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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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2
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Famulari A, Correddu D, Di Nardo G, Gilardi G, Mitrikas G, Chiesa M, García-Rubio I. Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study. Molecules 2024; 29:518. [PMID: 38276601 PMCID: PMC10819608 DOI: 10.3390/molecules29020518] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Affiliation(s)
- Antonino Famulari
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, 15341 Athens, Greece;
| | - Mario Chiesa
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Inés García-Rubio
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
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3
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Kanematsu Y, Kondo HX, Takano Y. Computational Exploration of Minimum Energy Reaction Pathway of N 2O Formation from Intermediate I of P450nor Using an Active Center Model. Int J Mol Sci 2023; 24:17172. [PMID: 38139001 PMCID: PMC10743073 DOI: 10.3390/ijms242417172] [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: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.
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Affiliation(s)
- Yusuke Kanematsu
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
| | - Hiroko X. Kondo
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
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Kondo HX, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y. Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network. Biomolecules 2023; 13:biom13010137. [PMID: 36671521 PMCID: PMC9855806 DOI: 10.3390/biom13010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure-function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure-function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB-OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure-function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
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Affiliation(s)
- Hiroko X. Kondo
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita 565-0874, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
| | - Hiroyuki Iizuka
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14, Nishi 9, Kitaku, Sapporo 060-0814, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yuichi Kabaya
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yusuke Kanematsu
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
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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: 18] [Impact Index Per Article: 9.0] [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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Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network. Biomolecules 2022; 12:biom12091172. [PMID: 36139011 PMCID: PMC9496533 DOI: 10.3390/biom12091172] [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: 07/30/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Heme proteins serve diverse and pivotal biological functions. Therefore, clarifying the mechanisms of these diverse functions of heme is a crucial scientific topic. Distortion of heme porphyrin is one of the key factors regulating the chemical properties of heme. Here, we constructed convolutional neural network models for predicting heme distortion from the tertiary structure of the heme-binding pocket to examine their correlation. For saddling, ruffling, doming, and waving distortions, the experimental structure and predicted values were closely correlated. Furthermore, we assessed the correlation between the cavity shape and molecular structure of heme and demonstrated that hemes in protein pockets with similar structures exhibit near-identical structures, indicating the regulation of heme distortion through the protein environment. These findings indicate that the tertiary structure of the heme-binding pocket is one of the factors regulating the distortion of heme porphyrin, thereby controlling the chemical properties of heme relevant to the protein function; this implies a structure–function correlation in heme proteins.
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Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022; 23:ijms23147684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.
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Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Correspondence:
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8
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Kondo HX, Kanematsu Y, Takano Y. Structure of Heme-binding Pocket in Heme Protein is Generally Rigid and can be Predicted by AlphaFold2. CHEM LETT 2022. [DOI: 10.1246/cl.220172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroko X. Kondo
- Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yusuke Kanematsu
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
- Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Yu Takano
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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Kondo HX, Fujii M, Tanioka T, Kanematsu Y, Yoshida T, Takano Y. Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. J Chem Inf Model 2022; 62:775-784. [PMID: 35157473 DOI: 10.1021/acs.jcim.1c01315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. Here, we tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes using machine learning. A correlation was detected in the three lowest vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure-function relationship of heme.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.,Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Masanori Fujii
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Takuma Tanioka
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takashi Yoshida
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. Life (Basel) 2022; 12:life12020210. [PMID: 35207496 PMCID: PMC8880375 DOI: 10.3390/life12020210] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations as well as statistical analysis of the protein structures of hemoglobin and myoglobin stored in Protein Data Bank. Our computation and statistical analysis showed that the protein environment for hemoglobin and myoglobin prominently affects the doming distortion of heme porphyrin, which correlates with its oxygen affinity, and that the magnitude of distortion is different between hemoglobin and myoglobin. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.
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