, Lemeza AM, Dzhagarov BM. The kinetics of molecular oxygen migration in the isolated α chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1279-88. [DOI: 10.1016/j.bbapap.2011.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
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Birukou I, Maillett DH, Birukova A, Olson JS. Modulating distal cavities in the α and β subunits of human HbA reveals the primary ligand migration pathway. Biochemistry 2011; 50:7361-74. [PMID: 21793487 DOI: 10.1021/bi200923k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The free volume in the active site of human HbA plays a crucial role in governing the bimolecular rates of O(2), CO, and NO binding, the fraction of geminate ligand recombination, and the rate of NO dioxygenation by the oxygenated complex. We have decreased the size of the distal pocket by mutating Leu(B10), Val(E11), and Leu(G8) to Phe and Trp and that of other more internal cavities by filling them with Xe at high gas pressures. Increasing the size of the B10 side chain reduces bimolecular rates of ligand binding nearly 5000-fold and inhibits CO geminate recombination due to both reduction of the capture volume in the distal pocket and direct steric hindrance of Fe-ligand bond formation. Phe and Trp(E11) mutations also cause a decrease in distal pocket volume but, at the same time, increase access to the Fe atom because of the loss of the γ2 CH(3) group of the native Val(E11) side chain. The net result of these E11 substitutions is a dramatic increase in the rate of geminate recombination because dissociated CO is sequestered close to the Fe atom and can rapidly rebind without steric resistance. However, the bimolecular rate constants for binding of ligand to the Phe and Trp(E11) mutants are decreased 5-30-fold, because of a smaller capture volume. Geminate and bimolecular kinetic parameters for Phe and Trp(G8) mutants are similar to those for the native HbA subunits because the aromatic rings at this position cause little change in distal pocket volume and because ligands do not move past this position into the globin interior of wild-type HbA subunits. The latter conclusion is verified by the observation that Xe binding to the α and β Hb subunits has little effect on either geminate or bimolecular ligand rebinding. All of these experimental results argue strongly against alternative ligand migration pathways that involve movements through the protein interior in HbA. Instead, ligands appear to enter through the His(E7) gate and are captured directly in the distal cavity.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and WM Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
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12
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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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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Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L. Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method. J Phys Chem B 2010; 114:7002-8. [DOI: 10.1021/jp908525s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonello Merlino
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alessandro Vergara
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Filomena Sica
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Massimiliano Aschi
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Andrea Amadei
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alfredo Di Nola
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Lelio Mazzarella
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
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15
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Dzhagarov BM, Lepeshkevich SV. Photonics of the hemoglobin active site. HIGH ENERGY CHEMISTRY 2010. [DOI: 10.1134/s0018143910020074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Savino C, Miele AE, Draghi F, Johnson KA, Sciara G, Brunori M, Vallone B. Pattern of cavities in globins: The case of human hemoglobin. Biopolymers 2009; 91:1097-107. [DOI: 10.1002/bip.21201] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Ligand migration through the internal hydrophobic cavities in human neuroglobin. Proc Natl Acad Sci U S A 2009; 106:18984-9. [PMID: 19850865 DOI: 10.1073/pnas.0905433106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb), a member of the globin superfamily, was found in the brain of vertebrates and is suggested to play a neuroprotective function under hypoxic conditions by scavenging nitrogen monoxide (NO) through a dioxygenase activity. In order for such a reaction to efficiently take place and to minimize the release of reactive intermediates in the cytosol, the cosubstrates O(2) and NO and other unstable reaction intermediates should bind sequentially to docking sites in the protein matrix. We have characterized the accessibility of these sites by analyzing the geminate CO rebinding kinetics to the heme moiety observed upon nanosecond flash photolysis of the Ngb-CO complex encapsulated in silica gels. The geminate rebinding phase showed a remarkable complexity, revealing the presence of a system of secondary docking sites where ligands are stored for hundreds of microseconds. Most kinetics steps display little temperature dependence, demonstrating that ligands can easily migrate through the cavities, except for the slowest reaction intermediate, possibly reflecting a structural conformational change reshaping the system of cavities. This conformational change is unrelated with distal His E7 binding to the heme, as it persists for the HE7L mutant. Overall, data are consistent with the presence of a discrete system of docking sites, possibly acting as reservoirs for the putative cosubstrates and for other reactive species involved in the physiologically relevant reaction.
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18
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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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19
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Caccia D, Ronda L, Frassi R, Perrella M, Del Favero E, Bruno S, Pioselli B, Abbruzzetti S, Viappiani C, Mozzarelli A. PEGylation Promotes Hemoglobin Tetramer Dissociation. Bioconjug Chem 2009; 20:1356-66. [DOI: 10.1021/bc900130f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dario Caccia
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Luca Ronda
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Raffaella Frassi
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Michele Perrella
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Elena Del Favero
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Barbara Pioselli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
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20
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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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21
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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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22
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Abbruzzetti S, Grandi E, Bruno S, Faggiano S, Spyrakis F, Mozzarelli A, Cacciatori E, Dominici P, Viappiani C. Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana. J Phys Chem B 2007; 111:12582-90. [PMID: 17924689 DOI: 10.1021/jp074954o] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AHb1 is a hexacoordinated type 1 nonsymbiotic hemoglobin recently discovered in Arabidopsis thaliana. To gain insight into the ligand migration inside the protein, we studied the CO rebinding kinetics of AHb1 encapsulated in silica gels, in the presence of glycerol. The CO rebinding kinetics after nanosecond laser flash photolysis exhibits complex ligand migration patterns, consistent with the existence of discrete docking sites in which ligands can temporarily be stored before rebinding to the heme at different times. This finding may be of relevance to the physiological NO dioxygenase activity of this protein, which requires sequential binding of two substrates, NO and O2, to the heme.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, NEST CNR-INFM, Parma, Italy
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23
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Samuni U, Roche CJ, Dantsker D, Friedman JM. Conformational dependence of hemoglobin reactivity under high viscosity conditions: the role of solvent slaved dynamics. J Am Chem Soc 2007; 129:12756-64. [PMID: 17910446 DOI: 10.1021/ja072342b] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The concept of protein dynamic states is introduced. This concept is based on (i) protein dynamics being organized hierarchically with respect to solvent slaving and (ii) which tier of dynamics is operative over the time window of a given measurement. The protein dynamic state concept is used to analyze the kinetic phases derived from the recombination of carbon monoxide to sol-gel-encapsulated human adult hemoglobin (HbA) and select recombinant mutants. The temperature-dependent measurements are made under very high viscosity conditions obtained by bathing the samples in an excess of glycerol. The results are consistent with a given tier of solvent slaved dynamics becoming operative at a time delay (with respect to the onset of the measurement) that is primarily solvent- and temperature-dependent. However, the functional consequences of the dynamics are protein- and conformation-specific. The kinetic traces from both equilibrium populations and trapped allosteric intermediates show a consistent progression that exposes the role of both conformation and hydration in the control of reactivity. Iron-zinc symmetric hybrid forms of HbA are used to show the dramatic difference between the kinetic patterns for T state alpha and beta subunits. The overall results support a model for allostery in HbA in which the ligand-binding-induced transition from the deoxy T state to the high -affinity R state proceeds through a progression of T state intermediates.
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Affiliation(s)
- Uri Samuni
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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24
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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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25
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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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26
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Bruno S, Faggiano S, Spyrakis F, Mozzarelli A, Abbruzzetti S, Grandi E, Viappiani C, Feis A, Mackowiak S, Smulevich G, Cacciatori E, Dominici P. The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities. J Am Chem Soc 2007; 129:2880-9. [PMID: 17298064 DOI: 10.1021/ja066638d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nonsymbiotic hemoglobins, AHb1 and AHb2, have recently been isolated from Arabidopsis thaliana. Using steady-state and time-resolved spectroscopic methods, we show that Fe2+ AHb1 contains a mixture of penta- and hexacoordinated heme, while Fe2+ AHb2 is fully hexacoordinated. In the CO complexes, polar interactions and H-bonds with the ligand are stronger for AHb1 than for AHb2. The ligand binding kinetics are substantially different, reflecting the distribution between the penta- and hexacoordinated species, and indicate that protein dynamics and ligand migration pathways are very specific for each of the two proteins. In particular, a very small, non-exponential geminate rebinding observed in AHb1 suggests that the distal heme cavity is connected with the exterior by a relatively open channel. The large, temperature-dependent geminate rebinding observed for AHb2 implies a major role of protein dynamics in the ligand migration from the distal cavity to the solvent. The structures of AHb1 and AHb2, modeled on the basis of the homologous rice hemoglobin, exhibit a different cavity system that is fully compatible with the observed ligand binding kinetics. Overall, these kinetic and structural data are consistent with the putative NO-dioxygenase activity previously attributed to AHb1, whereas the role of AHb2 remains elusive.
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Affiliation(s)
- Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, UniversitA degli Studi di Parma, Parma, Italy
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27
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Abbruzzetti S, Bruno S, Faggiano S, Grandi E, Mozzarelli A, Viappiani C. Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis. Photochem Photobiol Sci 2006; 5:1109-20. [PMID: 17136275 DOI: 10.1039/b610236k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haem proteins have long been the most studied proteins in biophysics, and have become paradigms for the characterization of fundamental biomolecular processes as ligand binding and regulatory conformational transitions. The presence of the haem prosthetic group, the absorbance spectrum of which has a ligation sensitive region conveniently located in the UV-visible range, has offered a powerful and sensitive tool for the investigation of molecular functions. The central Fe atom is capable of reversibly binding diatomic ligands, including O(2), CO, and NO. The Fe-ligand bond is photolabile, and a reactive unligated state can be transiently generated with a pulsed laser. The photodissociated ligands quickly rebind to the haem and the process can be monitored by transient absorbance methods. The ligand rebinding kinetics reflects protein dynamics and ligand migration within the protein inner cavities. The characterization of these processes was done in the past mainly by low temperature experiments. The use of silica gels to trap proteins allows the characterization of internal ligand dynamics at room temperature. In order to show the potential of the laser flash photolysis techniques, combined with modern numerical analysis methods, we report experiments conducted on two non-symbiotic haemoglobins from Arabidopsis thaliana. The comparison between time courses recorded on haemoglobins in solution and encapsulated in silica gels allows for the highlighting of different interplays between protein dynamics and ligand migration.
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