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Ri YK, Kim SA, Kye YH, Jong YC, Kang MS, Yu CJ. First-principles study of molecular hydrogen binding to heme in competition with O 2, NO and CO. RSC Adv 2024; 14:16629-16638. [PMID: 38784410 PMCID: PMC11110138 DOI: 10.1039/d4ra02091j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular hydrogen shows antioxidant activity and distinct efficacy towards vascular diseases, but the understanding of this is not yet satisfactory at the atomic level. In this work, we study the binding properties of H2 to the heme group in relation with other diatomic molecules (DMs), including O2, NO and CO, and their displacement reactions, using first-principles calculations. We carry out molecular modeling of the heme group, using iron-porphyrin with the imidazole ligand, i.e., FePIm, and smaller models of Fe(CnHn+2N2)2NH3 with n = 3 and 1, and of molecular complexes of heme-DM and -H. Through analysis of optimized geometries and energetics, it is found that the order of binding strength of DMs or H to the Fe of heme is NO > O2 > CO > H > H2 for FePIm-based systems, while it is H > O2 > NO > CO > H2 for model-based systems. We calculate the activation energies for displacement reactions of H2 and H by other DMs, revealing that the H2 displacements occur spontaneously while the H displacements require a large amount of energy. Finally, our calculations corroborate that the rate constants increase with increasing temperature according to the Arrhenius relation.
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Affiliation(s)
- Yun-Kyong Ri
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Song-Ae Kim
- Institute of Molecular Biology, Faculty of Life Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Yun-Hyok Kye
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Yu-Chol Jong
- Chair of Chemical Process, Faculty of Chemistry, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Myong-Su Kang
- Institute of Molecular Biology, Faculty of Life Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Chol-Jun Yu
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
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2
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Zhang L, Brown MC, Mutter AC, Greenland KN, Cooley JW, Koder RL. Protein dynamics govern the oxyferrous state lifetime of an artificial oxygen transport protein. Biophys J 2023; 122:4440-4450. [PMID: 37865818 PMCID: PMC10698322 DOI: 10.1016/j.bpj.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 10/23/2023] Open
Abstract
It has long been known that the alteration of protein side chains that occlude or expose the heme cofactor to water can greatly affect the stability of the oxyferrous heme state. Here, we demonstrate that the rate of dynamically driven water penetration into the core of an artificial oxygen transport protein also correlates with oxyferrous state lifetime by reducing global dynamics, without altering the structure of the active site, via the simple linking of the two monomers in a homodimeric artificial oxygen transport protein using a glycine-rich loop. The tethering of these two helices does not significantly affect the active site structure, pentacoordinate heme-binding affinity, reduction potential, or gaseous ligand affinity. It does, however, significantly reduce the hydration of the protein core, as demonstrated by resonance Raman spectroscopy, backbone amide hydrogen exchange, and pKa shifts in buried histidine side chains. This further destabilizes the charge-buried entatic state and nearly triples the oxyferrous state lifetime. These data are the first direct evidence that dynamically driven water penetration is a rate-limiting step in the oxidation of these complexes. It furthermore demonstrates that structural rigidity that limits water penetration is a critical design feature in metalloenzyme construction and provides an explanation for both the failures and successes of earlier attempts to create oxygen-binding proteins.
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Affiliation(s)
- Lei Zhang
- Department of Physics, The City College of New York, New York, New York
| | - Mia C Brown
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Andrew C Mutter
- Department of Biochemistry, The City College of New York, New York, New York
| | - Kelly N Greenland
- Department of Physics, The City College of New York, New York, New York
| | - Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York; Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, New York.
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3
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Kim CH, Ryu C, Ro YH, O SI, Yu CJ. First-principles study of mercaptoundecanoic acid molecule adsorption and gas molecule penetration onto silver surface: an insight for corrosion protection. RSC Adv 2023; 13:31224-31233. [PMID: 37886019 PMCID: PMC10598515 DOI: 10.1039/d3ra06040c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Recently, 11-mercaptoundecanoic acid (MUA) molecule has attracted attention as a promising passivation agent of Ag nanowire (NW) network electrode for corrosion inhibition, but the underneath mechanism has not been elaborated. In this work, we investigate adsorption of MUA molecule on Ag(1 0 0) and Ag(1 1 1) surface, adsorption of air gas molecules of H2O, H2S and O2 on MUA molecular end surface, and their penetrations into the Ag surface using the first-principles calculations. Our calculations reveal that the MUA molecule is strongly bound to the Ag surface with the binding energies ranging from -0.47 to -2.06 eV and the Ag-S bond lengths of 2.68-2.97 Å by Lewis acid-base reaction. Furthermore, we find attractive interactions between the gas molecules and the MUA@Ag complexes upon their adsorptions and calculate activation barriers for their migrations from the outermost end of the complexes to the top of Ag surface. It is found that the penetrations of H2O and H2S are more difficult than the O2 penetration due to their higher activation barriers, while the O2 penetration is still difficult, confirming the corrosion protection of Ag NW network by adsorbing the uniform monolayer of MUA. With these findings, this work can contribute to finding a better passivation agent in the strategy of corrosion protection of Ag NW network electrode.
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Affiliation(s)
- Chung-Hyok Kim
- Institute of Electronic Materials, High-Tech and Development Centre, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Chol Ryu
- Computational Materials Design (CMD), Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Yong-Hak Ro
- Institute of Electronic Materials, High-Tech and Development Centre, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Song-Il O
- Physics Department, O Jung Hub Chongjin University of Education Chongjin Hamgyong North Province Democratic People's Republic of Korea
| | - Chol-Jun Yu
- Computational Materials Design (CMD), Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
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4
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Kim SA, Jong YC, Kang MS, Yu CJ. Antioxidation activity of molecular hydrogen via protoheme catalysis in vivo: an insight from ab initio calculations. J Mol Model 2022; 28:287. [PMID: 36057001 DOI: 10.1007/s00894-022-05264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/12/2022] [Indexed: 01/29/2023]
Abstract
Recently, molecular hydrogen has been found to exhibit antioxidation activity through many clinical experiments, but the mechanism has not been fully understandable at atomic level. In this work, we perform systematic ab initio calculations of protoheme-hydrogen complexes to clarify the antioxidation mechanism of molecular hydrogen. We make molecular modeling of iron-protoporphyrin coordinated by imidazole, FeP(Im), and its hydrogen as well as dihydrogen complexes, together with reactive oxygen/nitrogen species (RONS). We carry out structural optimization and Mulliken charge analysis, revealing the two kinds of bonding characteristics between FeP(Im) and H[Formula: see text]: dihydrogen bonding in the end-on asymmetric configuration and Kubas bonding in the side-on symmetric configuration of H[Formula: see text] molecule. The activation barriers for adsorption and dissociation of H[Formula: see text] on and further desorption of H atom from FeP(Im) are found to be below 2.78 eV at most, which is remarkably lower than the H-H bond breaking energy of 4.64 eV in free H[Formula: see text] molecule. We find that the hydrogen bond dissociation energies of FeP(Im)-H[Formula: see text] and -H complexes are lower than those of RONS-H complexes, indicating the decisive role of protoheme as an effective catalyst in RONS antioxidation by molecular hydrogen in vivo.
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Affiliation(s)
- Song-Ae Kim
- Faculty of Chemistry, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, PO Box 76, Democratic People's Republic of Korea
| | - Yu-Chol Jong
- Faculty of Chemistry, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, PO Box 76, Democratic People's Republic of Korea
| | - Myong-Su Kang
- Faculty of Life Science, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, PO Box 76, Democratic People's Republic of Korea
| | - Chol-Jun Yu
- Faculty of Materials Science, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, PO Box 76, Democratic People's Republic of Korea.
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5
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Ovung A, Mavani A, Ghosh A, Chatterjee S, Das A, Suresh Kumar G, Ray D, Aswal VK, Bhattacharyya J. Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods. ACS OMEGA 2022; 7:4932-4944. [PMID: 35187312 PMCID: PMC8851458 DOI: 10.1021/acsomega.1c05554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/24/2022] [Indexed: 05/16/2023]
Abstract
Protein-ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure-function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 104 M-1. SMZ with two additional methyl (-CH3) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand-protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.
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Affiliation(s)
- Aben Ovung
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - A. Mavani
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - Ambarnil Ghosh
- UCD
Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Abhi Das
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Debes Ray
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Vinod K. Aswal
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Jhimli Bhattacharyya
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
- ,
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6
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Wang Z, Zhou H, Zhou K, Tu J, Xu B. An underlying softening mechanism in pale, soft and exudative - Like rabbit meat: The role of reactive oxygen species - Generating systems. Food Res Int 2022; 151:110853. [PMID: 34980389 DOI: 10.1016/j.foodres.2021.110853] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/02/2021] [Accepted: 11/27/2021] [Indexed: 01/01/2023]
Abstract
This work investigated the role of reactive oxygen species (ROS) - generating systems on the softening of the pale, soft and exudative-like (PSE-like) rabbit meat during aging. PSE-like meat was induced by incubation of post-mortem rabbit Longissimus thoracis et lumborum at 37 °C for 3 h. During aging, PSE-like meat samples had higher values in peroxides value, thiobarbituric acid-reactive substances, metmyoglobin percentage, ferrylmyoglobin content, non-heme iron content, hydroxyl radical content and ROS concentration compared with the normal ones, suggesting that PSE-like incubation could activate lipid-oxidizing system, myoglobin-mediated oxidation system, together with metal-catalyzed oxidation system. Additionally, higher protein carbonyl content was observed in PSE-like meat, along with a significant loss in sulfhydryl group. The results of SDS-PAGE suggested that more serious protein degradation occurred in PSE-like meat. It is plausible that the activated ROS-generating system played an underlying role in the softening texture during the aging period of PSE-like meat.
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Affiliation(s)
- Zhaoming Wang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hui Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Kai Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Juncai Tu
- Department of Wine, Food and Molecular Biosciences, Lincoln University, P O Box 84, Lincoln 7647, Christchurch, New Zealand
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; State Key Laboratory of Meat Processing and Quality Control, Nanjing, 211806, China.
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7
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Isogai Y, Imamura H, Nakae S, Sumi T, Takahashi KI, Shirai T. Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals. iScience 2021; 24:102920. [PMID: 34430810 PMCID: PMC8374505 DOI: 10.1016/j.isci.2021.102920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/04/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Myoglobin (Mb) is highly concentrated in the myocytes of diving mammals such as whales and seals, in comparison with land animals, and its molecular evolution has played a crucial role in their deep-sea adaptation. We previously resurrected ancestral whale Mbs and demonstrated the evolutional strategies for higher solubility under macromolecular crowding conditions. Pinnipeds, such as seals and sea lions, are also expert diving mammals with Mb-rich muscles. In the present study, we resurrected ancestral pinniped Mbs and investigated their biochemical and structural properties. Comparisons between pinniped and whale Mbs revealed the common and distinctive strategies for the deep-sea adaptation. The overall evolution processes, gaining precipitant tolerance and improving thermodynamic stability, were commonly observed. However, the strategies for improving the folding stability differed, and the pinniped Mbs exploited the shielding of hydrophobic surfaces more effectively than the whale Mbs.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
- Corresponding author
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Setsu Nakae
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Ken-ichi Takahashi
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
- Corresponding author
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8
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Julió Plana L, Martinez Grundman JE, Estrin DA, Lecomte JTJ, Capece L. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study. J Inorg Biochem 2021; 220:111455. [PMID: 33882423 DOI: 10.1016/j.jinorgbio.2021.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/26/2022]
Abstract
THB1 is a monomeric truncated hemoglobin from the green alga Chlamydomonas reinhardtii. In the absence of exogenous ligands and at neutral pH, the heme group of THB1 is coordinated by two protein residues, Lys53 and His77. THB1 is thought to function as a nitric oxide dioxygenase, and the distal binding of O2 requires the cleavage of the Fe-Lys53 bond accompanied by protonation and expulsion of the lysine from the heme cavity into the solvent. Nuclear magnetic resonance spectroscopy and crystallographic data have provided dynamic and structural insights of the process, but the details of the mechanism have not been fully elucidated. We applied a combination of computer simulations and site-directed mutagenesis experiments to shed light on this issue. Molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics restrained optimizations were performed to explore the nature of the transition between the decoordinated and lysine-bound states of the ferrous heme in THB1. Lys49 and Arg52, which form ionic interactions with the heme propionates in the X-ray structure of lysine-bound THB1, were observed to assist in maintaining Lys53 inside the protein cavity and play a key role in the transition. Lys49Ala, Arg52Ala and Lys49Ala/Arg52Ala THB1 variants were prepared, and the consequences of the replacements on the Lys (de)coordination equilibrium were characterized experimentally for comparison with computational prediction. The results reinforced the dynamic role of protein-propionate interactions and strongly suggested that cleavage of the Fe-Lys53 bond and ensuing conformational rearrangement is facilitated by protonation of the amino group inside the distal cavity.
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Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jaime E Martinez Grundman
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - 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
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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9
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Petrik ID, Davydov R, Kahle M, Sandoval B, Dwaraknath S, Ädelroth P, Hoffman B, Lu Y. An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Biochemistry 2021; 60:346-355. [PMID: 33464878 PMCID: PMC7888536 DOI: 10.1021/acs.biochem.0c00852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Efficiently carrying out the oxygen reduction reaction (ORR) is critical for many applications in biology and chemistry, such as bioenergetics and fuel cells, respectively. In biology, this reaction is carried out by large, transmembrane oxidases such as heme-copper oxidases (HCOs) and cytochrome bd oxidases. Common to these oxidases is the presence of a glutamate residue next to the active site, but its precise role in regulating the oxidase activity remains unclear. To gain insight into its role, we herein report that incorporation of glutamate next to a designed heme-copper center in two biosynthetic models of HCOs improves O2 binding affinity, facilitates protonation of reaction intermediates, and eliminates release of reactive oxygen species. High-resolution crystal structures of the models revealed extended, water-mediated hydrogen-bonding networks involving the glutamate. Electron paramagnetic resonance of the cryoreduced oxy-ferrous centers at cryogenic temperature followed by thermal annealing allowed observation of the key hydroperoxo intermediate that can be attributed to the hydrogen-bonding network. By demonstrating these important roles of glutamate in oxygen reduction biochemistry, this work offers deeper insights into its role in native oxidases, which may guide the design of more efficient artificial ORR enzymes or catalysts for applications such as fuel cells.
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Affiliation(s)
- Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Roman Davydov
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Braddock Sandoval
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sudharsan Dwaraknath
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brian Hoffman
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Ragucci S, Ruggiero A, Russo R, Landi N, Valletta M, Chambery A, Russo L, Di Maro A. Correlation of structure, function and protein dynamics in myoglobins from Eurasian woodcock, chicken and ostrich. J Biomol Struct Dyn 2020; 39:851-866. [DOI: 10.1080/07391102.2020.1719201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Alessio Ruggiero
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
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11
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Rodriguez-Mackenzie AD, Arbelo-Lopez HD, Wymore T, Lopez-Garriga J. A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64. J Mol Graph Model 2019; 94:107465. [PMID: 31670138 DOI: 10.1016/j.jmgm.2019.107465] [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: 08/09/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022]
Abstract
Myoglobin (Mb) binds oxygen with high affinity as a low spin singlet complex and thus functions as an oxygen storage protein. Yet, hybrid Density Functional Theory/Molecular Mechanical (DFT/MM) calculations of oxy-Mb models predict that the O2 bond is much less resistant to breaking in the presence of hydrogen sulfide (H2S) compared with water. Specifically, a hydrogen atom from H2S can be transferred to the distal oxygen atom through homolytic cleavage of the S-H bond to form the intermediate Compound (Cpd) 0 structure and a thiyl radical. In the presence of a neutral His64 (Nε protonation, His64-ε) and H2S, only a metastable Cpd 0 would be formed as the active site is devoid of any additional proton donor to fully break the O2 bond. In contrast, the calculations predict that the triplet state is significantly favored over the open shell singlet diradical state throughout the entire reaction coordinate in the presence of H2S and a positively charged His64. Furthermore, a positively charged His64 can readily donate a proton to Cpd 0 to fully break the O2 bond resulting in a configuration analogous to reported reaction models of a hemoglobin mutant bound to H2O2 with H2S present. Typically, exotic techniques are required to generate Cpd 0 but under the conditions just described the intermediate is readily detected in UV-Vis spectra at room temperature. The effect is observed as a 2 nm red shift of the Soret band from 414 nm to 416 nm (pH 5.0, His64-εδ) and from 416 nm to 418 nm (pH 6.6, His64-ε).
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Affiliation(s)
| | - Hector D Arbelo-Lopez
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico
| | - Troy Wymore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, United States.
| | - Juan Lopez-Garriga
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico.
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12
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Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions. Nat Commun 2019; 10:1396. [PMID: 30918256 PMCID: PMC6437160 DOI: 10.1038/s41467-019-09111-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/14/2019] [Indexed: 11/08/2022] Open
Abstract
Myoglobin, encoded by MB, is a small cytoplasmic globular hemoprotein highly expressed in cardiac myocytes and oxidative skeletal myofibers. Myoglobin binds O2, facilitates its intracellular transport and serves as a controller of nitric oxide and reactive oxygen species. Here, we identify a recurrent c.292C>T (p.His98Tyr) substitution in MB in fourteen members of six European families suffering from an autosomal dominant progressive myopathy with highly characteristic sarcoplasmic inclusions in skeletal and cardiac muscle. Myoglobinopathy manifests in adulthood with proximal and axial weakness that progresses to involve distal muscles and causes respiratory and cardiac failure. Biochemical characterization reveals that the mutant myoglobin has altered O2 binding, exhibits a faster heme dissociation rate and has a lower reduction potential compared to wild-type myoglobin. Preliminary studies show that mutant myoglobin may result in elevated superoxide levels at the cellular level. These data define a recognizable muscle disease associated with MB mutation. Myoglobin is a hemeprotein that reversibly binds oxygen and gives muscle its red color. Here, the authors report a genetic variant in the MB gene that associates with myoglobinopathy, an autosomal dominant progressive myopathy, and altered oxygen binding properties of the mutant protein.
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Isogai Y, Imamura H, Nakae S, Sumi T, Takahashi KI, Nakagawa T, Tsuneshige A, Shirai T. Tracing whale myoglobin evolution by resurrecting ancient proteins. Sci Rep 2018; 8:16883. [PMID: 30442991 PMCID: PMC6237822 DOI: 10.1038/s41598-018-34984-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan.
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Setsu Nakae
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Ken-Ichi Takahashi
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Taro Nakagawa
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Antonio Tsuneshige
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan.
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Watanabe M, Kanai Y, Nakamura S, Nishimura R, Shibata T, Momotake A, Yanagisawa S, Ogura T, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Synergistic Effect of Distal Polar Interactions in Myoglobin and Their Structural Consequences. Inorg Chem 2018; 57:14269-14279. [DOI: 10.1021/acs.inorgchem.8b02302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Affiliation(s)
- Mariette M. Pereira
- CQC, Coimbra Chemistry Centre, Department of Chemistry, Faculty of Science and Technology, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Lucas D. Dias
- CQC, Coimbra Chemistry Centre, Department of Chemistry, Faculty of Science and Technology, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Mário J. F. Calvete
- CQC, Coimbra Chemistry Centre, Department of Chemistry, Faculty of Science and Technology, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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16
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Tofteskov J, Hansen J, Bailey N. Modelling the autoxidation of myoglobin in fresh meat under modified atmosphere packing conditions. J FOOD ENG 2017. [DOI: 10.1016/j.jfoodeng.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Hanai S, Tsujino H, Yamashita T, Torii R, Sawai H, Shiro Y, Oohora K, Hayashi T, Uno T. Roles of N- and C-terminal domains in the ligand-binding properties of cytoglobin. J Inorg Biochem 2017; 179:1-9. [PMID: 29149638 DOI: 10.1016/j.jinorgbio.2017.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/04/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023]
Abstract
Cytoglobin (Cygb) is a member of the hexacoordinated globin protein family and is expressed ubiquitously in rat and human tissues. Although Cygb is reportedly upregulated under hypoxic conditions both in vivo and in vitro, suggesting a physiological function to protect cells under hypoxic/ischemic conditions by scavenging reactive oxygen species or by signal transduction, the mechanisms associated with this function have not been fully elucidated. Recent studies comparing Cygbs among several species suggest that mammalian Cygbs show a distinctly longer C-terminal domain potentially involved in unique physiological functions. In this study, we prepared human Cygb mutants (ΔC, ΔN, and ΔNC) with either one or both terminal domains truncated and investigated the enzymatic functions and structural features by spectroscopic methods. Evaluation of the superoxide-scavenging activity between Cygb variants showed that the ΔC and ΔNC mutants exhibited slightly higher activity involving superoxide scavenging as compared with wild-type Cygb. Subsequent experiments involving ligand titration, flash photolysis, and resonance Raman spectroscopic studies suggested that the truncation of the C- and N-terminal domains resulted in less effective to dissociation constants and binding rates for carbon monoxide, respectively. Furthermore, structural stability was assessed by guanidine hydrochloride and revealed that the C-terminal domain might play a vital role in improving structure, whereas the N-terminal domain did not exert a similar effect. These findings indicated that long terminal domains could be important not only in regulating enzymatic activity but also for structural stability, and that the domains might be relevant to other hypothesized physiological functions for Cygb.
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Affiliation(s)
- Shumpei Hanai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Taku Yamashita
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Hyogo, Japan.
| | - Ryo Torii
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | | | - Koji Oohora
- Department of Applied Chemistry, Osaka University, Osaka, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Osaka University, Osaka, Japan
| | - Tadayuki Uno
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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18
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations. Sci Rep 2017; 7:10926. [PMID: 28883619 PMCID: PMC5589765 DOI: 10.1038/s41598-017-11259-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of allosterism over 60 years ago, with the introduction of the MWC model based on Perutz structures of the oxy(R) and deoxy(T) states and the more recent Tertiary Two-State model that proposed the existence of individual subunit states -“r” and “t”-, whose structure is yet unknown. Cooperative oxygen binding is essential for Hb function, and despite decades of research there are still open questions related to how tertiary and quaternary changes regulate oxygen affinity. In the present work, we have determined the free energy profiles of oxygen migration and for HisE7 gate opening, with QM/MM calculations of the oxygen binding energy in order to address the influence of tertiary differences in the control of oxygen affinity. Our results show that in the α subunit the low to high affinity transition is achieved by a proximal effect that mostly affects oxygen dissociation and is the driving force of the allosteric transition, while in the β subunit the affinity change results from a complex interplay of proximal and distal effects, including an increase in the HE7 gate opening, that as shown by free energy profiles promotes oxygen uptake.
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Boubeta FM, Bari SE, Estrin DA, Boechi L. Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata. J Phys Chem B 2016; 120:9642-53. [DOI: 10.1021/acs.jpcb.6b06686] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando M. Boubeta
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Sara E. Bari
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Dario A. Estrin
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo/CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires,
Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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21
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Zhao C, Du W. Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations. J Biol Inorg Chem 2016; 21:251-61. [DOI: 10.1007/s00775-016-1334-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
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