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Adepu KK, Anishkin A, Adams SH, Chintapalli SV. A versatile delivery vehicle for cellular oxygen and fuels or metabolic sensor? A review and perspective on the functions of myoglobin. Physiol Rev 2024; 104:1611-1642. [PMID: 38696337 DOI: 10.1152/physrev.00031.2023] [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: 07/28/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/04/2024] Open
Abstract
A canonical view of the primary physiological function of myoglobin (Mb) is that it is an oxygen (O2) storage protein supporting mitochondrial oxidative phosphorylation, especially as the tissue O2 partial pressure (Po2) drops and Mb off-loads O2. Besides O2 storage/transport, recent findings support functions for Mb in lipid trafficking and sequestration, interacting with cellular glycolytic metabolites such as lactate (LAC) and pyruvate (PYR), and "ectopic" expression in some types of cancer cells and in brown adipose tissue (BAT). Data from Mb knockout (Mb-/-) mice and biochemical models suggest additional metabolic roles for Mb, especially regulation of nitric oxide (NO) pools, modulation of BAT bioenergetics, thermogenesis, and lipid storage phenotypes. From these and other findings in the literature over many decades, Mb's function is not confined to delivering O2 in support of oxidative phosphorylation but may serve as an O2 sensor that modulates intracellular Po2- and NO-responsive molecular signaling pathways. This paradigm reflects a fundamental change in how oxidative metabolism and cell regulation are viewed in Mb-expressing cells such as skeletal muscle, heart, brown adipocytes, and select cancer cells. Here, we review historic and emerging views related to the physiological roles for Mb and present working models illustrating the possible importance of interactions between Mb, gases, and small-molecule metabolites in regulation of cell signaling and bioenergetics.
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Affiliation(s)
- Kiran Kumar Adepu
- Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland, United States
| | - Sean H Adams
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, California, United States
- Center for Alimentary and Metabolic Science, School of Medicine, University of California Davis, Sacramento, California, United States
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States
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2
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Mathur S, Yadav SK, Yadav K, Bhatt S, Kundu S. A novel single sensor hemoglobin domain from the thermophilic cyanobacteria Thermosynechococcus elongatus BP-1 exhibits higher pH but lower thermal stability compared to globins from mesophilic organisms. Int J Biol Macromol 2023; 240:124471. [PMID: 37076076 DOI: 10.1016/j.ijbiomac.2023.124471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Thermosynechococcus elongatus-BP1 belongs to the class of photoautotrophic cyanobacterial organisms. The presence of chlorophyll a, carotenoids, and phycocyanobilin are the characteristics that categorize T. elongatus as a photosynthetic organism. Here, we report the structural and spectroscopic characteristics of novel hemoglobin (Hb) Synel Hb from T.elongatus, synonymous with Thermosynechococcus vestitus BP-1. The X-ray crystal structure (2.15 Å) of Synel Hb suggests the presence of a globin domain with a pre-A helix similar to the sensor domain (S) family of Hbs. The rich hydrophobic core accommodates heme in a penta-coordinated state and readily binds an extraneous ligand(imidazole). The absorption and circular dichroic spectral analysis of Synel Hb reiteratedthat the heme is in FeIII+ state with a predominantly α-helical structure similar to myoglobin. Synel Hb displays higher resistance to structural perturbations induced via external stresses like pH and guanidium hydrochloride, which is comparable to Synechocystis Hb. However, Synel Hb exhibited lower thermal stability compared to mesophilic hemoglobins. Overall, the data is suggestive of the structural sturdiness of Synel Hb, which probably corroborates its origin in extreme thermophilic conditions. The stable globin provides scope for further investigation and may lead to new insights with scope for engineering stability in hemoglobin-based oxygen carriers.
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Affiliation(s)
- Shruti Mathur
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi 110007, India
| | - Sanjeev Kumar Yadav
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Kajal Yadav
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi 110007, India; Birla Institute of Technology and Science Pilani, K.K.Birla Goa Campus, Goa 403726, India.
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3
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Foley EL, Hvitved AN, Eich RF, Olson JS. Mechanisms of nitric oxide reactions with Globins using mammalian myoglobin as a model system. J Inorg Biochem 2022; 233:111839. [DOI: 10.1016/j.jinorgbio.2022.111839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/15/2022]
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4
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Gardner PR. Ordered Motions in the Nitric-Oxide Dioxygenase Mechanism of Flavohemoglobin and Assorted Globins with Tightly Coupled Reductases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:45-96. [PMID: 36520413 DOI: 10.1007/5584_2022_751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nitric-oxide dioxygenases (NODs) activate and combine O2 with NO to form nitrate. A variety of oxygen-binding hemoglobins with associated partner reductases or electron donors function as enzymatic NODs. Kinetic and structural investigations of the archetypal two-domain microbial flavohemoglobin-NOD have illuminated an allosteric mechanism that employs selective tunnels for O2 and NO, gates for NO and nitrate, transient O2 association with ferric heme, and an O2 and NO-triggered, ferric heme spin crossover-driven, motion-controlled, and dipole-regulated electron-transfer switch. The proposed mechanism facilitates radical-radical coupling of ferric-superoxide with NO to form nitrate while preventing suicidal ferrous-NO formation. Diverse globins display the structural and functional motifs necessary for a similar allosteric NOD mechanism. In silico docking simulations reveal monomeric erythrocyte hemoglobin alpha-chain and beta-chain intrinsically matched and tightly coupled with NADH-cytochrome b5 oxidoreductase and NADPH-cytochrome P450 oxidoreductase, respectively, forming membrane-bound flavohemoglobin-like mammalian NODs. The neuroprotective neuroglobin manifests a potential NOD role in a close-fitting ternary complex with membrane-bound NADH-cytochrome b5 oxidoreductase and cytochrome b5. Cytoglobin interfaces weakly with cytochrome b5 for O2 and NO-regulated electron-transfer and coupled NOD activity. The mechanistic model also provides insight into the evolution of O2 binding cooperativity in hemoglobin and a basis for the discovery of allosteric NOD inhibitors.
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5
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Olson JS. Kinetic mechanisms for O 2 binding to myoglobins and hemoglobins. Mol Aspects Med 2021; 84:101024. [PMID: 34544605 DOI: 10.1016/j.mam.2021.101024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/29/2022]
Abstract
Antonini and Brunori's 1971 book "Hemoglobin and Myoglobin in Their Reactions with Ligands" was a truly remarkable publication that summarized almost 100 years of research on O2 binding to these globins. Over the ensuing 50 years, ultra-fast laser photolysis techniques, high-resolution and time resolved X-ray crystallography, molecular dynamics simulations, and libraries of recombinant myoglobin (Mb) and hemoglobin (Hb) variants have provided structural interpretations of O2 binding to these proteins. The resultant mechanisms provide quantitative descriptions of the stereochemical factors that govern overall affinity, including proximal and distal steric restrictions that affect iron reactivity and favorable positive electrostatic interactions that preferentially stabilize bound O2. The pathway for O2 uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O2 enters mammalian Mb and the α and β subunits of human HbA through a channel created by upward and outward rotation of the distal His at the E7 helical position, is non-covalently captured in the interior of the distal cavity, and then internally forms a bond with the heme Fe(II) atom. O2 dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O2 bond, and then competition between rebinding and escape through the E7-gate. The structural features that govern the rates of both the individual steps and overall reactions have been determined and provide the framework for: (1) defining the physiological functions of specific globins and their evolution; (2) understanding the clinical features of hemoglobinopathies; and (3) designing safer and more efficient acellular hemoglobin-based oxygen carriers (HBOCs) for transfusion therapy, organ preservation, and other commercially relevant O2 transport and storage processes.
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Affiliation(s)
- John S Olson
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
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6
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Mai NT, Lan NT, Vu TY, Duong PTM, Tung NT, Phung HTT. Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations. J Mol Graph Model 2020; 100:107648. [PMID: 32653524 DOI: 10.1016/j.jmgm.2020.107648] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.
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Affiliation(s)
- Nguyen Thi Mai
- Laboratory of Theoretical and Computational Biophysics, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Ngo Thi Lan
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Phuong Thi Mai Duong
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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7
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Abstract
Human hemoglobin is the textbook example of the stereochemistry of an allosteric protein and of the exquisite control that a protein can exert over ligand binding. However, the fundamental basis by which the protein facilitates the ligand movement remains unknown. In this study, we used cryogenic X-ray crystallography and a high-repetition pulsed laser irradiation technique to elucidate the atomic details of ligand migration processes in hemoglobin after photolysis of the bound CO. Our data clarify the distinct CO migration pathways in the individual subunits of hemoglobin and unravel the functional roles of the internal cavities and neighboring amino acid residues in ligand exit and entry. Our results also demonstrate the high gas permeability and porosity of hemoglobin, facilitating O2 delivery. Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.
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8
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Olson JS. Lessons Learned from 50 Years of Hemoglobin Research: Unstirred and Cell-Free Layers, Electrostatics, Baseball Gloves, and Molten Globules. Antioxid Redox Signal 2020; 32:228-246. [PMID: 31530172 PMCID: PMC6948003 DOI: 10.1089/ars.2019.7876] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Significance: Over the past 50 years, the mechanisms for O2 storage and transport have been determined quantitatively on distance scales from millimeters to tenths of nanometers and timescales from seconds to picoseconds. Recent Advances: In this review, I have described four key conclusions from work done by my group and our close colleagues. (i) O2 uptake by mammalian red cells is limited by diffusion through unstirred water layers adjacent to the cell surface and across cell-free layers adjacent to vessel walls. (ii) In most vertebrates, hemoglobins (Hbs) and myoglobins (Mbs), the distal histidine at the E7 helical position donates a strong hydrogen bond to bound O2, which selectively enhances O2 affinity, prevents carbon monoxide poisoning, and markedly slows autoxidation. (iii) O2 binding to mammalian Hbs and Mbs occurs by migration of the ligand through a channel created by upward rotation of the His(E7) side chain, capture in the empty space of the distal pocket, and then coordination with the ferroprotoporphyrin IX (heme) iron atom. (iv) The assembly of Mbs and Hbs occurs by formation of molten globule intermediates, in which the N- and C-terminal helices have almost fully formed secondary structures, but the heme pockets are disordered and followed by high-affinity binding of heme. Critical Issues: These conclusions indicate that there are often compromises between O2 transport function, holoprotein stability, and the efficiency of assembly. Future Directions: However, the biochemical mechanisms underlying these conclusions provide the framework for understanding globin evolution in greater detail and for engineering more efficient and stable globins.
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Affiliation(s)
- John S Olson
- BioSciences Department, Rice University, Houston, Texas
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9
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The nitrite reductase activity of ferrous human hemoglobin:haptoglobin 1-1 and 2-2 complexes. J Inorg Biochem 2018; 187:116-122. [DOI: 10.1016/j.jinorgbio.2018.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
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10
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Chintapalli SV, Anishkin A, Adams SH. Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin. Arch Biochem Biophys 2018; 655:56-66. [PMID: 30092229 DOI: 10.1016/j.abb.2018.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Myoglobin, besides its role in oxygen turnover, has gained recognition as a potential regulator of lipid metabolism. Previously, we confirmed the interaction of fatty acids and acylcarnitines with Oxy-Myoglobin, using both molecular dynamic simulations and Isothermal Titration Calorimetry studies. However, those studies were limited to testing only the binding sites derived from homology to fatty acid binding proteins and predictions using automated docking. To explore the entry mechanisms of the lipid ligands into myoglobin, we conducted molecular dynamic simulations of murine Oxy- and Deoxy-Mb structures with palmitate or palmitoylcarnitine starting at different positions near the protein surface. The simulations indicated that both ligands readily (under ∼10-20 ns) enter the Oxy-Mb structure through a dynamic area ("portal region") near heme, known to be the entry point for small molecule gaseous ligands like O2, CO and NO. The entry is not observed with Deoxy-Mb where lipid ligands move away from protein surface, due to a compaction of the entry portal and the heme-containing crevice in the Mb protein upon O2 removal. The results suggest quick spontaneous binding of lipids to Mb driven by hydrophobic interactions, strongly enhanced by oxygenation, and consistent with the emergent role of Mb in lipid metabolism.
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Affiliation(s)
- Sree V Chintapalli
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA.
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, USA
| | - Sean H Adams
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA
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11
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Terrell JR, Gumpper RH, Luo M. Hemoglobin crystals immersed in liquid oxygen reveal diffusion channels. Biochem Biophys Res Commun 2018; 495:1858-1863. [DOI: 10.1016/j.bbrc.2017.12.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 11/24/2022]
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12
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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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13
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Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016; 37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
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14
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Morrill GA, Kostellow AB. Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement. Front Physiol 2016; 7:360. [PMID: 27656147 PMCID: PMC5011150 DOI: 10.3389/fphys.2016.00360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/08/2016] [Indexed: 02/02/2023] Open
Abstract
Globins contain one or more cavities that control or affect such functions as ligand movement and ligand binding. Here we report that the extended globin family [cytoglobin (Cygb); neuroglobin (Ngb); myoglobin (Mb); hemoglobin (Hb) subunits Hba(α); and Hbb(β)] contain either a transmembrane (TM) helix or pore-lining region as well as internal cavities. Protein motif/domain analyses indicate that Ngb and Hbb each contain 5 cholesterol- binding (CRAC/CARC) domains and 1 caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding motifs. The Hb αβ-tetramer contains 14 cholesterol-binding domains. Computer algorithms indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions, whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba) and pore-lining region (Hbb). The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues, 55 of 154 Mb residues, and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to 8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities. Erythrocyte Hb αβ-tetramers are largely cytosolic but also bind to a membrane anion exchange protein, "band 3," which contains a large internal cavity and 12 TM helices (5 being pore-lining regions). The Hba TM helix may be the erythrocyte membrane "band 3" attachment site. "Band 3" contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO) movement within the large internal cavities and channels of the globins.
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Affiliation(s)
- Gene A Morrill
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Adele B Kostellow
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
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15
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Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
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16
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Arbelo-Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, Wymore T. Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme. J Phys Chem B 2016; 120:7319-31. [DOI: 10.1021/acs.jpcb.6b02839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hector D. Arbelo-Lopez
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Nikolay A. Simakov
- Center
for Computational Research, University of Buffalo, Buffalo, New York 14203, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Juan Lopez-Garriga
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Troy Wymore
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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17
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The nitrite reductase activity of horse heart carboxymethylated-cytochrome c is modulated by cardiolipin. J Biol Inorg Chem 2016; 21:421-32. [DOI: 10.1007/s00775-016-1351-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/28/2016] [Indexed: 10/22/2022]
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18
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Shadrina MS, English AM, Peslherbe GH. Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study. J Chem Theory Comput 2016; 12:2038-46. [PMID: 26938707 DOI: 10.1021/acs.jctc.5b01132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods.
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Affiliation(s)
- Maria S Shadrina
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
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19
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Bustamante JP, Radusky L, Boechi L, Estrin DA, ten Have A, Martí MA. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. PLoS Comput Biol 2016; 12:e1004701. [PMID: 26788940 PMCID: PMC4720485 DOI: 10.1371/journal.pcbi.1004701] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.
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Affiliation(s)
- Juan P. Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Radusky
- Departamento de Química Biológica e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Arjen ten Have
- Instituto de Investigación Biológica, CONICET, Universidad Nacional de Mar del Plata. Buenos Aires, Argentina
| | - Marcelo A. Martí
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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20
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Ascenzi P, Sbardella D, Fiocchetti M, Santucci R, Coletta M. NO2−-mediated nitrosylation of ferrous microperoxidase-11. J Inorg Biochem 2015; 153:121-127. [DOI: 10.1016/j.jinorgbio.2015.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/03/2015] [Accepted: 06/30/2015] [Indexed: 11/29/2022]
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21
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Shadrina MS, Peslherbe GH, English AM. Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin’s Gas Diffusion Tunnels. Biochemistry 2015; 54:5268-78. [DOI: 10.1021/acs.biochem.5b00368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Gilles H. Peslherbe
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Ann M. English
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
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22
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Wright TJ, Davis RW. Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals. ACTA ACUST UNITED AC 2015; 218:2180-9. [PMID: 25987728 DOI: 10.1242/jeb.119321] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/08/2015] [Indexed: 12/30/2022]
Abstract
Myoglobin (Mb) is an oxygen binding protein found in vertebrate skeletal muscle, where it facilitates intracellular transport and storage of oxygen. This protein has evolved to suit unique physiological needs in the muscle of diving vertebrates that express Mb at much greater concentrations than their terrestrial counterparts. In this study, we characterized Mb oxygen affinity (P50) from 25 species of aquatic and terrestrial birds and mammals. Among diving species, we tested for correlations between Mb P50 and routine dive duration. Across all species examined, Mb P50 ranged from 2.40 to 4.85 mmHg. The mean P50 of Mb from terrestrial ungulates was 3.72±0.15 mmHg (range 3.70-3.74 mmHg). The P50 of cetaceans was similar to terrestrial ungulates ranging from 3.54 to 3.82 mmHg, with the exception of the melon-headed whale, which had a significantly higher P50 of 4.85 mmHg. Among pinnipeds, the P50 ranged from 3.23 to 3.81 mmHg and showed a trend for higher oxygen affinity in species with longer dive durations. Among diving birds, the P50 ranged from 2.40 to 3.36 mmHg and also showed a trend of higher affinities in species with longer dive durations. In pinnipeds and birds, low Mb P50 was associated with species whose muscles are metabolically active under hypoxic conditions associated with aerobic dives. Given the broad range of potential globin oxygen affinities, Mb P50 from diverse vertebrate species appears constrained within a relatively narrow range. High Mb oxygen affinity within this range may be adaptive for some vertebrates that make prolonged dives.
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Affiliation(s)
- Traver J Wright
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX 77551, USA Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Randall W Davis
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX 77551, USA Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
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23
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Trujillo K, Papagiannopoulos T, Olsen KW. Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis. F1000Res 2015; 4:65. [PMID: 25866622 PMCID: PMC4376171 DOI: 10.12688/f1000research.6127.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 12/15/2022] Open
Abstract
Like many hemoglobins, the structure of the dimeric hemoglobin from the clam
Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.
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Affiliation(s)
- Kevin Trujillo
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Tasso Papagiannopoulos
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
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24
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Yu TQ, Lapelosa M, Vanden-Eijnden E, Abrams CF. Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations. J Am Chem Soc 2015; 137:3041-50. [PMID: 25664858 PMCID: PMC5508993 DOI: 10.1021/ja512484q] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments. We show semiquantitative agreement with experiment on entry and exit rates and in the identification of the so-called "histidine gate" at position 64 through which ≈90% of flux between solvent and the distal pocket passes. We also show with six-dimensional calculations that the minimum free-energy pathway of escape through the histidine gate is a "knock-on" mechanism in which motion of the ligand and the gate are sequential and interdependent. In total, these results suggest that such TPT simulations are indeed a promising approach to overcome the practical time-scale limitations of MD to allow reliable estimation of transition mechanisms and rates among metastable states.
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Affiliation(s)
- Tang-Qing Yu
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Mauro Lapelosa
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Eric Vanden-Eijnden
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Cameron F. Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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25
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Carbon monoxide binding properties of domain-swapped dimeric myoglobin. J Biol Inorg Chem 2015; 20:523-30. [DOI: 10.1007/s00775-014-1236-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/27/2014] [Indexed: 10/24/2022]
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26
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Abstract
Background Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common. Results Here, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein. Conclusions The majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0379-x) contains supplementary material, which is available to authorized users.
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27
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Abstract
![]()
Myoglobin
(Mb) binds diatomic ligands, like O2, CO,
and NO, in a cavity that is only transiently accessible. Crystallography
and molecular simulations show that the ligands can migrate through
an extensive network of transiently connected cavities but disagree
on the locations and occupancy of internal hydration sites. Here,
we use water 2H and 17O magnetic relaxation
dispersion (MRD) to characterize the internal water molecules in Mb
under physiological conditions. We find that equine carbonmonoxy Mb
contains 4.5 ± 1.0 ordered internal water molecules with a mean
survival time of 5.6 ± 0.5 μs at 25 °C. The likely
locations of these water molecules are the four polar hydration sites,
including one of the xenon-binding cavities, that are fully occupied
in all high-resolution crystal structures of equine Mb. The finding
that water escapes from these sites, located 17–31 Å apart
in the protein, on the same μs time scale suggests a global
exchange mechanism. We propose that this mechanism involves transient
penetration of the protein by H-bonded water chains. Such a mechanism
could play a functional role by eliminating trapped ligands. In addition,
the MRD results indicate that 2 or 3 of the 11 histidine residues
of equine Mb undergo intramolecular hydrogen exchange on a μs
time scale.
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Affiliation(s)
- Shuji Kaieda
- Department of Biophysical Chemistry, Lund University , P.O. Box 124, SE-22100 Lund, Sweden
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28
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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29
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Takayanagi M, Kurisaki I, Nagaoka M. Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin. J Phys Chem B 2013; 117:6082-91. [DOI: 10.1021/jp401459b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayoshi Takayanagi
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Ikuo Kurisaki
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
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30
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Spyrakis F, Lucas F, Bidon-Chanal A, Viappiani C, Guallar V, Luque FJ. Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1957-67. [PMID: 23583621 DOI: 10.1016/j.bbapap.2013.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
Abstract
This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1)→Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy.
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31
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Nienhaus K, Olson JS, Nienhaus GU. An engineered heme-copper center in myoglobin: CO migration and binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1824-31. [PMID: 23459127 DOI: 10.1016/j.bbapap.2013.02.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
Abstract
We have investigated CO migration and binding in CuBMb, a copper-binding myoglobin double mutant (L29H-F43H), by using Fourier transform infrared spectroscopy and flash photolysis over a wide temperature range. This mutant was originally engineered with the aim to mimic the catalytic site of heme-copper oxidases. Comparison of the wild-type protein Mb and CuBMb shows that the copper ion in the distal pocket gives rise to significant effects on ligand binding to the heme iron. In Mb and copper-free CuBMb, primary and secondary ligand docking sites are accessible upon photodissociation. In copper-bound CuBMb, ligands do not migrate to secondary docking sites but rather coordinate to the copper ion. Ligands entering the heme pocket from the outside normally would not be captured efficiently by the tight distal pocket housing the two additional large imidazole rings. Binding at the Cu ion, however, ensures efficient trapping in CuBMb. The Cu ion also restricts the motions of the His64 side chain, which is the entry/exit door for ligand movement into the active site, and this restriction results in enhanced geminate and slow bimolecular CO rebinding. These results support current mechanistic views of ligand binding in hemoglobins and the role of the CuB in the active of heme-copper oxidases. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
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32
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Lucas MF, Guallar V. Single vs. multiple ligand pathways in globins: a computational view. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1739-43. [PMID: 23388390 DOI: 10.1016/j.bbapap.2013.01.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 11/30/2022]
Abstract
Diatomic ligand migration in globins has been the subject of numerous studies. Still, a consensus picture for the ligand entrance is not clear, with a growing concern among experimental researchers that computational simulations always show multiple pathways for any globin. Modeling non-biased ligand entrance from conventional molecular dynamics techniques, however, has shown to be difficult (and expensive). Here we use our Monte Carlo methodology, capable of freely mapping ligand diffusion and the description of rare events, to two well-studied systems: myoglobin and the mini-hemoglobin from the sea worm Cerebratulus lacteus. Our results clearly show that the simulations are specific to the system providing a different trend in the entrance pathway, as expected from experiments. While Mb presents multiple entrance pathways, populating the well-known xenon cavities, in CerHb the ligand enters the protein only by one apolar channel. Most of the trajectories (64%) visiting myoglobin's active site though, are gated by the distal histidine. Such detailed information, accessible through the state of the art algorithms in PELE, is computationally inexpensive and available to all non-profit researchers. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- M Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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33
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Grivennikova VG, Vinogradov AD. Partitioning of superoxide and hydrogen peroxide production by mitochondrial respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:446-54. [PMID: 23313413 DOI: 10.1016/j.bbabio.2013.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/24/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
Membrane-bound respiratory complex I in inside-out submitochondrial particles (SMP) catalyzes both superoxide and hydrogen peroxide formation in NADH- and/or succinate-supported reactions. At optimal NADH concentration (50μM), the complex I-mediated process results in a formation of two superoxide anions and H(2)O(2) as the reaction products in approximately 0.7 ratio. Almost the same ratio is found for purified complex I (0.6) and for the aerobic succinate-supported reverse electron transfer reaction. Superoxide production is depressed at high, more physiologically relevant NADH concentrations, whereas hydrogen peroxide formation is insensitive to the elevated level of NADH. The rates of H(2)O(2) formation at variable NAD(+)/NADH ratios satisfactorily fit the Nernst equation for a single reactive two-electron donor component equilibrated with ambient midpoint redox potential of -347mV (0.13 NAD(+)/NADH ratio, pH 8.0). Half-maximal superoxide production rate proceeds at significantly higher NAD(+)/NADH ratio (0.33). Guanidine strongly stimulates NADH-supported hydrogen peroxide and superoxide production at any NADH concentration and activates NADH:ferricyanide and inhibits NADH:hexaammineruthenium (III) reductase activities while showing no effects on NADH oxidase of SMP. In the low range of NADH concentration, superoxide production rate shows a simple hyperbolic dependence on NADH with apparent K(m)(NADH) of 0.5μM, whereas sigmoidal dependence of hydrogen peroxide production is seen with half-maximal rate at 25μM NADH. We interpret the data as to suggest that at least two sites participate in complex I-mediated ROS generation: FMNH(-) that produces hydrogen peroxide, and an iron-sulfur center (likely N-2) that produces superoxide anion.
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Affiliation(s)
- Vera G Grivennikova
- Department of Biochemistry, Moscow State University, Moscow, Russian Federation
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34
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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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