1
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Frankenfield K, Marchany-Rivera D, Flanders KG, Cruz-Balberdy A, Lopez-Garriga J, Cerda JF. Fluoride binding to characteristic heme-pocket centers: Insights into ligand stability. J Inorg Biochem 2021; 224:111578. [PMID: 34481348 PMCID: PMC8463504 DOI: 10.1016/j.jinorgbio.2021.111578] [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: 02/28/2021] [Revised: 07/17/2021] [Accepted: 08/10/2021] [Indexed: 11/20/2022]
Abstract
The studies on the L. pectinata hemoglobins (HbI, HbII, and HbIII) are essential because of their biological roles in hydrogen sulfide transport and metabolism. Variation in the pH could also play a role in the transport of hydrogen sulfide by HbI and oxygen by HbII and HbIII, respectively. Here, fluoride binding was used to further understand the structural properties essential for the molecular mechanism of ligand stabilization as a function of pH. The data allowed us to gain insights into how the physiological roles of HbI, HbII, HbIII, adult hemoglobin (A-Hb), and horse heart myoglobin (Mb) have an impact on the heme-bound fluoride stabilization. In addition, analysis of the vibrational assignments of the met-cyano heme complexes shows varied strength interactions of the heme-bound ligand. The heme pocket composition properties differ between HbI (GlnE7 and PheB10) and HbII/HbIII (GlnE7 and TyrB10). Also, the structural GlnE7 stereo orientation changes between HbI and HbII/HbIII. In HbI, its carbonyl group orients towards the heme iron, while in HbII/HbIII, the amino group occupies this position. Therefore, in HbI, the interactions to the heme-bound fluoride ion, cyanide, and oxygen with GlnE7 via H-bonding are not probable. Still, the aromatic cage PheB10, PheCD1, and PheE11 may contribute to the observed stabilization. However, a robust H-bonding networking stabilizes HbII and HbIII, heme-bound fluoride, cyanide, and oxygen ligand with the OH and NH2 groups of TyrB10 and GlnE7, respectively. At the same time, A-Hb and Mb have moderate but similar ligand interactions controlled by their respective distal E7 histidine.
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Affiliation(s)
| | - Darya Marchany-Rivera
- Department of Chemistry/Industrial Biotechnology, P.O. Box 9000, University of Puerto Rico, Mayagüez Campus, 00681, Puerto Rico.
| | - Kayla G Flanders
- Department of Chemistry, Saint Joseph's University, 5600 City Ave., Philadelphia, PA 19131, USA.
| | | | - Juan Lopez-Garriga
- Department of Chemistry/Industrial Biotechnology, P.O. Box 9000, University of Puerto Rico, Mayagüez Campus, 00681, Puerto Rico.
| | - Jose F Cerda
- Department of Chemistry, Saint Joseph's University, 5600 City Ave., Philadelphia, PA 19131, USA.
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2
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Thompson MK, Shay MR, de Serrano V, Dumarieh R, Ghiladi RA, Franzen S. A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.
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Affiliation(s)
- Matthew K. Thompson
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Madeline R. Shay
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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3
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4
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Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond. Int J Mol Sci 2020; 21:ijms21072512. [PMID: 32260401 PMCID: PMC7177771 DOI: 10.3390/ijms21072512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/23/2022] Open
Abstract
Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.
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5
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Schaffner I, Mlynek G, Flego N, Pühringer D, Libiseller-Egger J, Coates L, Hofbauer S, Bellei M, Furtmüller PG, Battistuzzi G, Smulevich G, Djinović-Carugo K, Obinger C. Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies. ACS Catal 2017; 7:7962-7976. [PMID: 29142780 PMCID: PMC5678291 DOI: 10.1021/acscatal.7b01749] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/22/2017] [Indexed: 01/19/2023]
Abstract
![]()
The
heme enzyme chlorite dismutase (Cld) catalyzes the degradation
of chlorite to chloride and dioxygen. Although structure and steady-state
kinetics of Clds have been elucidated, many questions remain (e.g.,
the mechanism of chlorite cleavage and the pH dependence of the reaction).
Here, we present high-resolution X-ray crystal structures of a dimeric
Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and
the neutron structure at pH 9.0 together with the pH dependence of
the Fe(III)/Fe(II) couple, and the UV–vis and resonance Raman
spectral features. We demonstrate that the distal Arg127 cannot act
as proton acceptor and is fully ionized even at pH 9.0 ruling out
its proposed role in dictating the pH dependence of chlorite degradation.
Stopped-flow studies show that (i) Compound I and hypochlorite do
not recombine and (ii) Compound II is the immediately formed redox
intermediate that dominates during turnover. Homolytic cleavage of
chlorite is proposed.
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Affiliation(s)
- Irene Schaffner
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Georg Mlynek
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Nicola Flego
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Julian Libiseller-Egger
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Leighton Coates
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Stefan Hofbauer
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Marzia Bellei
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
103, 41125 Modena, Italy
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Gianantonio Battistuzzi
- Department
of Chemistry and Geology, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Kristina Djinović-Carugo
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Christian Obinger
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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6
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Geeraerts Z, Rodgers KR, DuBois JL, Lukat-Rodgers GS. Active Sites of O 2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations. Biochemistry 2017; 56:4509-4524. [PMID: 28758386 DOI: 10.1021/acs.biochem.7b00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O2-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO2- to O2 and Cl-. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate- and chlorate-respiring bacteria. The Cld from the Gram-negative human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their fluorides, chlorides, and hydroxides. Cooperative binding of Cl- to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(FeIII-F) bands at 385 and 390 cm-1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond donation to the F- ligand, indicating that atoms directly coordinated to heme iron are accessible to distal H-bond donation. New vibrational frequency correlations between either ν(FeIII-F) or ν(FeIII-OH) and ν(FeII-His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe-X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.
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Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Kenton R Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
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7
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Liao F, Yuan H, Du KJ, You Y, Gao SQ, Wen GB, Lin YW, Tan X. Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin. MOLECULAR BIOSYSTEMS 2016; 12:3139-45. [PMID: 27476534 DOI: 10.1039/c6mb00537c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.
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Affiliation(s)
- Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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8
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From chlorite dismutase towards HemQ - the role of the proximal H-bonding network in haeme binding. Biosci Rep 2016; 36:BSR20150330. [PMID: 26858461 PMCID: PMC4793301 DOI: 10.1042/bsr20150330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.
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9
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Bennett EH, Akbas N, Adrian SA, Lukat-Rodgers GS, Collins DP, Dawson JH, Allen CE, Schmitt MP, Rodgers KR, Dixon DW. Heme Binding by Corynebacterium diphtheriae HmuT: Function and Heme Environment. Biochemistry 2015; 54:6598-609. [PMID: 26478504 PMCID: PMC4943319 DOI: 10.1021/acs.biochem.5b00666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The heme uptake pathway (hmu) of Corynebacterium diphtheriae utilizes multiple proteins to bind and transport heme into the cell. One of these proteins, HmuT, delivers heme to the ABC transporter HmuUV. In this study, the axial ligation of the heme in ferric HmuT is probed by examination of wild-type (WT) HmuT and a series of conserved heme pocket residue mutants, H136A, Y235A, and M292A. Characterization by UV-visible, resonance Raman, and magnetic circular dichroism spectroscopies indicates that H136 and Y235 are the axial ligands in ferric HmuT. Consistent with this assignment of axial ligands, ferric WT and H136A HmuT are difficult to reduce while Y235A is reduced readily in the presence of dithionite. The FeCO Raman shifts in WT, H136A, and Y235A HmuT-CO complexes provide further evidence of the axial ligand assignments. Additionally, these frequencies provide insight into the nonbonding environment of the heme pocket. Ferrous Y235A and the Y235A-CO complex reveal that the imidazole of H136 exists in two forms, one neutral and one with imidazolate character, consistent with a hydrogen bond acceptor on the H136 side of the heme. The ferric fluoride complex of Y235A reveals the presence of at least one hydrogen bond donor on the Y235 side of the heme. Hemoglobin utilization assays showed that the axial Y235 ligand is required for heme uptake in HmuT.
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Affiliation(s)
| | - Neval Akbas
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965
| | - Seth A. Adrian
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Daniel P. Collins
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Courtni E. Allen
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation, and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Michael P. Schmitt
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation, and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Dabney W. Dixon
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965
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10
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Zhao J, Moretto J, Le P, Franzen S. Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium. J Phys Chem B 2015; 119:2827-38. [DOI: 10.1021/jp512996v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Justin Moretto
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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11
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Howes BD, Boechi L, Boffi A, Estrin DE, Smulevich G. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO. Adv Microb Physiol 2015; 67:85-126. [PMID: 26616516 DOI: 10.1016/bs.ampbs.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche, Università "Sapienza", Rome, Italy
| | - Dario E Estrin
- Departamento de Química Inorgánica, Analítica y Química Física and Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy.
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12
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Hydrogen-bonding network in heme active site regulates the hydrolysis activity of myoglobin. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Nicoletti FP, Bustamante JP, Droghetti E, Howes BD, Fittipaldi M, Bonamore A, Baiocco P, Feis A, Boffi A, Estrin DA, Smulevich G. Interplay of the H-Bond Donor–Acceptor Role of the Distal Residues in Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin. Biochemistry 2014; 53:8021-30. [DOI: 10.1021/bi501132a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | | | - Enrica Droghetti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Barry D. Howes
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Maria Fittipaldi
- INSTM
and Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - Alessandra Bonamore
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Paola Baiocco
- Center of
Life Nano Sciences, Italian Institute of Technology, Viale Regina
Elena 291, I-00161 Rome, Italy
| | - Alessandro Feis
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | | | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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14
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Du JF, Li W, Li L, Wen GB, Lin YW, Tan X. Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network. ChemistryOpen 2014; 4:97-101. [PMID: 25969804 PMCID: PMC4420578 DOI: 10.1002/open.201402108] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 01/03/2023] Open
Abstract
Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.
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Affiliation(s)
- Jun-Fang Du
- School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China))
| | - Wei Li
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University Liaocheng, 252059, (P. R. China)
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China)
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China)) ; Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China)
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
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15
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Meininger DJ, Muzquiz N, Arman HD, Tonzetich ZJ. A convenient procedure for the synthesis of fluoro-iron(III) complexes of common synthetic porphyrinates. J PORPHYR PHTHALOCYA 2014. [DOI: 10.1142/s108842461450014x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We report here an improved method for the preparation of fluoro-iron(III) porphyrinate complexes. Treatment of [ Fe 2( P )2(μ- O )] (P = tetraphenylporphyrinate {TPP}, tetra-p-tolylporphyrinate {TTP}, or octaethylporphyrinate {OEP}) or [ Fe ( OH )( OH 2)( TMP )] (TMP = tetramesitylporphyrinate) with the commercially available fluorinating agent, Et 3 N ·3 HF , in dichloromethane affords the desired [ FeF ( P )] complexes in a straightforward fashion and in good yield while avoiding the use of aqueous hydrofluoric acid. All fluoro-iron(III) complexes have been completely characterized by a series of different spectroscopic techniques including cyclic voltammetry. Reaction of a representative complex, [ FeF ( OEP )], with various chloride reagents demonstrates that halide exchange with chloride is facile, but only proceeds at an appreciable rate in the presence of proton sources. Unexpectedly, treatment of [ FeF ( OEP )] with NOBF 4 did not to lead formation of an oxidized species, but rather to formation of the { Fe – NO }6 complex, [ Fe ( NO )( OEP )]( BF 4).
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Affiliation(s)
- Daniel J. Meininger
- Department of Chemistry, University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, TX 78249, USA
| | - Nicanor Muzquiz
- Department of Chemistry, University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, TX 78249, USA
| | - Hadi D. Arman
- Department of Chemistry, University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, TX 78249, USA
| | - Zachary J. Tonzetich
- Department of Chemistry, University of Texas at San Antonio (UTSA), One UTSA Circle, San Antonio, TX 78249, USA
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16
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Cerda JF, Roeder MH, Houchins DN, Guzman CX, Amendola EJ, Castorino JD, Fritz AL. Electrochemical determination of heme-linked pKa values and the importance of using fluoride binding in heme proteins. Anal Biochem 2013; 443:75-7. [DOI: 10.1016/j.ab.2013.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 11/25/2022]
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17
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Insights into the distal heme pocket of H-NOX using fluoride as a probe for H-bonding interactions. J Inorg Biochem 2013; 126:91-5. [DOI: 10.1016/j.jinorgbio.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022]
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18
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Nicoletti FP, Droghetti E, Howes BD, Bustamante JP, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1901-9. [PMID: 23467007 DOI: 10.1016/j.bbapap.2013.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN(-) have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH(-) and Fe-CN(-) frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH(-) ligand, CN(-) binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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19
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Small ligand-globin interactions: reviewing lessons derived from computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1722-38. [PMID: 23470499 DOI: 10.1016/j.bbapap.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/24/2022]
Abstract
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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20
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Cametti M, Rissanen K. Highlights on contemporary recognition and sensing of fluoride anion in solution and in the solid state. Chem Soc Rev 2012. [PMID: 23188119 DOI: 10.1039/c2cs35439j] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The fluoride anion has recently gained well deserved attention among the scientific community for its importance in many fields of human activities, but also for concerns on its effect on health and the environment. Although surprisingly overlooked in systematic studies in the past, fluoride has nowadays become a topical target in the field of anion recognition. A multitude of scientific reports are published every year where the establishment of efficient and specific interaction with fluoride is sought in polar and aqueous media. Here, the emphasis is directed to a detailed description of the most interesting contemporary studies in the field, with a particular focus given to those published in the last few years.
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Affiliation(s)
- Massimo Cametti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, I-20131, Milan, Italy.
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21
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Insights into the anomalous heme pocket of rainbow trout myoglobin. J Inorg Biochem 2012; 109:1-8. [DOI: 10.1016/j.jinorgbio.2012.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/22/2011] [Accepted: 01/18/2012] [Indexed: 11/22/2022]
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22
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Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. J Am Chem Soc 2011; 133:20970-80. [DOI: 10.1021/ja209312k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Enrica Droghetti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandra Bonamore
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Natascia Sciamanna
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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