1
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Leavens MJ, Spang LE, Cherney MM, Bowler BE. Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues. Biochemistry 2021; 60:3071-3085. [PMID: 34606713 PMCID: PMC8751257 DOI: 10.1021/acs.biochem.1c00400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris cytochrome c', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome c (iso-1-Cytc). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cytc domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.
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Affiliation(s)
- Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Lisa E. Spang
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Melisa M. Cherney
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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2
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Fry HC, Peters BL, Ferguson AL. Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles. J Phys Chem B 2021; 125:1317-1330. [PMID: 33529038 DOI: 10.1021/acs.jpcb.0c07713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies, it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger, which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies.
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Affiliation(s)
- H Christopher Fry
- Center for Nansocale Materials, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Brandon L Peters
- Materials Science Division, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
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3
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Maglio O, Chino M, Vicari C, Pavone V, Louro RO, Lombardi A. Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts. Chem Commun (Camb) 2021; 57:990-993. [PMID: 33399143 DOI: 10.1039/d0cc06676a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fe-Mimochrome VI*a is a synthetic peroxidase and peroxygenase, featuring two different peptides that are covalently-linked to deuteroheme. To perform a systematic structure/function correlation, we purposely shortened the distance between the distal peptide and the heme, allowing for the separation and characterization of two regioisomers. They differ in both His axial-ligand orientation, as determined by paramagnetic NMR shifts, and activity. These findings highlight that synthetic metalloenzymes may provide an efficient tool for disentangling the role of axial ligand orientation over peroxidase activity.
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Affiliation(s)
- Ornella Maglio
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy. and IBB-CNR, Via Mezzocannone 16, Naples, 80134, Italy
| | - Marco Chino
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Claudia Vicari
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Vincenzo Pavone
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Ricardo O Louro
- ITQB-UNL, Av. da Republica (EAN), Oeiras 2780-157, Portugal.
| | - Angela Lombardi
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
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4
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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5
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Kielmann M, Senge MO. Molecular Engineering of Free-Base Porphyrins as Ligands-The N-H⋅⋅⋅X Binding Motif in Tetrapyrroles. Angew Chem Int Ed Engl 2019; 58:418-441. [PMID: 30067890 PMCID: PMC6391963 DOI: 10.1002/anie.201806281] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 12/15/2022]
Abstract
The core N-H units of planar porphyrins are often inaccessible to forming hydrogen-bonding complexes with acceptor molecules. This is due to the fact that the amine moieties are "shielded" by the macrocyclic system, impeding the formation of intermolecular H-bonds. However, methods exist to modulate the tetrapyrrole conformations and to reshape the vector of N-H orientation outwards, thus increasing their availability and reactivity. Strategies include the use of porpho(di)methenes and phlorins (calixphyrins), as well as saddle-distorted porphyrins. The former form cavities due to interruption of the aromatic system. The latter are highly basic systems and capable of binding anions and neutral molecules via N-H⋅⋅⋅X-type H-bonds. This Review discusses the role of porphyrin(oid) ligands in various coordination-type complexes, means to access the core for hydrogen bonding, the concept of conformational control, and emerging applications, such as organocatalysis and sensors.
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Affiliation(s)
- Marc Kielmann
- School of ChemistrySFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152–160 Pearse StreetDublin 2Ireland
| | - Mathias O. Senge
- School of ChemistrySFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152–160 Pearse StreetDublin 2Ireland
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6
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Kielmann M, Senge MO. Molekulares Engineering freier Porphyrinbasen als Liganden - das N-H⋅⋅⋅X-Bindungsmotiv in Tetrapyrrolen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Marc Kielmann
- School of Chemistry; SFI Tetrapyrrole Laboratory; Trinity Biomedical Sciences Institute; Trinity College Dublin; The University of Dublin; 152-160 Pearse Street Dublin 2 Irland
| | - Mathias O. Senge
- School of Chemistry; SFI Tetrapyrrole Laboratory; Trinity Biomedical Sciences Institute; Trinity College Dublin; The University of Dublin; 152-160 Pearse Street Dublin 2 Irland
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7
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Nye DB, Lecomte JTJ. Replacement of the Distal Histidine Reveals a Noncanonical Heme Binding Site in a 2-on-2 Hemoglobin. Biochemistry 2018; 57:5785-5796. [PMID: 30213188 PMCID: PMC6217817 DOI: 10.1021/acs.biochem.8b00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme ligation in hemoglobin is typically assumed by the "proximal" histidine. Hydrophobic contacts, ionic interactions, and the ligation bond secure the heme between two α-helices denoted E and F. Across the hemoglobin superfamily, several proteins also use a "distal" histidine, making the native state a bis-histidine complex. The group 1 truncated hemoglobin from Synechocystis sp. PCC 6803, GlbN, is one such bis-histidine protein. Ferric GlbN, in which the distal histidine (His46 or E10) has been replaced with a leucine, though expected to bind a water molecule and yield a high-spin iron complex at neutral pH, has low-spin spectral properties. Here, we applied nuclear magnetic resonance and electronic absorption spectroscopic methods to GlbN modified with heme and amino acid replacements to identify the distal ligand in H46L GlbN. We found that His117, a residue located in the C-terminal portion of the protein and on the proximal side of the heme, is responsible for the formation of an alternative bis-histidine complex. Simultaneous coordination by His70 and His117 situates the heme in a binding site different from the canonical site. This new holoprotein form is achieved with only local conformational changes. Heme affinity in the alternative site is weaker than in the normal site, likely because of strained coordination and a reduced number of specific heme-protein interactions. The observation of an unconventional heme binding site has important implications for the interpretation of mutagenesis results and globin homology modeling.
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Affiliation(s)
- Dillon B. Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Juliette T. J. Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
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8
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Nye DB, Preimesberger MR, Majumdar A, Lecomte JTJ. Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates. Biochemistry 2018; 57:631-644. [PMID: 29271191 DOI: 10.1021/acs.biochem.7b01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The hemoglobin of Synechococcus sp. PCC 7002, GlbN, is a monomeric group I truncated protein (TrHb1) that coordinates the heme iron with two histidine ligands at neutral pH. One of these is the distal histidine (His46), a residue that can be displaced by dioxygen and other small molecules. Here, we show with mutagenesis, electronic absorption spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy that at high pH and exclusively in the ferrous state, Lys42 competes with His46 for the iron coordination site. When b heme is originally present, the population of the lysine-bound species remains too small for detailed characterization; however, the population can be increased significantly by using dimethyl-esterified heme. Electronic absorption and NMR spectroscopies showed that the reversible ligand switching process occurs with an apparent pKa of 9.3 and a Lys-ligated population of ∼60% at the basic pH limit in the modified holoprotein. The switching rate, which is slow on the chemical shift time scale, was estimated to be 20-30 s-1 by NMR exchange spectroscopy. Lys42-His46 competition and attendant conformational rearrangement appeared to be related to weakened bis-histidine ligation and enhanced backbone dynamics in the ferrous protein. The pH- and redox-dependent ligand exchange process observed in GlbN illustrates the structural plasticity allowed by the TrHb1 fold and demonstrates the importance of electrostatic interactions at the heme periphery for achieving axial ligand selection. An analogy is drawn to the alkaline transition of cytochrome c, in which Lys-Met competition is detected at alkaline pH, but, in contrast to GlbN, in the ferric state only.
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Affiliation(s)
- Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Matthew R Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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9
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Danielson TA, Stine JM, Dar TA, Briknarova K, Bowler BE. Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-cytochrome c. Biochemistry 2017; 56:6662-6676. [PMID: 29148740 DOI: 10.1021/acs.biochem.7b01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54 → His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional nuclear magnetic resonance methods to assign 1H and 15N backbone amide and 13C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54 → His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6.4, where the His54-heme loop is formed, and pH 3.6, where the His54-heme loop is broken. Using the secondary structure propensity score, with the 6 M guanidine hydrochloride chemical shift data as a random coil reference state for data collected in 3 M guanidine hydrochloride, we found residual helical structure in the denatured state for the 60s helix and the C-terminal helix, but not in the N-terminal helix in the presence or absence of the His54-heme loop. Non-native helical structure is observed in two regions that form Ω-loops in the native state. There is more residual helical structure in the C-terminal helix at pH 6.4 when the loop is formed. Loop formation also appears to stabilize helical structure near His54, consistent with induction of helical structure observed when His-heme bonds form in heme-peptide model systems. The results are discussed in the context of the folding mechanism of cytochrome c.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Jessica M Stine
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Tanveer A Dar
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Klara Briknarova
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
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10
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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11
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Affiliation(s)
- Kandala Laxman
- Department of Chemistry; Indian Institute of Technology, Bombay; 400076 Powai, Mumbai India
- IIT Bombay; IITB-Monash Research Academy; 400076 Powai, Mumbai India
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12
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Solomon LA, Kronenberg JB, Fry HC. Control of Heme Coordination and Catalytic Activity by Conformational Changes in Peptide-Amphiphile Assemblies. J Am Chem Soc 2017; 139:8497-8507. [PMID: 28505436 DOI: 10.1021/jacs.7b01588] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling peptide materials have gained significant attention, due to well-demonstrated applications, but they are functionally underutilized. To advance their utility, we use noncovalent interactions to incorporate the biological cofactor heme-B for catalysis. Heme-proteins achieve differing functions through structural and coordinative variations. Here, we replicate this phenomenon by highlighting changes in heme reactivity as a function of coordination, sequence, and morphology (micelles versus fibers) in a series of simple peptide amphiphiles with the sequence c16-xyL3K3-CO2H where c16 is a palmitoyl moiety and xy represents the heme binding region: AA, AH, HH, and MH. The morphology of this peptide series is characterized using transmission electron and atomic force microscopies as well as dynamic light scattering. Within this small library of peptide constructs, we show that three spectroscopically (UV/visible and electron paramagnetic resonance) distinct heme environments were generated: noncoordinated/embedded high-spin, five-coordinate high-spin, and six-coordinate low-spin. The resulting material's functional dependence on sequence and supramolecular morphology is highlighted 2-fold. First, the heme active site binds carbon monoxide in both micelles and fibers, demonstrating that the heme active site in both morphologies is accessible to small molecules for catalysis. Second, peroxidase activity was observed in heme-containing micelles yet was significantly reduced in heme-containing fibers. We briefly discuss the implications these findings have in the production of functional, self-assembling peptide materials.
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Affiliation(s)
- Lee A Solomon
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jacob B Kronenberg
- Illinois Math and Science Academy , 1500 West Sullivan Road, Aurora, Illinois 60506, United States
| | - H Christopher Fry
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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13
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Preimesberger MR, Majumdar A, Lecomte JTJ. Dynamics of Lysine as a Heme Axial Ligand: NMR Analysis of the Chlamydomonas reinhardtii Hemoglobin THB1. Biochemistry 2017; 56:551-569. [DOI: 10.1021/acs.biochem.6b00926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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14
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Christoforidis KC, Pantazis DA, Bonilla LL, Bletsa E, Louloudi M, Deligiannakis Y. Axial ligand effect on the catalytic activity of biomimetic Fe-porphyrin catalyst: An experimental and DFT study. J Catal 2016. [DOI: 10.1016/j.jcat.2016.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Honorio-Felício N, Carepo MS, de F. Paulo T, de França Lopes LG, Sousa EH, Diógenes IC, Bernhardt PV. The Heme-Based Oxygen Sensor Rhizobium etli FixL: Influence of Auxiliary Ligands on Heme Redox Potential and Implications on the Enzyme Activity. J Inorg Biochem 2016; 164:34-41. [DOI: 10.1016/j.jinorgbio.2016.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/05/2016] [Accepted: 08/22/2016] [Indexed: 12/09/2022]
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16
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Amdursky N. Electron Transfer across Helical Peptides. Chempluschem 2015; 80:1075-1095. [DOI: 10.1002/cplu.201500121] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/06/2015] [Indexed: 02/05/2023]
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17
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Rice SL, Preimesberger MR, Johnson EA, Lecomte JTJ. Introduction of a covalent histidine-heme linkage in a hemoglobin: a promising tool for heme protein engineering. J Inorg Biochem 2014; 141:198-207. [PMID: 25304367 DOI: 10.1016/j.jinorgbio.2014.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/15/2014] [Accepted: 09/15/2014] [Indexed: 11/28/2022]
Abstract
The hemoglobins of the cyanobacteria Synechococcus and Synechocystis (GlbNs) are capable of spontaneous and irreversible attachment of the b heme to the protein matrix. The reaction, which saturates the heme 2-vinyl by addition of a histidine residue, is reproduced in vitro by preparing the recombinant apoprotein, adding ferric heme, and reducing the iron to the ferrous state. Spontaneous covalent attachment of the heme is potentially useful for protein engineering purposes. Thus, to explore whether the histidine-heme linkage can serve in such applications, we attempted to introduce it in a test protein. We selected as our target the heme domain of Chlamydomonas eugametos LI637 (CtrHb), a eukaryotic globin that exhibits less than 50% sequence identity with the cyanobacterial GlbNs. We chose two positions, 75 in the FG corner and 111 in the H helix, to situate a histidine near a vinyl group. We characterized the proteins with gel electrophoresis, absorbance spectroscopy, and NMR analysis. Both T111H and L75H CtrHbs reacted upon reduction of the ferric starting material containing cyanide as the distal ligand to the iron. With L75H CtrHb, nearly complete (>90%) crosslinking was observed to the 4-vinyl as expected from the X-ray structure of wild-type CtrHb. Reaction of T111H CtrHb also occurred at the 4-vinyl, in a 60% yield indicating a preference for the flipped heme orientation in the starting material. The work suggests that the His-heme modification will be applicable to the design of proteins with a non-dissociable heme group.
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Affiliation(s)
- Selena L Rice
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Eric A Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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18
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Distal-proximal crosstalk in the heme binding pocket of the NO sensor DNR. Biometals 2014; 27:763-73. [PMID: 25007853 DOI: 10.1007/s10534-014-9770-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/25/2014] [Indexed: 01/10/2023]
Abstract
In the opportunistic pathogen Pseudomonas aeruginosa the denitrification process is triggered by nitric oxide (NO) and plays a crucial role for the survival in chronic infection sites as a microaerobic-anaerobic biofilm. This respiratory pathway is transcriptionally induced by DNR, an heme-based gas sensor which positively responds to NO. Molecular details of the NO sensing mechanism employed by DNR are now emerging: we recently reported an in vitro study which dissected, for the first time, the heme-iron environment and identified one of the heme axial ligand (i.e. His187), found to be crucial to respond to NO. Nevertheless, the identification of the second heme axial ligand has been unsuccessful, given that a peculiar phenomenon of ligand switching around the heme-iron presumably occurs in DNR. The unusual heme binding properties of DNR could be due to the remarkable flexibility in solution of DNR itself, which, in turns, is crucial for the sensing activity; protein flexibility and dynamics indeed represent a common strategy employed by heme-based redox sensors, which present features deeply different from those of "canonical" hemeproteins. The capability of DNR to deeply rearrange around the heme-iron as been here demonstrated by means of spectroscopic characterization of the H167A/H187A DNR double mutant, which shows unusual kinetics of binding of NO and CO. Moreover, we show that the alteration (such as histidines mutations) of the distal side of the heme pocket is perceived by the proximal one, possibly via the DNR protein chain.
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19
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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20
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Bhowmik S, Dey S, Sahoo D, Rath SP. Unusual Stabilization of an Intermediate Spin State of Iron upon the Axial Phenoxide Coordination of a Diiron(III)-Bisporphyrin: Effect of Heme-Heme Interactions. Chemistry 2013; 19:13732-44. [DOI: 10.1002/chem.201301242] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Indexed: 11/06/2022]
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21
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Kepp KP, Dasmeh P. Effect of Distal Interactions on O2 Binding to Heme. J Phys Chem B 2013; 117:3755-70. [DOI: 10.1021/jp400260u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Pouria Dasmeh
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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22
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Wang L, Luan Q, Yang D, Yao X, Zhou K. Strong electron-conjugation interaction facilitates electron transfer of hemoglobin by Ce(OH)3 nanorods. RSC Adv 2013. [DOI: 10.1039/c3ra40336j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Rinaldo S, Castiglione N, Giardina G, Caruso M, Arcovito A, Longa SD, D'Angelo P, Cutruzzolà F. Unusual heme binding properties of the dissimilative nitrate respiration regulator, a bacterial nitric oxide sensor. Antioxid Redox Signal 2012; 17:1178-89. [PMID: 22424265 DOI: 10.1089/ars.2011.4226] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIMS In the opportunistic pathogen Pseudomonas aeruginosa, nitric oxide (NO) triggers the respiration of nitrate (denitrification), thus allowing survival in chronic infection sites as a microaerobic-anaerobic biofilm. The NO-dependent induction of denitrification is mediated by the dissimilative nitrate respiration regulator (DNR), a transcription factor forming a stable complex with heme, which is required to sense the physiological messenger (i.e., NO). The molecular details of NO sensing in DNR and, more in general, in this class of sensors are largely unknown, and a study aimed at integrating microbiology and biochemistry is needed. RESULTS Here we present a comprehensive study, including in vivo results and spectroscopy, kinetics, and protein engineering, that demonstrates the direct involvement of a histidine residue in heme iron coordination. Moreover, a peculiar phenomenon of ligand switching around heme iron, which hampers the identification of the second heme axial ligand, is also suggested. These results indicate that DNR is characterized by a remarkable flexibility in solution, as observed for other cAMP receptor protein/fumarate and nitrate reductase regulators (CRP-FNR) to which DNR belongs. INNOVATION The present work represents one of the few studies focused on the biochemistry of NO sensing by bacterial transcriptional regulators. The data presented demonstrate that structural plasticity of DNR is crucial for the sensing activity and confers to the protein unusual heme binding properties. CONCLUSIONS Protein flexibility and dynamics is a key structural feature essential to explain the evolutionary success and adaptability of CRP-FNR, and may represent a common strategy employed by heme-based redox sensors, which presents features deeply different from those of canonical hemeproteins.
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Affiliation(s)
- Serena Rinaldo
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
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24
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Pond MP, Majumdar A, Lecomte JTJ. Influence of heme post-translational modification and distal ligation on the backbone dynamics of a monomeric hemoglobin. Biochemistry 2012; 51:5733-47. [PMID: 22775272 DOI: 10.1021/bi300624a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The cyanobacterium Synechococcus sp. PCC 7002 uses a hemoglobin of the truncated lineage (GlbN) in the detoxification of reactive species generated in the assimilation of nitrate. In view of a sensing or enzymatic role, several states of GlbN are of interest with respect to its structure-activity relationship. Nuclear magnetic resonance spectroscopy was applied to compare the structure and backbone dynamics of six GlbN forms differing in their oxidation state [Fe(II) or Fe(III)], distal ligand to the iron (histidine, carbon monoxide, or cyanide), or heme post-translational modification (b heme or covalently attached heme). Structural properties were assessed with pseudocontact shift calculations. (15)N relaxation data were analyzed by reduced spectral density mapping (picosecond to nanosecond motions) and by inspection of elevated R(2) values (microsecond to millisecond motions). On the picosecond to nanosecond time scale, GlbN exhibited little flexibility and was unresponsive to the differences among the various forms. Regions of slightly higher mobility were the CE turn, the EF loop, and the H-H' kink. In contrast, fluctuations on the microsecond to millisecond time scale depended on the form. Cyanide binding to the ferric state did not enhance motions, whereas reduction to the ferrous bis-histidine state resulted in elevated R(2) values for several amides. This response was attributed, at least in part, to a weakening of the distal histidine coordination. Carbon monoxide binding quenched some of these fluctuations. The results emphasized the role of the distal ligand in dictating backbone flexibility and illustrated the multiple ways in which motions are controlled by the hemoglobin fold.
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Affiliation(s)
- Matthew P Pond
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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25
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Abstract
The density functional calculations suggest that the expansion of the corrin macrocycle's N(4) core by 0.06-0.10 Å leads to an appreciable lowering of 100-150 mV vs. saturated calomel electrode in the reduction potentials of two biologically important B(12) cofactors namely methylcobalamin and adenosylcobalamin respectively. This redox tuning of B(12) cofactors may encourage the electron transfer-based activation mechanism for B(12)-dependent enzymes.
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Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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26
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Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2012; 17:741-60. [DOI: 10.1007/s00775-012-0893-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
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27
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Shinde S, Cordova JM, Woodrum BW, Ghirlanda G. Modulation of function in a minimalist heme-binding membrane protein. J Biol Inorg Chem 2012; 17:557-64. [PMID: 22307279 DOI: 10.1007/s00775-012-0876-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 01/14/2012] [Indexed: 12/21/2022]
Abstract
De novo designed heme-binding proteins have been used successfully to recapitulate features of natural hemoproteins. This approach has now been extended to membrane-soluble model proteins. Our group designed a functional hemoprotein, ME1, by engineering a bishistidine binding site into a natural membrane protein, glycophorin A (Cordova et al. in J Am Chem Soc 129:512-518, 2007). ME1 binds iron(III) protoporphyrin IX with submicromolar affinity, has a redox potential of -128 mV, and displays peroxidase activity. Here, we show the effect of aromatic residues in modulating the redox potential in the context of a membrane-soluble model system. We designed aromatic interactions with the heme through a single-point mutant, G25F, in which a phenylalanine is designed to dock against the porphyrin ring. This mutation results in roughly tenfold tighter binding to iron(III) protoporphyrin IX (K(d,app) = 6.5 × 10(-8) M), and lowers the redox potential of the cofactor to -172 mV. This work demonstrates that specific design features aimed at controlling the properties of bound cofactors can be introduced in a minimalist membrane hemoprotein model. The ability to modulate the redox potential of cofactors embedded in artificial membrane proteins is crucial for the design of electron transfer chains across membranes in functional photosynthetic devices.
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Affiliation(s)
- Sandip Shinde
- Department of Chemistry and Biochemistry, ASU, Tempe, AZ 85287, USA
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28
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Zhang L, Anderson JLR, Ahmed I, Norman JA, Negron C, Mutter AC, Dutton PL, Koder RL. Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein. Biochemistry 2011; 50:10254-61. [PMID: 22004125 DOI: 10.1021/bi201242a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the mutational analysis of an artificial oxygen transport protein, HP7, which operates via a mechanism akin to that of human neuroglobin and cytoglobin. This protein destabilizes one of two heme-ligating histidine residues by coupling histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Replacement of these glutamate residues with alanine, which is uncharged, increases the affinity of the distal histidine ligand by a factor of 13. Paradoxically, it also decreases heme binding affinity by a factor of 5 in the reduced state and 60 in the oxidized state. Application of a three-state binding model, in which an initial pentacoordinate binding event is followed by a protein conformational change to hexacoordinate, provides insight into the mechanism of this seemingly counterintuitive result: the initial pentacoordinate encounter complex is significantly destabilized by the loss of the glutamate side chains, and the increased affinity for the distal histidine only partially compensates for that. These results point to the importance of considering each oxidation and conformational state in the design of functional artificial proteins.
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Affiliation(s)
- Lei Zhang
- Department of Physics, The City College of New York, New York, New York 10031, United States
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29
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Probing the local electronic and geometric properties of the heme iron center in a H-NOX domain. J Inorg Biochem 2011; 105:784-92. [PMID: 21497576 DOI: 10.1016/j.jinorgbio.2011.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/03/2011] [Accepted: 03/04/2011] [Indexed: 11/23/2022]
Abstract
Heme-Nitric oxide and/or OXygen binding (H-NOX) proteins are a family of diatomic gas binding hemoproteins that have attracted intense research interest. Here we employ X-ray absorption near-edge structure (XANES) spectroscopy to study the nitric oxide (NO) binding site of H-NOX. This is the first time this technique has been utilized to examine the NO/H-NOX signaling pathway. XANES spectra of wildtype and a point mutant (proline 115 to alanine, P115A) of the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) were obtained and analyzed for ferrous and ferric complexes of the protein. This work provides specific structural characterization of the solution state of several Tt H-NOX ferrous complexes (-unligated, -NO, and -CO) that were previously unavailable. Our iron K-edges indicate effective charge on the iron center in the various complexes and report on the electronic environment of heme iron. We analyzed the ligand field indicator ratio (LFIR), which is extracted from XANES spectra, for each complex, providing an understanding of ligand field strength, spin state of the central iron, movement of the iron atom upon ligation, and ligand binding properties. In particular, our LFIRs indicate that the heme iron is dramatically displaced towards the distal pocket during ligand binding. Based on these results, we propose that iron displacement towards the distal heme pocket is an essential step in signal initiation in H-NOX proteins. This provides a mechanistic link between ligand binding and the changes in heme and protein conformation that have been observed for H-NOX family members during signaling.
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30
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Chemical reactivity of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 hemoglobins: covalent heme attachment and bishistidine coordination. J Biol Inorg Chem 2011; 16:539-52. [PMID: 21240532 DOI: 10.1007/s00775-011-0754-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/03/2011] [Indexed: 12/16/2022]
Abstract
In the absence of an exogenous ligand, the hemoglobins from the cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 coordinate the heme group with two axial histidines (His46 and His70). These globins also form a covalent linkage between the heme 2-vinyl substituent and His117. The in vitro mechanism of heme attachment to His117 was examined with a combination of site-directed mutagenesis, NMR spectroscopy, and optical spectroscopy. The results supported an electrophilic addition with vinyl protonation being the rate-determining step. Replacement of His117 with a cysteine demonstrated that the reaction could occur with an alternative nucleophile. His46 (distal histidine) was implicated in the specificity of the reaction for the 2-vinyl group as well as protection of the protein from oxidative damage caused by exposure to exogenous H(2)O(2).
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31
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Olea C, Kuriyan J, Marletta MA. Modulating heme redox potential through protein-induced porphyrin distortion. J Am Chem Soc 2011; 132:12794-5. [PMID: 20735135 DOI: 10.1021/ja106252b] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoproteins are ubiquitous in biology and are commonly involved in critical processes such as electron transfer, oxidative phosphorylation, and signal transduction. Both the protein environment and the heme cofactor contribute to generate the range of chemical properties needed for these diverse functions. Using the heme nitric oxide/oxygen binding (H-NOX) protein from the thermophilic bacterium Thermoanaerobacter tengcongensis, we have shown that heme electronic properties can be modulated by porphyrin distortion within the same protein scaffold without changing the heme ligation state or heme environment. The degree of heme distortion was found to be directly correlated to the electron density at the heme iron, as evidenced by dramatic changes in the heme redox potential and pK(a) of the distal ligand ((-)OH vs H(2)O). Protein-induced porphyrin distortion represents a new strategy to rationally tune the electronic properties of protein-bound porphyrins and could be used to engineer proteins with desired reactivity or functionality.
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Affiliation(s)
- Charles Olea
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, and Division of Physical Biosciences, University of California, Berkeley, Berkeley, California 94720-3220, USA
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32
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Bowman SEJ, Bren KL. Variation and analysis of second-sphere interactions and axial histidinate character in c-type cytochromes. Inorg Chem 2010; 49:7890-7. [PMID: 20666367 PMCID: PMC2933145 DOI: 10.1021/ic100899k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The electron-donating properties of the axial His ligand to heme iron in cytochromes c (cyts c) are found to be correlated with the midpoint reduction potential (E(m)) in variants of Hydrogenobacter thermophilus cytochrome c(552) (Ht cyt c(552)) in which mutations have been made in and near the Cys-X-X-Cys-His (CXXCH) heme-binding motif. To probe the strength of the His-Fe(III) interaction, we have measured (13)C nuclear magnetic resonance (NMR) chemical shifts for (13)CN(-) bound to heme iron trans to the axial His in Ht Fe(III) cyt c(552) variants. We observe a linear relationship between these (13)C chemical shifts and E(m), indicating that the His-Fe(III) bond strength correlates with E(m). To probe a conserved hydrogen bonding interaction between the axial His Hdelta1 and the backbone carbonyl of a Pro residue, we measured the pK(a) of the axial His Hdelta1 proton (pK(a(2))), which we propose to relate to the His-Fe(III) interaction, reduction potential, and local electrostatic effects. The observed linear relationship between the axial His (13)Cbeta chemical shift and E(m) is proposed to reflect histidinate (anionic) character of the ligand. A linear relationship also is seen between the average heme methyl (1)H chemical shift and E(m) which may reflect variation in axial His electron-donating properties or in the ruffling distortion of the heme plane. In summary, chemical shifts of the axial His and exogenous CN(-) bound trans to His are shown to be sensitive probes of the His-Fe(III) interaction in variants of Ht cyt c(552) and display trends that correlate with E(m).
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Affiliation(s)
- Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
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33
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Christoforidis KC, Louloudi M, Deligiannakis Y. Substrate and co-catalyst effects on the local coordination environment of a Fe–porphyrin catalyst. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Sturms R, Kakar S, Trent J, Hargrove MS. Trema and parasponia hemoglobins reveal convergent evolution of oxygen transport in plants. Biochemistry 2010; 49:4085-93. [PMID: 20377207 DOI: 10.1021/bi1002844] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All plants contain hemoglobins that fall into distinct phylogenetic classes. The subset of plants that carry out symbiotic nitrogen fixation expresses hemoglobins that scavenge and transport oxygen to bacterial symbiotes within root nodules. These "symbiotic" oxygen transport hemoglobins are distinct in structure and function from the nonoxygen transport ("nonsymbiotic") Hbs found in all plants. Hemoglobins found in two closely related plants present a paradox concerning hemoglobin structure and function. Parasponia andersonii is a nitrogen-fixing plant that expresses a symbiotic hemoglobin (ParaHb) characteristic of oxygen transport hemoglobins in having a pentacoordinate ferrous heme iron, moderate oxygen affinity, and a relatively rapid oxygen dissociation rate constant. A close relative that does not fix nitrogen, Trema tomentosa, expresses hemoglobin (TremaHb) sharing 93% amino acid identity to ParaHb, but its phylogeny predicts a typical nonsymbiotic hemoglobin with a hexacoordinate heme iron, high oxygen affinity, and slow oxygen dissociation rate constant. Here we characterize heme coordination and oxygen binding in TremaHb and ParaHb to investigate whether or not two hemoglobins with such high sequence similarity are actually so different in functional behavior. Our results indicate that the two proteins resemble nonsymbiotic hemoglobins in the ferric oxidation state and symbiotic hemoglobins in the ferrous oxidation state. They differ from each other only in oxygen affinity and oxygen dissociation rate constants, two factors key to their different functions. These results demonstrate distinct mechanisms for convergent evolution of oxygen transport in different phylogenetic classes of plant hemoglobins.
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Affiliation(s)
- Ryan Sturms
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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35
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Li CZ, Taniguchi I, Mulchandani A. Redox properties of engineered ruthenium myoglobin. Bioelectrochemistry 2009; 75:182-8. [DOI: 10.1016/j.bioelechem.2009.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 04/10/2009] [Accepted: 04/16/2009] [Indexed: 11/28/2022]
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36
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Negron C, Fufezan C, Koder RL. Geometric constraints for porphyrin binding in helical protein binding sites. Proteins 2009; 74:400-16. [PMID: 18636480 DOI: 10.1002/prot.22143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.
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Affiliation(s)
- Christopher Negron
- Department of Physics, the City College of New York, New York, New York 10031, USA
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37
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Engineering heme binding sites in monomeric rop. J Biol Inorg Chem 2009; 14:497-505. [PMID: 19152012 DOI: 10.1007/s00775-009-0465-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
Heme ligands were introduced in the hydrophobic core of an engineered monomeric ColE1 repressor of primer (rop-S55) in two different layers of the heptad repeat. Mutants rop-L63M/F121H (layer 1) and rop-L56H/L113H (layer 3) were found to bind heme with a K (D) of 1.1 +/- 0.2 and 0.47 +/- 0.07 microM, respectively. The unfolding of heme-bound and heme-free mutants, in the presence of guanidinium hydrochloride, was monitored by both circular dichroism and fluorescence spectroscopy. For the heme-bound rop mutants, the total free energy change was 0.5 kcal/mol higher in the layer 3 mutant compared with that in the layer1 mutant. Heme binding also stabilized these mutants by increasing the [DGobsH2O] by 1.4 and 1.8 kcal/mol in rop-L63M/F121H and rop-L56H/L113H, respectively. The reduction potentials measured by spectroelectrochemical titrations were calculated to be -154 +/- 2 mV for rop-56H/113H and -87.5 +/- 1.2 mV for rop-L63M/F121H. The mutant designed to bind heme in a more buried environment (layer 3) showed tighter heme binding, a higher stability, and a different reduction potential compared with the mutant designed to bind heme in layer 1.
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38
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Olea C, Boon EM, Pellicena P, Kuriyan J, Marletta MA. Probing the function of heme distortion in the H-NOX family. ACS Chem Biol 2008; 3:703-10. [PMID: 19032091 DOI: 10.1021/cb800185h] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoproteins carry out diverse functions utilizing a wide range of chemical reactivity while employing the same heme prosthetic group. It is clear from high-resolution crystal structures and biochemical studies that protein-bound hemes are not planar and adopt diverse conformations. The crystal structure of an H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) contains the most distorted heme reported to date. In this study, Tt H-NOX was engineered to adopt a flatter heme by mutating proline 115, a conserved residue in the H-NOX family, to alanine. Decreasing heme distortion in Tt H-NOX increases affinity for oxygen and decreases the reduction potential of the heme iron. Additionally, flattening the heme is associated with significant shifts in the N-terminus of the protein. These results show a clear link between the heme conformation and Tt H-NOX structure and demonstrate that heme distortion is an important determinant for maintaining biochemical properties in H-NOX proteins.
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Affiliation(s)
| | - Elizabeth M. Boon
- Department of Chemistry, California Institute for Quantitative Biosciences
| | | | - John Kuriyan
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael A. Marletta
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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39
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Bowman SEJ, Bren KL. The chemistry and biochemistry of heme c: functional bases for covalent attachment. Nat Prod Rep 2008; 25:1118-30. [PMID: 19030605 DOI: 10.1039/b717196j] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A discussion of the literature concerning the synthesis, function, and activity of heme c-containing proteins is presented. Comparison of the properties of heme c, which is covalently bound to protein, is made to heme b, which is bound noncovalently. A question of interest is why nature uses biochemically expensive heme c in many proteins when its properties are expected to be similar to heme b. Considering the effects of covalent heme attachment on heme conformation and on the proximal histidine interaction with iron, it is proposed that heme attachment influences both heme reduction potential and ligand-iron interactions.
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Affiliation(s)
- Sarah E J Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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40
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Investigation of ascorbate-mediated iron release from ferric phytosiderophores in the presence of nicotianamine. Biometals 2008; 21:503-13. [DOI: 10.1007/s10534-008-9137-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 02/14/2008] [Indexed: 12/22/2022]
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41
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Wang L, Cowley AB, Benson DR. Enhancing the thermal stability of mitochondrial cytochrome b5 by introducing a structural motif characteristic of the less stable microsomal isoform. Protein Eng Des Sel 2007; 20:511-20. [PMID: 17962223 DOI: 10.1093/protein/gzm053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Outer mitochondrial membrane cytochrome b5 (OM b5) is the most thermostable cytochrome b5 isoform presently known. Herein, we show that OM b5 thermal stability is substantially enhanced by swapping an apparently invariant motif in its heme-independent folding core with the corresponding motif characteristic of its less stable evolutionary relative, microsomal cytochrome b5 (Mc b5). The motif swap involved replacing two residues, Arg15 with His and Glu20 with Ser, thereby introducing a Glu11-His15-Ser20 H-bonding triad on the protein surface along with a His15/Trp22 pi-stacking interaction. The ferric and ferrous forms of the OM b5 R15H/E20S double mutant have thermal denaturation midpoints (Tm values) of approximately 93 degrees C and approximately 104 degrees C, respectively. A 15 degrees C increase in apoprotein Tm plays a key role in the holoprotein thermal stability enhancement, and is achieved by one of the most common natural mechanisms for stabilization of thermophilic versus mesophilic proteins: raising the unfolding free energy along the entire stability curve.
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Affiliation(s)
- Lijun Wang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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42
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Michel LV, Ye T, Bowman SEJ, Levin BD, Hahn MA, Russell BS, Elliott SJ, Bren KL. Heme attachment motif mobility tunes cytochrome c redox potential. Biochemistry 2007; 46:11753-60. [PMID: 17900177 PMCID: PMC2606054 DOI: 10.1021/bi701177j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen exchange (HX) rates and midpoint potentials (Em) of variants of cytochrome c from Pseudomonas aeruginosa (Pa cyt c551) and Hydrogenobacter thermophilus (Ht cyt c552) have been characterized in an effort to develop an understanding of the impact of properties of the Cys-X-X-Cys-His pentapeptide c-heme attachment (CXXCH) motif on heme redox potential. Despite structural conservation of the CXXCH motif, Ht cyt c552 exhibits a low level of protection from HX for amide protons within this motif relative to Pa cyt c551. Site-directed mutants have been prepared to determine the structural basis for and functional implications of these variations on HX behavior. The double mutant Ht-M13V/K22M displays suppressed HX within the CXXCH motif as well as a decreased Em (by 81 mV), whereas the corresponding double mutant of Pa cyt c551 (V13M/M22K) exhibits enhanced HX within the CXXCH pentapeptide and a modest increase in Em (by 30 mV). The changes in Em correlate with changes in axial His chemical shifts in the ferric proteins reflecting the extent of histidinate character. Thus, the mobility of the CXXCH pentapeptide is found to impact the His-Fe(III) interaction and therefore the heme redox potential.
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Affiliation(s)
| | | | | | | | | | | | | | - Kara L. Bren
- To whom correspondence should be addressed: Department of Chemistry, University of Rochester, Rochester, NY 14627-0216. Telephone: (585) 275-4335. Fax: (585) 276-0205. e-mail:
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Hoy JA, Robinson H, Trent JT, Kakar S, Smagghe BJ, Hargrove MS. Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport. J Mol Biol 2007; 371:168-79. [PMID: 17560601 DOI: 10.1016/j.jmb.2007.05.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 05/07/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Abstract
The evolution of oxygen transport hemoglobins occurred on at least two independent occasions. The earliest event led to myoglobin and red blood cell hemoglobin in animals. In plants, oxygen transport "leghemoglobins" evolved much more recently. In both events, pentacoordinate heme sites capable of inert oxygen transfer evolved from hexacoordinate hemoglobins that have unrelated functions. High sequence homology between hexacoordinate and pentacoordinate hemoglobins in plants has poised them for potential structural analysis leading to a molecular understanding of this important evolutionary event. However, the lack of a plant hexacoordinate hemoglobin structure in the exogenously ligand-bound form has prevented such comparison. Here we report the crystal structure of the cyanide-bound hexacoordinate hemoglobin from barley. This presents the first opportunity to examine conformational changes in plant hexacoordinate hemoglobins upon exogenous ligand binding, and reveals structural mechanisms for stabilizing the high-energy pentacoordinate heme conformation critical to the evolution of reversible oxygen binding hemoglobins.
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Affiliation(s)
- Julie A Hoy
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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