1
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De Simone G, di Masi A, Pasquadibisceglie A, Coletta A, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Nitrobindin versus myoglobin: A comparative structural and functional study. J Inorg Biochem 2024; 250:112387. [PMID: 37914583 DOI: 10.1016/j.jinorgbio.2023.112387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/03/2023]
Abstract
Most hemoproteins display an all-α-helical fold, showing the classical three on three (3/3) globin structural arrangement characterized by seven or eight α-helical segments that form a sandwich around the heme. Over the last decade, a completely distinct class of heme-proteins called nitrobindins (Nbs), which display an all-β-barrel fold, has been identified and characterized from both structural and functional perspectives. Nbs are ten-stranded anti-parallel all-β-barrel heme-proteins found across the evolutionary ladder, from bacteria to Homo sapiens. Myoglobin (Mb), commonly regarded as the prototype of monomeric all-α-helical globins, is involved along with the oligomeric hemoglobin (Hb) in diatomic gas transport, storage, and sensing, as well as in the detoxification of reactive nitrogen and oxygen species. On the other hand, the function(s) of Nbs is still obscure, even though it has been postulated that they might participate to O2/NO signaling and metabolism. This function might be of the utmost importance in poorly oxygenated tissues, such as the eye's retina, where a delicate balance between oxygenation and blood flow (regulated by NO) is crucial. Dysfunction in this balance is associated with several pathological conditions, such as glaucoma and diabetic retinopathy. Here a detailed comparison of the structural, spectroscopic, and functional properties of Mb and Nbs is reported to shed light on the similarities and differences between all-α-helical and all-β-barrel heme-proteins.
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Affiliation(s)
| | | | | | | | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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2
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Luo Y, Liu C, Li D, Yang B, Shi J, Guo X, Fan H, Lv Q. Progress in the Diagnostic and Predictive Evaluation of Crush Syndrome. Diagnostics (Basel) 2023; 13:3034. [PMID: 37835777 PMCID: PMC10572195 DOI: 10.3390/diagnostics13193034] [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: 07/17/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Crush syndrome (CS), also known as traumatic rhabdomyolysis, is a syndrome with a wide clinical spectrum; it is caused by external compression, which often occurs in earthquakes, wars, and traffic accidents, especially in large-scale disasters. Crush syndrome is the second leading cause of death after direct trauma in earthquakes. A series of clinical complications caused by crush syndrome, including hyperkalemia, myoglobinuria, and, in particular, acute kidney injury (AKI), is the main cause of death in crush syndrome. The early diagnosis of crush syndrome, the correct evaluation of its severity, and accurate predictions of a poor prognosis can provide personalized suggestions for rescuers to carry out early treatments and reduce mortality. This review summarizes various methods for the diagnostic and predictive evaluation of crush syndrome, including urine dipstick tests for a large number of victims, traditional and emerging biomarkers, imaging-assisted diagnostic methods, and developed evaluation models, with the aim of providing materials for scholars in this research field.
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Affiliation(s)
- Yu Luo
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Chunli Liu
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Duo Li
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Bofan Yang
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Jie Shi
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Xiaoqin Guo
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Haojun Fan
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
| | - Qi Lv
- Institution of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Y.L.)
- Key Laboratory of Medical Rescue Key Technology and Equipment, Ministry of Emergency Management, Wenzhou 325000, China
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3
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Ishizuka T, Grover N, Kingsbury CJ, Kotani H, Senge MO, Kojima T. Nonplanar porphyrins: synthesis, properties, and unique functionalities. Chem Soc Rev 2022; 51:7560-7630. [PMID: 35959748 DOI: 10.1039/d2cs00391k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Porphyrins are variously substituted tetrapyrrolic macrocycles, with wide-ranging biological and chemical applications derived from metal chelation in the core and the 18π aromatic surface. Under suitable conditions, the porphyrin framework can deform significantly from regular planar shape, owing to steric overload on the porphyrin periphery or steric repulsion in the core, among other structure modulation strategies. Adopting this nonplanar porphyrin architecture allows guest molecules to interact directly with an exposed core, with guest-responsive and photoactive electronic states of the porphyrin allowing energy, information, atom and electron transfer within and between these species. This functionality can be incorporated and tuned by decoration of functional groups and electronic modifications, with individual deformation profiles adapted to specific key sensing and catalysis applications. Nonplanar porphyrins are assisting breakthroughs in molecular recognition, organo- and photoredox catalysis; simultaneously bio-inspired and distinctly synthetic, these molecules offer a new dimension in shape-responsive host-guest chemistry. In this review, we have summarized the synthetic methods and design aspects of nonplanar porphyrin formation, key properties, structure and functionality of the nonplanar aromatic framework, and the scope and utility of this emerging class towards outstanding scientific, industrial and environmental issues.
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Affiliation(s)
- Tomoya Ishizuka
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
| | - Nitika Grover
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Christopher J Kingsbury
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Hiroaki Kotani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
| | - Mathias O Senge
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Focus Group - Molecular and Interfacial Engineering of Organic Nanosystems, Lichtenbergstrasse 2a, 85748 Garching, Germany.
| | - Takahiko Kojima
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
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4
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Abiological catalysis by myoglobin mutant with a genetically incorporated unnatural amino acid. Biochem J 2021; 478:1795-1808. [PMID: 33821889 PMCID: PMC10071548 DOI: 10.1042/bcj20210091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022]
Abstract
To inculcate biocatalytic activity in the oxygen-storage protein myoglobin (Mb), a genetically engineered myoglobin mutant H64DOPA (DOPA = L-3,4-dihydroxyphenylalanine) has been created. Incorporation of unnatural amino acids has already demonstrated their ability to accomplish many non-natural functions in proteins efficiently. Herein, the presence of redox-active DOPA residue in the active site of mutant Mb presumably stabilizes the compound I in the catalytic oxidation process by participating in an additional hydrogen bonding (H-bonding) as compared to the WT Mb. Specifically, a general acid-base catalytic pathway was achieved due to the availability of the hydroxyl moieties of DOPA. The reduction potential values of WT (E° = -260 mV) and mutant Mb (E° = -300 mV), w.r.t. Ag/AgCl reference electrode, in the presence of hydrogen peroxide, indicated an additional H-bonding in the mutant protein, which is responsible for the peroxidase activity of the mutant Mb. We observed that in the presence of 5 mM H2O2, H64DOPA Mb oxidizes thioanisole and benzaldehyde with a 10 and 54 folds higher rate, respectively, as opposed to WT Mb. Based on spectroscopic, kinetic, and electrochemical studies, we deduce that DOPA residue, when present within the distal pocket of mutant Mb, alone serves the role of His/Arg-pair of peroxidases.
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5
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Kitagishi H, Kano K. Synthetic heme protein models that function in aqueous solution. Chem Commun (Camb) 2021; 57:148-173. [DOI: 10.1039/d0cc07044k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supramolecular porphyrin–cyclodextrin complexes act as biomimetic heme protein models in aqueous solution.
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Affiliation(s)
- Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry
- Faculty of Science and Engineering
- Doshisha University
- Kyoto 610-0321
- Japan
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry
- Faculty of Science and Engineering
- Doshisha University
- Kyoto 610-0321
- Japan
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6
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De Simone G, Ascenzi P, di Masi A, Polticelli F. Nitrophorins and nitrobindins: structure and function. Biomol Concepts 2018; 8:105-118. [PMID: 28574374 DOI: 10.1515/bmc-2017-0013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/03/2017] [Indexed: 12/23/2022] Open
Abstract
Classical all α-helical globins are present in all living organisms and are ordered in three lineages: (i) flavohemoglobins and single domain globins, (ii) protoglobins and globin coupled sensors and (iii) truncated hemoglobins, displaying the 3/3 or the 2/2 all α-helical fold. However, over the last two decades, all β-barrel and mixed α-helical-β-barrel heme-proteins displaying heme-based functional properties (e.g. ligand binding, transport and sensing) closely similar to those of all α-helical globins have been reported. Monomeric nitrophorins (NPs) and α1-microglobulin (α1-m), belonging to the lipocalin superfamily and nitrobindins (Nbs) represent prototypical heme-proteins displaying the all β-barrel and mixed α-helical-β-barrel folds. NPs are confined to the Reduviidae and Cimicidae families of Heteroptera, whereas α1-m and Nbs constitute heme-protein families spanning bacteria to Homo sapiens. The structural organization and the reactivity of the stable ferric solvent-exposed heme-Fe atom suggest that NPs and Nbs are devoted to NO transport, storage and sensing, whereas Hs-α1-m participates in heme metabolism. Here, the structural and functional properties of NPs and Nbs are reviewed in parallel with those of sperm whale myoglobin, which is generally taken as the prototype of monomeric globins.
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7
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Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y. Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor. Biochemistry 2017; 56:4500-4508. [DOI: 10.1021/acs.biochem.7b00457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kanai
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ayaka Harada
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kosuke Namiki
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Miho Watanabe
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shunpei Nakamura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Fumiaki Yumoto
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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8
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Shibata T, Kanai Y, Nishimura R, Xu L, Moritaka Y, Suzuki A, Neya S, Nakamura M, Yamamoto Y. Characterization of Ground State Electron Configurations of High-Spin Quintet Ferrous Heme Iron in Deoxy Myoglobin Reconstituted with Trifluoromethyl Group-Substituted Heme Cofactors. Inorg Chem 2016; 55:12128-12136. [DOI: 10.1021/acs.inorgchem.6b01360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Kanai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Liyang Xu
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Moritaka
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of
Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Mikio Nakamura
- Department
of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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9
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Chintapalli SV, Jayanthi S, Mallipeddi PL, Gundampati R, Suresh Kumar TK, van Rossum DB, Anishkin A, Adams SH. Novel Molecular Interactions of Acylcarnitines and Fatty Acids with Myoglobin. J Biol Chem 2016; 291:25133-25143. [PMID: 27758871 DOI: 10.1074/jbc.m116.754978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/29/2016] [Indexed: 11/06/2022] Open
Abstract
Previous research has indicated that long-chain fatty acids can bind myoglobin (Mb) in an oxygen-dependent manner. This suggests that oxy-Mb may play an important role in fuel delivery in Mb-rich muscle fibers (e.g. type I fibers and cardiomyocytes), and raises the possibility that Mb also serves as an acylcarnitine-binding protein. We report for the first time the putative interaction and affinity characteristics for different chain lengths of both fatty acids and acylcarnitines with oxy-Mb using molecular dynamic simulations and isothermal titration calorimetry experiments. We found that short- to medium-chain fatty acids or acylcarnitines (ranging from C2:0 to C10:0) fail to achieve a stable conformation with oxy-Mb. Furthermore, our results indicate that C12:0 is the minimum chain length essential for stable binding of either fatty acids or acylcarnitines with oxy-Mb. Importantly, the empirical lipid binding studies were consistent with structural modeling. These results reveal that: (i) the lipid binding affinity for oxy-Mb increases as the chain length increases (i.e. C12:0 to C18:1), (ii) the binding affinities of acylcarnitines are higher when compared with their respective fatty acid counterparts, and (iii) both fatty acids and acylcarnitines bind to oxy-Mb in 1:1 stoichiometry. Taken together, our results support a model in which oxy-Mb is a novel regulator of long-chain acylcarnitine and fatty acid pools in Mb-rich tissues. This has important implications for physiological fuel management during exercise, and relevance to pathophysiological conditions (e.g. fatty acid oxidation disorders and cardiac ischemia) where long-chain acylcarnitine accumulation is evident.
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Affiliation(s)
- Sree V Chintapalli
- From the Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72202,
| | - Srinivas Jayanthi
- the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Prema L Mallipeddi
- the Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204
| | - Ravikumar Gundampati
- the Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | | | - Damian B van Rossum
- the Center for Computational Proteomics and.,the Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, and
| | - Andriy Anishkin
- the Department of Biology, University of Maryland, College Park, Maryland 20742
| | - Sean H Adams
- From the Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72202,
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10
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Hu B, He M, Yao Z, Schulz CE, Li J. Unique Axial Imidazole Geometries of Fully Halogenated Iron(II) Porphyrin Complexes: Crystal Structures and Mössbauer Spectroscopic Studies. Inorg Chem 2016; 55:9632-9643. [DOI: 10.1021/acs.inorgchem.6b01364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bin Hu
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Mingrui He
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Zhen Yao
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Charles E. Schulz
- Department
of Physics, Knox College, Galesburg, Illinois 61401, United States
| | - Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
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11
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Abstract
If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
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Affiliation(s)
- Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche “Alessandro Rossi Fanelli” and Istituto Pasteur — Fondazione Cenci, Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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12
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Bondarenko AS, Jansen TLC. Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins. J Chem Phys 2016; 142:212437. [PMID: 26049457 DOI: 10.1063/1.4919716] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.
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Affiliation(s)
- Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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13
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Chintapalli SV, Bhardwaj G, Patel R, Shah N, Patterson RL, van Rossum DB, Anishkin A, Adams SH. Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin. PLoS One 2015; 10:e0128496. [PMID: 26030763 PMCID: PMC4451517 DOI: 10.1371/journal.pone.0128496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state.
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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, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
| | - Gaurav Bhardwaj
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Reema Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Natasha Shah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Randen L. Patterson
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Damian B. van Rossum
- Center for Computational Proteomics, The Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Sean H. Adams
- Arkansas Children’s Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
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14
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Interaction of apoNeuroglobin with heme–Aβ complexes relevant to Alzheimer’s disease. J Biol Inorg Chem 2015; 20:563-74. [DOI: 10.1007/s00775-015-1241-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/13/2015] [Indexed: 01/09/2023]
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15
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Nagai M, Kobayashi C, Nagai Y, Imai K, Mizusawa N, Sakurai H, Neya S, Kayanuma M, Shoji M, Nagatomo S. Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical Analyses. J Phys Chem B 2015; 119:1275-87. [DOI: 10.1021/jp5086203] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masako Nagai
- Research
Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
- School
of Health Sciences, College of Medical, Pharmaceutical and Health
Sciences, Kanazawa University, Kanazawa 920-0942, Japan
| | - Chika Kobayashi
- Department
of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Yukifumi Nagai
- Research
Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Kiyohiro Imai
- Department
of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Naoki Mizusawa
- Research
Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
- Department
of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Hiroshi Sakurai
- School
of Health Sciences, College of Medical, Pharmaceutical and Health
Sciences, Kanazawa University, Kanazawa 920-0942, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Inohana, Chuo-Ku, Chiba 260-8675, Japan
| | - Megumi Kayanuma
- Department
of Computer Science, Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Mitsuo Shoji
- Department
of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigenori Nagatomo
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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16
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Wang YQ, Zhang HM, Cao J. Binding of hydroxylated single-walled carbon nanotubes to two hemoproteins, hemoglobin and myoglobin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:26-35. [PMID: 25313539 DOI: 10.1016/j.jphotobiol.2014.08.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 01/05/2023]
Abstract
Herein, we studied the binding interactions between hydroxylated single-walled carbon nanotubes and hemoglobin and myoglobin by the use of multi-spectral techniques and molecular modeling. The ultraviolet-vis absorbance and circular dichroism spectral results indicated that the binding interactions existed between hydroxylated single-walled carbon nanotubes and hemoglobin/myoglobin. These binding interactions partially affected the soret/heme bands of hemoglobin and myoglobin. The secondary structures of hemoproteins were partially destroyed by hydroxylated single-walled carbon nanotubes. Fluorescence studies suggested that the complexes formed between hydroxylated single-walled carbon nanotubes and hemoglobin/myoglobin by hydrogen bonding, hydrophobic, and π-π stacking interactions. In addition, molecular modeling analysis well supported the experimental results.
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Affiliation(s)
- Yan-Qing Wang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China.
| | - Hong-Mei Zhang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China
| | - Jian Cao
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province 224002, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China
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17
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Nishimura R, Shibata T, Tai H, Ishigami I, Yanagisawa S, Ogura T, Neya S, Suzuki A, Yamamoto Y. Effect of the Electron Density of the Heme Fe Atom on the Fe–Histidine Coordination Bond in Deoxy Myoglobin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Hulin Tai
- Department of Chemistry, University of Tsukuba
| | - Izumi Ishigami
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Sachiko Yanagisawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology
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18
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Maj M, Oh Y, Park K, Lee J, Kwak KW, Cho M. Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin. J Chem Phys 2014; 140:235104. [DOI: 10.1063/1.4883505] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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19
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Choi J, Tojo S, Fujitsuka M, Majima T. Dynamics in the heme geometry of myoglobin induced by the one-electron reduction. Int J Radiat Biol 2014; 90:459-67. [DOI: 10.3109/09553002.2013.876115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Roy J, Sen Santara S, Bose M, Mukherjee S, Saha R, Adak S. The ferrous–dioxy complex of Leishmania major globin coupled heme containing adenylate cyclase: The role of proximal histidine on its stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:615-22. [DOI: 10.1016/j.bbapap.2014.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 11/16/2022]
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21
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Moin ST, Hofer TS. Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations. ACTA ACUST UNITED AC 2014; 10:117-27. [DOI: 10.1039/c3mb70300b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Forman A, Davis MS, Fujita I, Hanson LK, Smith KM, Fajer J. Mechanisms of Energy Transduction in Plant Photosynthesis: ESR, ENDOR and MOs of the Primary Acceptors. Isr J Chem 2013. [DOI: 10.1002/ijch.198100049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Banerjee S. Induction of protein conformational change inside the charged electrospray droplet. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:193-204. [PMID: 23378092 DOI: 10.1002/jms.3148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 06/01/2023]
Abstract
The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process.
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Affiliation(s)
- Shibdas Banerjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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24
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Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
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Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
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25
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Huang X, Appelhans D, Formanek P, Simon F, Voit B. Tailored synthesis of intelligent polymer nanocapsules: an investigation of controlled permeability and pH-dependent degradability. ACS NANO 2012; 6:9718-9726. [PMID: 23102500 DOI: 10.1021/nn3031723] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, we present a new route to synthesize an intelligent polymer nanocapsule with an ultrathin membrane based on surface-initiated reversible addition-fragmentation chain-transfer polymerization. The key concept of our report is to use pH-responsive polydiethylaminoethylmethacrylate as a main membrane-generating component and a degradable disulfide bond to cross-link the membrane. The permeability of membrane, tuned by adjusting pH and using different lengths of the cross-linkers, was proven by showing a dramatic swelling behavior of the nanocapsules with the longest cross-linker from 560 nm at pH 8.0 to 780 nm at pH 4.0. Also, due to the disulfide cross-linker, degradation of the capsules using GSH as reducing agent was achieved which is further significantly promoted at pH 4.0. Using a rather long-chain dithiol cross-linker, the synthesized nanocapsules demonstrated a good permeability allowing that an enzyme myoglobin can be postencapsulated, where the pH controlled enzyme activity by switching membrane permeability was also shown.
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Affiliation(s)
- Xin Huang
- Leibniz Institute of Polymer Research Dresden, Hohe Strasse 6, 01069 Dresden, Germany.
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26
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Kim S, Lim M. Protein Conformation-Controlled Rebinding Barrier of NO and Its Binding Trajectories in Myoglobin and Hemoglobin at Room Temperature. J Phys Chem B 2012; 116:5819-30. [DOI: 10.1021/jp300176q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
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27
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Lucas MF, Guallar V. An atomistic view on human hemoglobin carbon monoxide migration processes. Biophys J 2012; 102:887-96. [PMID: 22385860 DOI: 10.1016/j.bpj.2012.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 01/02/2012] [Accepted: 01/11/2012] [Indexed: 10/28/2022] Open
Abstract
A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed.
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Affiliation(s)
- M Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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28
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Oganesyan VS. A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein. Phys Chem Chem Phys 2011; 13:4724-37. [PMID: 21279205 DOI: 10.1039/c0cp01068e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.
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29
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30
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Stevens JA, Link JJ, Kao YT, Zang C, Wang L, Zhong D. Ultrafast Dynamics of Resonance Energy Transfer in Myoglobin: Probing Local Conformation Fluctuations. J Phys Chem B 2010; 114:1498-505. [PMID: 20047308 DOI: 10.1021/jp910013f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jeffrey A. Stevens
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
| | - Justin J. Link
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
| | - Ya-Ting Kao
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
| | - Chen Zang
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
| | - Lijuan Wang
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
| | - Dongping Zhong
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 191 West Woodruff Avenue, The Ohio State University, Columbus, Ohio 43210
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31
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Bergmann N, Bonhommeau S, Lange KM, Greil SM, Eisebitt S, de Groot F, Chergui M, Aziz EF. Retracted Article: On the enzymatic activity of catalase: an iron L-edge X-ray absorption study of the active centre. Phys Chem Chem Phys 2010; 12:4827-32. [DOI: 10.1039/b924245g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe L2,3-edge X-ray absorption spectra of a catalase active centre in a physiological solution reveals a partial ferryl character, which stems from the proximal tyrosine residue.
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Affiliation(s)
- Nora Bergmann
- Max-Delbrück-Center for Molecular Medicine
- D-13125 Berlin-Buch
- Germany
| | - Sébastien Bonhommeau
- Institut des Sciences Moléculaires-UMR 5255 CNRS
- Université Bordeaux 1
- 33405 Talence Cedex
- France
| | - Kathrin M. Lange
- Helmholtz-Zentrum Berlin für Materialen und Energie c/o BESSY II
- 12489 Berlin
- Germany
| | - Stefanie M. Greil
- Helmholtz-Zentrum Berlin für Materialen und Energie c/o BESSY II
- 12489 Berlin
- Germany
| | - Stefan Eisebitt
- Helmholtz-Zentrum Berlin für Materialen und Energie c/o BESSY II
- 12489 Berlin
- Germany
- Technical University Berlin
- 10623 Berlin
| | - Frank de Groot
- Department of Inorganic Chemistry and Catalysis
- Utrecht University
- 3584 CA Utrecht
- The Netherlands
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne
- Laboratoire de Spectroscopie Ultrarapide
- Faculté des Sciences de Base
- ISIC-BSP
- CH-1015 Lausanne-Dorigny
| | - Emad F. Aziz
- Helmholtz-Zentrum Berlin für Materialen und Energie c/o BESSY II
- 12489 Berlin
- Germany
- Ecole Polytechnique Fédérale de Lausanne
- Laboratoire de Spectroscopie Ultrarapide
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32
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Electron-electron distances in spin-labeled low-spin metmyoglobin variants by relaxation enhancement. Biophys J 2008; 95:5306-16. [PMID: 18775958 DOI: 10.1529/biophysj.108.141887] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirteen single-cysteine variants of myoglobin were prepared by overexpression of apoprotein, spin labeling, and reconstitution with hemin. This procedure resulted in a protein with fewer hemichrome impurities than was obtained by an overexpression of holo-protein followed by spin labeling. Coordination of cyanide to the met heme formed low-spin complexes. Iron-nitroxyl interspin distances in the range of 17-30 A were determined by saturation recovery measurements of the enhancement of the nitroxyl spin lattice relaxation rates between approximately 30-140 K, and by spin-echo measurements of the enhancement of spin-spin relaxation rates at 10-30 K. Interspin distances were also calculated, using the molecular modeling program Insight II (Accelrys, San Diego, CA). For most variants, distances determined from the temperature dependence of spin-echo intensities at a pulse spacing of 200 ns agree with distances measured by saturation recovery and calculated with Insight II within about an angstrom, which is within experimental uncertainties. Measurements of interspin distances via spin-spin relaxation enhancement have the advantages that maximum effects are observed for slower metal relaxation rates than are required for spin-lattice relaxation enhancement, and the impact diminishes as r(-3) instead of r(-6), as with spin-lattice relaxation enhancement, which permits measurements at longer distances.
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33
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Hoy JA, Hargrove MS. The structure and function of plant hemoglobins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:371-9. [PMID: 18321722 DOI: 10.1016/j.plaphy.2007.12.016] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Indexed: 05/24/2023]
Abstract
Plants, like humans, contain hemoglobin. Three distinct types of hemoglobin exist in plants: symbiotic, non-symbiotic, and truncated hemoglobins. Crystal structures and other structural and biophysical techniques have revealed important knowledge about ligand binding and conformational stabilization in all three types. In symbiotic hemoglobins (leghemoglobins), ligand binding regulatory mechanisms have been shown to differ dramatically from myoglobin and red blood cell hemoglobin. In the non-symbiotic hemoglobins found in all plants, crystal structures and vibrational spectroscopy have revealed the nature of the structural transition between the hexacoordinate and ligand-bound states. In truncated hemoglobins, the abbreviated globin is porous, providing tunnels that may assist in ligand binding, and the bound ligand is stabilized by more than one distal pocket residue. Research has implicated these plant hemoglobins in a number of possible functions differing among hemoglobin types, and possibly between plant species.
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Affiliation(s)
- Julie A Hoy
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50014, USA
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34
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Zahran ZN, Chooback L, Copeland DM, West AH, Richter-Addo GB. Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations. J Inorg Biochem 2008; 102:216-33. [PMID: 17905436 PMCID: PMC2771112 DOI: 10.1016/j.jinorgbio.2007.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Revised: 08/03/2007] [Accepted: 08/16/2007] [Indexed: 01/17/2023]
Abstract
Nitrite is now recognized as a storage pool of bioactive nitric oxide (NO). Hemoglobin (Hb) and myoglobin (Mb) convert, under certain conditions, nitrite to NO. This newly discovered nitrite reductase activity of Hb and Mb provides an attractive alternative to mammalian NO synthesis from the NO synthase pathway that requires dioxygen. We recently reported the X-ray crystal structure of the nitrite adduct of ferric horse heart Mb, and showed that the nitrite ligand binds in an unprecedented O-binding (nitrito) mode to the d(5) ferric center in Mb(III)(ONO) [D.M. Copeland, A. Soares, A.H. West, G.B. Richter-Addo, J. Inorg. Biochem. 100 (2006) 1413-1425]. We also showed that the distal pocket in Mb allows for different conformations of the NO ligand (120 degrees and 144 degrees ) in Mb(II)NO depending on the mode of preparation of the compound. In this article, we report the crystal structures of the nitrite and NO adducts of manganese-substituted hh Mb (a d(4) system) and of the nitrite adduct of cobalt-substituted hh Mb (a d(6) system). We show that the distal His64 residue directs the nitrite ligand towards the rare nitrito O-binding mode in Mn(III)Mb and Co(III)Mb. We also report that the distal pocket residues allow a stabilization of an unprecendented bent MnNO moiety in Mn(II)MbNO. These crystal structural data, when combined with the data for the aquo, methanol, and azide MnMb derivatives, provide information on the role of distal pocket residues in the observed binding modes of nitrite and NO ligands to wild-type and metal-substituted Mb.
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Affiliation(s)
- Zaki N. Zahran
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019
| | - Lilian Chooback
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019
| | - Daniel M. Copeland
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019
| | - Ann H. West
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019
| | - George B. Richter-Addo
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019
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35
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Marques HM. Insights into porphyrin chemistry provided by the microperoxidases, the haempeptides derived from cytochrome c. Dalton Trans 2007:4371-85. [PMID: 17909648 DOI: 10.1039/b710940g] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The water-soluble haem-containing peptides obtained by proteolytic digestion of cytochrome c, the microperoxidases, have been used to explore aspects of the chemistry of iron porphyrins, and as mimics for some reactions catalysed by the haemoproteins, including the reactions catalysed by the peroxidases and the cytochromes P450. The preparation of the microperoxidases, their physical and chemical properties including their electronic structure, the kinetics and thermodynamics of their reactions with ligands, electrochemical studies and examples of their uses as haemoproteins mimics, is reviewed.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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36
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Dirama TE, Curtis JE, Carri GA, Sokolov AP. Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations. J Chem Phys 2007; 124:034901. [PMID: 16438608 DOI: 10.1063/1.2159471] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.
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Affiliation(s)
- Taner E Dirama
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, USA
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Effects of Solvent Viscosity on Conformational Dynamics of Heme-pocket in Myoglobin and Hemoglobin. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.11.1825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gao Y, El-Mashtoly SF, Pal B, Hayashi T, Harada K, Kitagawa T. Pathway of Information Transmission from Heme to Protein upon Ligand Binding/Dissociation in Myoglobin Revealed by UV Resonance Raman Spectroscopy. J Biol Chem 2006; 281:24637-46. [PMID: 16774917 DOI: 10.1074/jbc.m603198200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gas sensory heme proteins respond to their environment by binding a specific gas molecule to heme and transmitting this primary binding signal to the protein. How the binding signal is transmitted from the heme to the protein remains to be clarified. Using UV resonance Raman (UVRR) spectroscopy, we investigated this pathway in sperm whale myoglobin as a model gas sensory heme protein. Based on the UVRR data and the effects of deleting one of three important pathways (His-93, 6-propionate, or 7-propionate), we determined the changes in the conformation of globin that occur upon binding of CO, nitric oxide (NO), or O(2) to heme and how they are transmitted from heme to globin. The UVRR results show that heme discriminates different ligands, resulting in different conformations in the globin protein. Specifically, NO induces changes in the spectrum of Trp residues in the A-helix that are significantly different from those induced by O(2) or CO binding. On the other hand, binding of O(2) to heme produces changes in the Tyr residues of the H-helix that are different from those induced by CO or NO binding. Furthermore, we found that cleavage of the Fe-His-93 covalent bond eliminates communication to the terminal region of the H-helix and that the 7-propionate hydrogen-bonding network is essential for transmitting the CO or NO binding signal to the N and C termini. Finally, the 6-propionate is important only for NO binding. Thus, the hydrogen-bonding network in the protein appears to be critical for intramolecular signal transduction in gas sensory heme proteins.
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Affiliation(s)
- Ying Gao
- School of Advanced Sciences, the Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
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Bondarenko V, Wang J, Kalish H, Balch AL, La Mar GN. Solution 1H NMR study of the accommodation of the side chain of n-butyl-etiohemin-I incorporated into the active site of cyano-metmyoglobin. J Biol Inorg Chem 2005; 10:283-93. [PMID: 15821940 DOI: 10.1007/s00775-005-0640-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 03/01/2005] [Indexed: 11/24/2022]
Abstract
In order to identify the most readily deformable portion of the heme pocket in myoglobin, equine myoglobin was reconstituted with a meso-n-butyl substituent on centrosymmetric etiohemin-I. Solution 1H NMR data for the low-spin iron(III) cyanide complex of oxidized myoglobin that include 2D nuclear Overhauser enhancement spectroscopy contacts, paramagnetic relaxation, and dipolar shifts resulting from magnetic anisotropy show that the heme binds uniquely to the iron in a manner that arranges the methyl and ethyl substituents on a given pyrrole in a clockwise manner when viewed from the proximal side, and with the n-butyl group seated at the canonical alpha-meso position of native protohemin-IX. The butyl group is oriented sharply toward the proximal side and its protein contacts demonstrate that it is oriented largely into the "xenon hole" in myoglobin. The location of the n-butyl group on the proximal side near the vacancies places it within the region found to be most flexible in molecular dynamics simulation. A small, counterclockwise rotation of the pyrrole N-Fe-N vector of n-butyl-etiohemin-I relative to that for native protohemin, indicated by both the prosthetic group methyl contact shift pattern and the prosthetic group contacts to heme pocket residues, is proposed to allow the xenon hole to accommodate better the n-butyl group. In contrast to previous work, which showed that a bulky polar substituent on etiohemin-I preferentially seats at the canonical gamma-meso position, the nonpolar n-butyl group selects the alpha-meso position.
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Affiliation(s)
- Vasyl Bondarenko
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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41
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Madden PW, Babcock MJ, Vayda ME, Cashon RE. Structural and kinetic characterization of myoglobins from eurythermal and stenothermal fish species. Comp Biochem Physiol B Biochem Mol Biol 2005; 137:341-50. [PMID: 15050521 DOI: 10.1016/j.cbpc.2003.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Revised: 12/15/2003] [Accepted: 12/31/2003] [Indexed: 11/20/2022]
Abstract
Teleost myoglobin (Mb) proteins from four fish species inhabiting different temperature environments were used to investigate the relationship between protein function and thermal stability. Mb was isolated from yellowfin tuna (homeothermal warm), mackerel (eurythermal warm), and the Antarctic teleost Notothenia coriiceps (stenothermal cold). Zebrafish (stenothermal tropical) myoglobin was expressed from cloned cDNA. These proteins differed in oxygen affinity, as measured by O2 dissociation rates and P50 values, and thermal stability as measured by autooxidation rates. Mackerel Mb had the highest P50 value at 25 degrees C (3.7 mmHg), corresponding to the lowest O2 affinity, followed by zebrafish (1.0 mmHg), yellowfin tuna (1.0 mmHg), and N. coriiceps (0.6 mmHg). Oxygen dissociation rates and Arrhenius plots were similar between all teleost species in this study, with the exception of mackerel myoglobin, which was two-fold faster at all temperatures tested. Myoglobin from the Antarctic teleost had the highest autooxidation rate (0.44 h(-1)), followed by mackerel (0.26 h(-1)), zebrafish (0.22 h(-1)), and yellowfin tuna (0.088 h(-1)). Primary structural analysis revealed residue differences distributed throughout the polypeptide sequences, making it difficult to identify, which, if any, residues contribute to structural flexibility. However, analysis of molecular dynamics trajectories indicates that Mb from the eurythermal mackerel is predicted to be the most flexible protein within the D loop and FG turn. At the same time, it has the lowest O2 affinity and the highest O2 dissociation rates when compared to myoglobins from teleosts that appear to be less flexible in our dynamics simulations.
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Affiliation(s)
- Peter W Madden
- Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, 5735 Hitchner Hall, Orono, ME 04469-5735, USA
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Manderson GA, Johansson JS. Towards a three-alpha-helix bundle protein that binds volatile general anesthetics. Biopolymers 2004; 75:338-54. [PMID: 15372486 DOI: 10.1002/bip.20138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The general anesthetics halothane and chloroform are capable of binding to synthetic water-soluble four-alpha-helix bundles, which model the putative in vivo receptors. In this study, we investigate the binding of these anesthetics to synthetic water-soluble three-alpha-helix bundles. A series of variants containing up to four X-to-Ala and up to four X-to-Met substitutions was made; and the effect of these substitutions on structure, stability and anesthetic binding affinity was examined. Generally, the amount of alpha-helix and the stability of the three-alpha-helix bundles decreased as the number of X-to-Ala substitutions increased. A concomitant red-shift in tryptophan fluorescence lambdamax was seen, suggesting an increased flexibility of the native structure. Up to four X-to-Met substitutions had little effect on the amount of alpha-helix, but an increase in tryptophan lambdamax was seen for the variants with three and four methionine substitutions. The exceptions were a) a variant with a clustering of alanine and methionine residues at one end of the three-alpha-helix bundle, suggesting a gate structure that can admit ligand molecules; and b) a variant with a single Leu35Ala substitution, suggesting that at select positions, the size of the side chain is important for defining anesthetic binding affinity.
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Affiliation(s)
- Gavin A Manderson
- University of Pennsylvania, Department of Anesthesia and the Johnson Research Foundation, Philadelphia, PA 19104, USA
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Picotti P, Marabotti A, Negro A, Musi V, Spolaore B, Zambonin M, Fontana A. Modulation of the structural integrity of helix F in apomyoglobin by single amino acid replacements. Protein Sci 2004; 13:1572-85. [PMID: 15152090 PMCID: PMC2279989 DOI: 10.1110/ps.04635304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 03/08/2004] [Accepted: 03/09/2004] [Indexed: 01/19/2023]
Abstract
The conformational features of native and mutant forms of sperm-whale apomyoglobin (apoMb) at neutral pH were probed by limited proteolysis experiments utilizing up to eight proteases of different substrate specificities. It was shown that all proteases selectively cleave apoMb at the level of chain segment 82-94 (HEAELKPLAQSHA), encompassing helix F in the X-ray structure of the holo form of the native protein; for example, thermolysin cleaves the Pro 88-Leu 89 peptide bond. These results indicate that helix F is highly flexible or largely disrupted in apoMb. Because helix F contains the helix-breaking Pro 88 residue, we propose that helix F is kept in place in the native holo protein by a variety of helix-heme stabilizing interactions. To modulate the stability of helix F, the Pro88Ala and Pro88Gly mutants were prepared by site-directed mutagenesis, and their conformational properties investigated by both far-UV circular dichroism spectroscopy and limited proteolysis. The helix content of the Pro88Ala mutant was somewhat enhanced with respect to that of both native and Pro88Gly mutant, as expected from the fact that Ala is the strongest helix inducer among the 20 amino acid residues. The rate of limited proteolysis of the three apoMb variants by thermolysin and proteinase K was in the order native > Pro88Gly >> Pro88Ala, in agreement with the scale of helix propensity of Ala, Gly, and Pro. The possible role of the flexible/unfolded chain segment 82-94 for the function and fate of apoMb at the cellular level is discussed.
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Affiliation(s)
- Paola Picotti
- CRIBI Biotechnology Centre, University of Padua, Viale G. Colombo 3, I-35121 Padua, Italy
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45
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Walker FA. Models of the Bis-Histidine-Ligated Electron-Transferring Cytochromes. Comparative Geometric and Electronic Structure of Low-Spin Ferro- and Ferrihemes. Chem Rev 2004; 104:589-615. [PMID: 14871136 DOI: 10.1021/cr020634j] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F Ann Walker
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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Yamamoto Y, Nagao S, Hirai Y, Inose T, Terui N, Mita H, Suzuki A. NMR investigation of the heme electronic structure in deoxymyoglobin possessing a fluorinated heme. J Biol Inorg Chem 2003; 9:152-60. [PMID: 14685828 DOI: 10.1007/s00775-003-0508-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2003] [Accepted: 10/14/2003] [Indexed: 10/26/2022]
Abstract
The heme electronic structures of deoxymyoglobins (deoxy-Mbs) reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-(trifluoromethyl)porphyrinatoiron(III) (7-PF), 13,17-bis(2-carboxylatoethyl)-3,7-difluoro-2,8,12,18-tetramethylporphyrinatoiron(III) (3,7-DF), and 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2-fluoro-7,12,18-trimethylporphyrinatoiron(III) (2-MF) have been characterized by (1)H and (19)F NMR. The analysis of heme methyl proton shift patterns of the hemes in their bis-cyano forms demonstrated that, owing to the substitution of a strongly electron-withdrawing perfluoromethyl group, CF(3), to porphyrin, the porphyrin pi-system of 7-PF is more significantly distorted from four-fold symmetry than those of the ring-fluorinated hemes, 3,7-DF and 2-MF. The presence of the heme orientation disorder resulted in the observation of the two well-resolved (19)F signals in the spectra of deoxy-Mbs possessing 7-PF and 2-MF. The (19)F signals of deoxy-Mb possessing 7-PF exhibited a relatively large difference in paramagnetic shift (approximately 30 ppm), despite their small paramagnetic shifts (approximately 30 ppm), supporting the significant contribution of a pi spin delocalization mechanism in this Mb due to the d-electron configuration derived from the (5)E ground state. On the other hand, (19)F signals of deoxy-Mbs with 3,7-DF as well as 2-MF exhibited large paramagnetic shifts (approximately 250 ppm) with a relatively small difference in the paramagnetic shift (approximately 20 ppm), indicating the predominant contribution of spin delocalization, due to a d-electron configuration derived from the (5)B(2) ground state. These results demonstrate for the first time that the relative contributions of the orbital ground states derived from (5)E and (5)B(2) states to the heme electronic structure in deoxy-Mb are affected by the distortion of the porphyrin pi-system exerted by chemical properties of the heme peripheral side-chains.
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Affiliation(s)
- Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, 305-8571 Tsukuba, Japan.
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Structural Dynamics of Myoglobin Probed by Femtosecond Infrared Spectroscopy of the Amide Band. B KOREAN CHEM SOC 2003. [DOI: 10.5012/bkcs.2003.24.10.1470] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kundu S, Hargrove MS. Distal heme pocket regulation of ligand binding and stability in soybean leghemoglobin. Proteins 2003; 50:239-48. [PMID: 12486718 DOI: 10.1002/prot.10277] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Leghemoglobins facilitate diffusion of oxygen through root tissue to a bacterial terminal oxidase in much the same way that myoglobin transports oxygen from blood to muscle cell mitochondria. Leghemoglobin serves an additional role as an oxygen scavenger to prevent inhibition of nitrogen fixation. For this purpose, the oxygen affinity of soybean leghemoglobin is 20-fold greater than myoglobin, resulting from an 8-fold faster association rate constant combined with a 3-fold slower dissociation rate constant. Although the biochemical mechanism used by myoglobin to bind oxygen has been described in elegant detail, an explanation for the difference in affinity between these two structurally similar proteins is not obvious. The present work demonstrates that, despite their similar structures, leghemoglobin uses methods different from myoglobin to regulate ligand affinity. Oxygen and carbon monoxide binding to a comprehensive set of leghemoglobin distal heme pocket mutant proteins in comparison to their myoglobin counterparts has revealed some of these mechanisms. The "distal histidine" provides a crucial hydrogen bond to stabilize oxygen in myoglobin but has little effect on bound oxygen in leghemoglobin and is retained mainly for reasons of protein stability and prevention of heme loss. Furthermore, soybean leghemoglobin uses an unusual combination of HisE7 and TyrB10 to sustain a weak stabilizing interaction with bound oxygen. Thus, the leghemoglobin distal heme pocket provides a much lower barrier to oxygen association than occurs in myoglobin and oxygen dissociation is regulated from the proximal heme pocket.
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Affiliation(s)
- Suman Kundu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Mizutani Y, Kitagawa T. Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy. CHEM REC 2002; 1:258-75. [PMID: 11895123 DOI: 10.1002/tcr.1012] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described.
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Affiliation(s)
- Y Mizutani
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Japan
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Kundu S, Snyder B, Das K, Chowdhury P, Park J, Petrich JW, Hargrove MS. The leghemoglobin proximal heme pocket directs oxygen dissociation and stabilizes bound heme. Proteins 2002; 46:268-77. [PMID: 11835502 DOI: 10.1002/prot.10048] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Sperm whale myoglobin (Mb) and soybean leghemoglobin (Lba) are two small, monomeric hemoglobins that share a common globin fold but differ widely in many other aspects. Lba has a much higher affinity for most ligands, and the two proteins use different distal and proximal heme pocket regulatory mechanisms to control ligand binding. Removal of the constraint provided by covalent attachment of the proximal histidine to the F-helices of these proteins decreases oxygen affinity in Lba and increases oxygen affinity in Mb, mainly because of changes in oxygen dissociation rate constants. Hence, Mb and Lba use covalent constraints in opposite ways to regulate ligand binding. Swapping the F-helices of the two proteins brings about similar effects, highlighting the importance of this helix in proximal heme pocket regulation of ligand binding. The F7 residue in Mb is capable of weaving a hydrogen-bonding network that holds the proximal histidine in a fixed orientation. On the contrary, the F7 residue in Lba lacks this property and allows the proximal histidine to assume a conformation favorable for higher ligand binding affinity. Geminate recombination studies indicate that heme iron reactivity on picosecond timescales is not the dominant cause for the effects observed in each mutation. Results also indicate that in Lba the proximal and distal pocket mutations probably influence ligand binding independently. These results are discussed in the context of current hypotheses for proximal heme pocket structure and function.
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Affiliation(s)
- Suman Kundu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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