1
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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2
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Pletzer-Zelgert J, Ehrt C, Fender I, Griewel A, Flachsenberg F, Klebe G, Rarey M. LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments. Acta Crystallogr D Struct Biol 2023; 79:837-856. [PMID: 37561404 PMCID: PMC10478636 DOI: 10.1107/s205979832300582x] [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: 04/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Due to the structural complexity of proteins, their corresponding crystal arrangements generally contain a significant amount of solvent-occupied space. These areas allow a certain degree of intracrystalline protein flexibility and mobility of solutes. Therefore, knowledge of the geometry of solvent-filled channels and cavities is essential whenever the dynamics inside a crystal are of interest. Especially in soaking experiments for structure-based drug design, ligands must be able to traverse the crystal solvent channels and reach the corresponding binding pockets. Unsuccessful screenings are sometimes attributed to the geometry of the crystal packing, but the underlying causes are often difficult to understand. This work presents LifeSoaks, a novel tool for analyzing and visualizing solvent channels in protein crystals. LifeSoaks uses a Voronoi diagram-based periodic channel representation which can be efficiently computed. The size and location of channel bottlenecks, which might hinder molecular diffusion, can be directly derived from this representation. This work presents the calculated bottleneck radii for all crystal structures in the PDB and the analysis of a new, hand-curated data set of structures obtained by soaking experiments. The results indicate that the consideration of bottleneck radii and the visual inspection of channels are beneficial for planning soaking experiments.
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Affiliation(s)
| | - Christiane Ehrt
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Inken Fender
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Axel Griewel
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Universität Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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3
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Günsel U, Klöpfer K, Häusler E, Hitzenberger M, Bölter B, Sperl LE, Zacharias M, Soll J, Hagn F. Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21. Nat Struct Mol Biol 2023:10.1038/s41594-023-00984-y. [PMID: 37156968 DOI: 10.1038/s41594-023-00984-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
Triose phosphates (TPs) are the primary products of photosynthetic CO2 fixation in chloroplasts, which need to be exported into the cytosol across the chloroplast inner envelope (IE) and outer envelope (OE) membranes to sustain plant growth. While transport across the IE is well understood, the mode of action of the transporters in the OE remains unclear. Here we present the high-resolution nuclear magnetic resonance (NMR) structure of the outer envelope protein 21 (OEP21) from garden pea, the main exit pore for TPs in C3 plants. OEP21 is a cone-shaped β-barrel pore with a highly positively charged interior that enables binding and translocation of negatively charged metabolites in a competitive manner, up to a size of ~1 kDa. ATP stabilizes the channel and keeps it in an open state. Despite the broad substrate selectivity of OEP21, these results suggest that control of metabolite transport across the OE might be possible.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Kai Klöpfer
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elisabeth Häusler
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Manuel Hitzenberger
- Lehrstuhl für Theoretische Biophysik (T38), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Bettina Bölter
- Biozentrum, LMU München, Department of Biology, Planegg-Martinsried, Germany
| | - Laura E Sperl
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Lehrstuhl für Theoretische Biophysik (T38), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Jürgen Soll
- Biozentrum, LMU München, Department of Biology, Planegg-Martinsried, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany.
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4
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Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures. Int J Mol Sci 2022; 23:ijms232315149. [PMID: 36499474 PMCID: PMC9741079 DOI: 10.3390/ijms232315149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.
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5
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Goode-Romero G, Dominguez L. Computational study of the conformational ensemble of CX3C chemokine receptor 1 (CX3CR1) and its interactions with antagonist and agonist ligands. J Mol Graph Model 2022; 117:108278. [PMID: 35988439 DOI: 10.1016/j.jmgm.2022.108278] [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: 12/05/2021] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/14/2023]
Abstract
The CX3C chemokine receptor 1 (CX3CR1), a member of the class A of G Protein-Coupled Receptors (GPCR) superfamily, and its ligand fractalkine constitute an important biochemical axis that influence many cellular pathways involving homeostatic and inflammatory processes. They participate in the activation, chemotaxis and recruitment of multiple immunological cells such as microglia, macrophages and monocytes, and play a critical role in neuroinflammatory conditions such as Alzheimer's disease and multiple sclerosis, in the recovery from central nervous system injuries, in several chronic, peripheral inflammatory entities and in some infective processes including HIV-AIDS. In this work we present the study of the CX3CR1 receptor employing extensive atomistic Molecular Dynamics (MD) simulations with the aim to characterize the conformational ensemble of the receptor in the presence of its antagonist and agonist ligands. We analyzed the receptor conformational changes and described interactions within its key regions and the bounded ligands to identify their notable differences. Finally, we classify the features that would allow the identification of patterns that characterize a functional state to contribute to the understanding of the complexity of the GPCR superfamily.
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Affiliation(s)
- Guillermo Goode-Romero
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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6
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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7
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Goode-Romero G, Dominguez L. Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands. PLoS One 2022; 17:e0275269. [PMID: 36251708 PMCID: PMC9576088 DOI: 10.1371/journal.pone.0275269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
CC Chemokine receptor 5 (CCR5), a member of the Superfamily of G Protein-Coupled Receptors (GPCRs), is an important effector in multiple physiopathological processes such as inflammatory and infectious entities, including central nervous system neuroinflammatory diseases such as Alzheimer's disease, recovery from nervous injuries, and in the HIV-AIDS infective processes. Thus, CCR5 is an attractive target for pharmacological modulation. Since maraviroc was described as a CCR5 ligand that modifies the HIV-AIDS progression, multiple efforts have been developed to describe the functionality of the receptor. In this work, we characterized key structural features of the CCR5 receptor employing extensive atomistic molecular dynamics (MD) in its apo form and in complex with an endogenous agonist, the chemokine CCL5/RANTES, an HIV entry inhibitor, the partial inverse agonist maraviroc, and the experimental antagonists Compound 21 and 34, aiming to elucidate the structural features and mechanistic processes that constitute its functional states, contributing with structural details and a general understanding of this relevant system.
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Affiliation(s)
- Guillermo Goode-Romero
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
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8
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Shahbazi M, Tohidfar M, Azimzadeh Irani M, Moheb Seraj RG. Functional annotation and evaluation of hypothetical proteins in cyanobacterium Synechocystis sp. PCC 6803. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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The computational analyses, molecular dynamics of fatty-acid transport mechanism to the CD36 receptor. Sci Rep 2021; 11:23207. [PMID: 34853341 PMCID: PMC8636502 DOI: 10.1038/s41598-021-01373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/21/2021] [Indexed: 01/08/2023] Open
Abstract
The transmembrane glycoprotein CD36, which is responsible of the metabolic disorders, and the elevated intake of fat induces lipid buildup, is a multifunctional scavenger receptor signaling those functions in high-affinity tissue uptake of long-chain fatty acids. In this study, we used series of molecular dynamics simulations of the wild type and mutants types K164A CD36 protein interacting with one palmitic acid (PLM) besides simulations of the wild type interacting with the three PLM to find out the mechanism of the functioning of the complex CD36/Fatty acids and the unraveling of the role of the mutation. Additionally we determined whether Lys164, mostly exposed to protein surface, played important roles in fatty acid uptake. These simulations revealed, the conformational changes induced by Lys164 residue and the altered interactions induced by the mutagenesis of surface lysine that was badly influencing the folding, utility, solubility, and stability form of the variant. Furthermore, Lys164 residue provided the structural basis of forming an opening at the region of principal portal for the dissociation of palmitic acid. The results of our simulations revealed hole two fatty acids found in CD36 cavity structure and it was the most preferred to CD36 structure stabilization.
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10
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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Sedlák E, Žár T, Varhač R, Musatov A, Tomášková N. Anion-Specific Effects on the Alkaline State of Cytochrome c. BIOCHEMISTRY (MOSCOW) 2021; 86:59-73. [PMID: 33705282 DOI: 10.1134/s0006297921010065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Specific effects of anions on the structure, thermal stability, and peroxidase activity of native (state III) and alkaline (state IV) cytochrome c (cyt c) have been studied by the UV-VIS absorbance spectroscopy, intrinsic tryptophan fluorescence, and circular dichroism. Thermal and isothermal denaturation monitored by the tryptophan fluorescence and circular dichroism, respectively, implied lower stability of cyt c state IV in comparison with the state III. The pKa value of alkaline isomerization of cyt c depended on the present salts, i.e., kosmotropic anions increased and chaotropic anions decreased pKa (Hofmeister effect on protein stability). The peroxidase activity of cyt c in the state III, measured by oxidation of guaiacol, showed clear dependence on the salt position in the Hofmeister series, while cyt c in the alkaline state lacked the peroxidase activity regardless of the type of anions present in the solution. The alkaline isomerization of cyt c in the presence of 8 M urea, measured by Trp59 fluorescence, implied an existence of a high-affinity non-native ligand for the heme iron even in a partially denatured protein conformation. The conformation of the cyt c alkaline state in 8 M urea was considerably modulated by the specific effect of anions. Based on the Trp59 fluorescence quenching upon titration to alkaline pH in 8 M urea and molecular dynamics simulation, we hypothesize that the Lys79 conformer is most likely the predominant alkaline conformer of cyt c. The high affinity of the sixth ligand for the heme iron is likely a reason of the lack of peroxidase activity of cyt c in the alkaline state.
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Affiliation(s)
- Erik Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia. .,Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia
| | - Tibor Žár
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Andrej Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, 040 01, Slovakia.
| | - Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
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12
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Nouri-Nejad D, O’Donnell BL, Patil CS, Sanchez-Pupo RE, Johnston D, Sayedyahossein S, Jurcic K, Lau R, Gyenis L, Litchfield DW, Jackson MF, Gloor GB, Penuela S. Pannexin 1 mutation found in melanoma tumor reduces phosphorylation, glycosylation, and trafficking of the channel-forming protein. Mol Biol Cell 2021; 32:376-390. [PMID: 33405952 PMCID: PMC8098850 DOI: 10.1091/mbc.e19-10-0585] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/17/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Pannexin 1 (PANX1) is a glycoprotein that forms large pore channels capable of passing ions and metabolites such as ATP for cellular communication. PANX1 has been implicated in many diseases including breast cancer and melanoma, where inhibition or deletion of PANX1 reduced the tumorigenic and metastatic properties of the cancer cells. We interrogated the effect of single amino acid changes in various PANX1 domains using naturally occurring variants reported in cancer patient tumors. We found that a previously reported variant (Q5H) is present in cancer cells, but was not different from the wild type (Q5) in glycosylation, trafficking, or channel function and did not affect cellular properties. We discovered that the Q5H variant is in fact the highly conserved ancestral allele of PANX1 with 89% of humans carrying at least one Q5H allele. Another mutated form Y150F, found in a melanoma patient tumor, prevented phosphorylation at Y150 as well as complex N-glycosylation while increasing intracellular localization. Sarcoma (SRC) is the predicted kinase to phosphorylate the Y150 residue, and its phosphorylation is not likely to be constitutive, but rather dynamically regulated. The Y150 phosphorylation site is the first one reported to play a role in regulating posttranslational modifications and trafficking of PANX1, with potential consequences on its large-pore channel structure and function in melanoma cells.
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Affiliation(s)
- Daniel Nouri-Nejad
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
| | - Brooke L. O’Donnell
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
| | - Chetan S. Patil
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
- Kleysen Institute for Advanced Medicine, Health Sciences Centre, Winnipeg, MB R3E 0Z3, Canada
| | | | - Danielle Johnston
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
| | - Samar Sayedyahossein
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada
| | - Rebecca Lau
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
| | - Laszlo Gyenis
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada
| | - David W. Litchfield
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada
- Department of Oncology, Division of Experimental Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Michael F. Jackson
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
- Kleysen Institute for Advanced Medicine, Health Sciences Centre, Winnipeg, MB R3E 0Z3, Canada
| | - Gregory B. Gloor
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada
| | - Silvia Penuela
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 5C1, Canada
- Department of Oncology, Division of Experimental Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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13
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Tomášková N, Novák P, Kožár T, Petrenčáková M, Jancura D, Yassaghi G, Man P, Sedlák E. Early modification of cytochrome c by hydrogen peroxide triggers its fast degradation. Int J Biol Macromol 2021; 174:413-423. [PMID: 33529629 DOI: 10.1016/j.ijbiomac.2021.01.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/16/2022]
Abstract
Cytochrome c (cyt c), in addition to its function as an electron shuttle in respiratory chain, is able to perform as a pseudo-peroxidase with a critical role during apoptosis. Incubation of cyt c with an excess of hydrogen peroxide leads to a suicide inactivation of the protein, which is accompanied by heme destruction and covalent modification of numerous amino acid residues. Although steady-state reactions of cyt c with an excess of hydrogen peroxide represent non-physiological conditions, they might be used for analysis of the first-modified amino acid in in vivo. Here, we observed oxidation of tyrosine residues 67 and 74 and heme as the first modifications found upon incubation with hydrogen peroxide. The positions of the oxidized tyrosines suggest a possible migration pathway of hydrogen peroxide-induced radicals from the site of heme localization to the protein surface. Analysis of a size of folded fraction of cyt c upon limited incubation with hydrogen peroxide indicates that the early oxidation of amino acids triggers an accelerated destruction of cyt c. Position of channels from molecular dynamics simulation structures of cyt c points to a location of amino acid residues exposed to reactive oxidants that are thus more prone to covalent modification.
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Affiliation(s)
- Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Petr Novák
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Martina Petrenčáková
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Daniel Jancura
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Ghazaleh Yassaghi
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Man
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Erik Sedlák
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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14
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Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Computational design of enzymes for biotechnological applications. Biotechnol Adv 2021; 47:107696. [PMID: 33513434 DOI: 10.1016/j.biotechadv.2021.107696] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their natural effectiveness has been fine-tuned as a result of millions of years of natural evolution. Such catalytic effectiveness has prompted the use of biocatalysts from multiple sources on different applications, including the industrial production of goods (food and beverages, detergents, textile, and pharmaceutics), environmental protection, and biomedical applications. Natural enzymes often need to be improved by protein engineering to optimize their function in non-native environments. Recent technological advances have greatly facilitated this process by providing the experimental approaches of directed evolution or by enabling computer-assisted applications. Directed evolution mimics the natural selection process in a highly accelerated fashion at the expense of arduous laboratory work and economic resources. Theoretical methods provide predictions and represent an attractive complement to such experiments by waiving their inherent costs. Computational techniques can be used to engineer enzymatic reactivity, substrate specificity and ligand binding, access pathways and ligand transport, and global properties like protein stability, solubility, and flexibility. Theoretical approaches can also identify hotspots on the protein sequence for mutagenesis and predict suitable alternatives for selected positions with expected outcomes. This review covers the latest advances in computational methods for enzyme engineering and presents many successful case studies.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic; IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
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15
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Rahbar MR, Zarei M, Jahangiri A, Khalili S, Nezafat N, Negahdaripour M, Fattahian Y, Savardashtaki A, Ghasemi Y. Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae. Front Microbiol 2020; 11:560667. [PMID: 33281759 PMCID: PMC7688925 DOI: 10.3389/fmicb.2020.560667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Brucella species are Gram-negative, facultative intracellular pathogens. They are the main cause of brucellosis, which has led to a global health burden. Adherence of the pathogen to the host cells is the first step in the infection process. The bacteria can adhere to various biotic and abiotic surfaces using their outer membrane proteins. Trimeric autotransporter adhesins (TAAs) are modular homotrimers of various length and domain complexity. They are a diverse, and widespread gene family constituting the type Vc secretion pathway. These adhesins have been established as virulence factors in Brucellaceae. To date, no comprehensive and exhaustive study has been performed on the trimeric autotransporter family in the genus. In the present study, various bioinformatics tools were used to provide a novel evolutionary insight into the sequence and structure of this protein family in Brucellaceae. To this end, a dataset of all trimeric autotransporters from the Brucella genomes was built. Analyses included but were not limited to sequence alignment, phylogenetic tree constructions, codon-based test for selection, clustering of the sequences, and structure (primary to quaternary) predictions. Batch analyzes of the dataset suggested the existence of a few structural domains within the whole population. BatA from the B. abortus 2308 genome was selected as a reference to describe the features of these structural domains. Furthermore, we examined the structural basis for the observed rigidity and resiliency of the protein structure through a molecular dynamics evaluation, which led us to deduce that the random drift results in the non-adaptive evolution of the trimeric autotransporter genes in the Brucella genus. Notably, the modifications have occurred across the genus without interference of gene transmission.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yaser Fattahian
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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16
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Dey D, Borkotoky S, Banerjee M. In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor. Comput Biol Med 2020; 127:104063. [PMID: 33126128 PMCID: PMC7574788 DOI: 10.1016/j.compbiomed.2020.104063] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/25/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and Picornavirus 2B, form discrete aqueous passageways which mediate ion and small molecule transport in infected cells. The alterations in host membrane structures induced by viroporins is essential for key steps in the virus life cycle like entry, replication and egress. Any disruption in viroporin functionality severely compromises viral pathogenesis. The envelope (E) protein encoded by coronaviruses is a viroporin with ion channel activity and has been shown to be crucial for the assembly and pathophysiology of coronaviruses. We used a combination of virtual database screening, molecular docking, all-atom molecular dynamics simulation and MM-PBSA analysis to test four FDA approved drugs - Tretinoin, Mefenamic Acid, Ondansetron and Artemether - as potential inhibitors of ion channels formed by SARS-CoV-2 E protein. Interaction and binding energy analysis showed that electrostatic interactions and polar solvation energy were the major driving forces for binding of the drugs, with Tretinoin being the most promising inhibitor. Tretinoin bound within the lumen of the channel formed by E protein, which is lined by hydrophobic residues like Phe, Val and Ala, indicating its potential for blocking the channel and inhibiting the viroporin functionality of E. In control simulations, tretinoin demonstrated a lower binding energy with a known target as compared to SARS-CoV-2 E protein. This work thus highlights the possibility of exploring Tretinoin as a potential SARS-CoV-2 E protein ion channel blocker and virus assembly inhibitor, which could be an important therapeutic strategy in the treatment for coronaviruses. Screened a database of 1806 small molecule compounds from DrugBank for potential SARS CoV-2 E protein inhibitors. Tested four FDA-approved drugs Tetinoin, Mefenamic acid, Ondansetron and Artemether as SARS CoV-2 E protein inhibitors. Used a combination of molecular docking, MD simulations and MM-PBSA analysis to propose Tretinoin as a promising inhibitor.
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Affiliation(s)
- Debajit Dey
- School of Medicine, University of Maryland Baltimore, United States
| | - Subhomoi Borkotoky
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India.
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17
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Masood TB, Ray T, Natarajan V. Parallel computation of alpha complexes for biomolecules. COMPUTATIONAL GEOMETRY 2020; 90:101651. [DOI: 10.1016/j.comgeo.2020.101651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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18
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Kim G, Lee SG, Han S, Jung J, Jeong HS, Hyun JK, Rhee DK, Kim HM, Lee S. ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones. FASEB J 2020; 34:14353-14370. [PMID: 32910525 DOI: 10.1096/fj.202000843r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023]
Abstract
AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones.
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Affiliation(s)
- Gyuhee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seong-Gyu Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Jaeeun Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | | | - Jae-Kyung Hyun
- Korea Basic Science Institute, Cheongju, Korea.,Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Dong-Kwon Rhee
- School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.,Biomedical Institute for Convergence at SKKU, Sungkyunkwan University, Suwon, Korea
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19
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Tsutsumi N, Mukherjee S, Waghray D, Janda CY, Jude KM, Miao Y, Burg JS, Aduri NG, Kossiakoff AA, Gati C, Garcia KC. Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. eLife 2020; 9:e58464. [PMID: 32762848 PMCID: PMC7442489 DOI: 10.7554/elife.58464] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/06/2020] [Indexed: 01/19/2023] Open
Abstract
Frizzleds (Fzd) are the primary receptors for Wnt morphogens, which are essential regulators of stem cell biology, yet the structural basis of Wnt signaling through Fzd remains poorly understood. Here we report the structure of an unliganded human Fzd5 determined by single-particle cryo-EM at 3.7 Å resolution, with the aid of an antibody chaperone acting as a fiducial marker. We also analyzed the topology of low-resolution XWnt8/Fzd5 complex particles, which revealed extreme flexibility between the Wnt/Fzd-CRD and the Fzd-TM regions. Analysis of Wnt/β-catenin signaling in response to Wnt3a versus a 'surrogate agonist' that cross-links Fzd to LRP6, revealed identical structure-activity relationships. Thus, canonical Wnt/β-catenin signaling appears to be principally reliant on ligand-induced Fzd/LRP6 heterodimerization, versus the allosteric mechanisms seen in structurally analogous class A G protein-coupled receptors, and Smoothened. These findings deepen our mechanistic understanding of Wnt signal transduction, and have implications for harnessing Wnt agonism in regenerative medicine.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
| | - Claudia Y Janda
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Princess Máxima Center for Pediatric OncologyUtrechtNetherlands
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - John S Burg
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Nanda Gowtham Aduri
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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20
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21
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Stourac J, Vavra O, Kokkonen P, Filipovic J, Pinto G, Brezovsky J, Damborsky J, Bednar D. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res 2020; 47:W414-W422. [PMID: 31114897 PMCID: PMC6602463 DOI: 10.1093/nar/gkz378] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/24/2019] [Accepted: 05/05/2019] [Indexed: 12/29/2022] Open
Abstract
Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands’ transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands’ passages can be calculated and visualized. The tool is very fast (2–20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.
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Affiliation(s)
- Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiri Filipovic
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - Gaspar Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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22
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Cryo-EM structure of the Shigella type III needle complex. PLoS Pathog 2020; 16:e1008263. [PMID: 32092125 PMCID: PMC7058355 DOI: 10.1371/journal.ppat.1008263] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 03/05/2020] [Accepted: 12/09/2019] [Indexed: 12/22/2022] Open
Abstract
The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces. Diarrheal diseases evoke about 2.2. million dead people annually and are the second leading cause of postneonatal child mortality worldwide. Shigella causing dysentery utilizes the type 3-secretion system (T3SS) to inject virulence factors into the gut cells. The T3SS needle complex is a syringe-shaped nanomachine consisting of two membrane-embedded ring systems that sheath a central export apparatus and a hollow needle-like structure through which the virulence factors are transported. We present here the structure of the Shigella T3SS needle complex obtained by high-end electron microscopy. The outer membrane (OM) ring system adopts a mixed 15- and 16-fold cyclic symmetry and the near-atomic structure shows the connection of the inner membrane (IM) and OM rings. Conserved channels in the IM ring connect the bacterial periplasm with the central export apparatus. Similar to the Salmonella flagellar system, the export apparatus and its connected needle-like structure assemble in a helical manner. This study advances our understanding of the role of essential structural elements in the T3SS assembly and function.
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23
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Molecular Cavity Topological Representation for Pattern Analysis: A NLP Analogy-Based Word2Vec Method. Int J Mol Sci 2019; 20:ijms20236019. [PMID: 31795343 PMCID: PMC6928730 DOI: 10.3390/ijms20236019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
Cavity analysis in molecular dynamics is important for understanding molecular function. However, analyzing the dynamic pattern of molecular cavities remains a difficult task. In this paper, we propose a novel method to topologically represent molecular cavities by vectorization. First, a characterization of cavities is established through Word2Vec model, based on an analogy between the cavities and natural language processing (NLP) terms. Then, we use some techniques such as dimension reduction and clustering to conduct an exploratory analysis of the vectorized molecular cavity. On a real data set, we demonstrate that our approach is applicable to maintain the topological characteristics of the cavity and can find the change patterns from a large number of cavities.
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24
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Structure of a Tc holotoxin pore provides insights into the translocation mechanism. Proc Natl Acad Sci U S A 2019; 116:23083-23090. [PMID: 31666324 DOI: 10.1073/pnas.1909821116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Tc toxins are modular toxin systems of insect and human pathogenic bacteria. They are composed of a 1.4-MDa pentameric membrane translocator (TcA) and a 250-kDa cocoon (TcB and TcC) encapsulating the 30-kDa toxic enzyme (C terminus of TcC). Binding of Tc toxins to target cells and a pH shift trigger the conformational transition from the soluble prepore state to the membrane-embedded pore. Subsequently, the toxic enzyme is translocated and released into the cytoplasm. A high-resolution structure of a holotoxin embedded in membranes is missing, leaving open the question of whether TcB-TcC has an influence on the conformational transition of TcA. Here we show in atomic detail a fully assembled 1.7-MDa Tc holotoxin complex from Photorhabdus luminescens in the membrane. We find that the 5 TcA protomers conformationally adapt to fit around the cocoon during the prepore-to-pore transition. The architecture of the Tc toxin complex allows TcB-TcC to bind to an already membrane-embedded TcA pore to form a holotoxin. Importantly, assembly of the holotoxin at the membrane results in spontaneous translocation of the toxic enzyme, indicating that this process is not driven by a proton gradient or other energy source. Mammalian lipids with zwitterionic head groups are preferred over other lipids for the integration of Tc toxins. In a nontoxic Tc toxin variant, we can visualize part of the translocating toxic enzyme, which transiently interacts with alternating negative charges and hydrophobic stretches of the translocation channel, providing insights into the mechanism of action of Tc toxins.
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25
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Gatsogiannis C, Balogh D, Merino F, Sieber SA, Raunser S. Cryo-EM structure of the ClpXP protein degradation machinery. Nat Struct Mol Biol 2019; 26:946-954. [PMID: 31582852 PMCID: PMC6783313 DOI: 10.1038/s41594-019-0304-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
The ClpXP machinery is a two component protease complex performing
targeted protein degradation in bacteria and mitochondria. The complex consists
of the AAA+ chaperone ClpX and the peptidase ClpP. The hexameric ClpX utilizes
the energy of ATP binding and hydrolysis to engage, unfold and translocate
substrates into the catalytic chamber of tetradecameric ClpP where they are
degraded. Formation of the complex involves a symmetry mismatch, since hexameric
AAA+ rings bind axially to the opposing stacked heptameric rings of the
tetradecameric ClpP. Here we present the cryo-EM structure of ClpXP from
Listeria monocytogenes. We unravel the heptamer-hexamer
binding interface and provide novel insights into the ClpX-ClpP crosstalk and
activation mechanism. The comparison with available crystal structures of ClpP
and ClpX in different states allows us to understand important aspects of
ClpXP’s complex mode of action and provides a structural framework for
future pharmacological applications.
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Affiliation(s)
- Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dora Balogh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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26
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Leidreiter F, Roderer D, Meusch D, Gatsogiannis C, Benz R, Raunser S. Common architecture of Tc toxins from human and insect pathogenic bacteria. SCIENCE ADVANCES 2019; 5:eaax6497. [PMID: 31663026 PMCID: PMC6795518 DOI: 10.1126/sciadv.aax6497] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family.
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Affiliation(s)
- F. Leidreiter
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - D. Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - D. Meusch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - C. Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - R. Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - S. Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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Guerriero G, Deshmukh R, Sonah H, Sergeant K, Hausman JF, Lentzen E, Valle N, Siddiqui KS, Exley C. Identification of the aquaporin gene family in Cannabis sativa and evidence for the accumulation of silicon in its tissues. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110167. [PMID: 31481224 DOI: 10.1016/j.plantsci.2019.110167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 05/08/2023]
Abstract
Cannabis sativa is an economically important crop providing bast fibres for the textile and biocomposite sector. Length is a fundamental characteristic determining the properties of bast fibres. Aquaporins, channel-forming proteins facilitating the passage of water, urea, as well as elements such as boron and silicon, are known to play a role in the control of fibre length in other species, like cotton. By mining the available genome, we here identify, for the first time, the aquaporin gene family of C. sativa. The analysis of published RNA-Seq data and targeted qPCR on a textile variety reveal an organ-specific expression of aquaporin genes. Computational analyses, including homology-based search, phylogeny and protein modelling, identify two NOD26-like intrinsic proteins harbouring the Gly-Ser-Gly-Arg (GSGR) aromatic/Arg selectivity filter and 108 amino acid NPA (Asn-Pro-Ala) spacing, features reported to be associated with silicon permeability. SIMS nano-analysis and silica extraction coupled to fluorescence microscopy performed on hemp plantlets reveal the presence of silicon in the bast fibres of the hypocotyl and in leaves. The accumulation of silica in the distal cell walls of bast fibres and in the basal cells of leaf trichomes is indicative of a mechanical role.
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Affiliation(s)
- Gea Guerriero
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), P.O. Manauli, S.A.S. Nagar, Mohali, 140306, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), P.O. Manauli, S.A.S. Nagar, Mohali, 140306, Punjab, India
| | - Kjell Sergeant
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
| | - Jean-Francois Hausman
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
| | - Esther Lentzen
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
| | - Nathalie Valle
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
| | - Khawar Sohail Siddiqui
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), 31261, Dhahran, Saudi Arabia
| | - Christopher Exley
- The Birchall Centre, Lennard Jones Laboratories, Keele University, Keele, Staffordshire, ST5 5BG, UK
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28
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Pierce into the Native Structure of Ata, a Trimeric Autotransporter of Acinetobacter baumannii ATCC 17978. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09920-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Sánchez-Aparicio JE, Sciortino G, Herrmannsdoerfer DV, Chueca PO, Pedregal JRG, Maréchal JD. GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm. Int J Mol Sci 2019; 20:E3155. [PMID: 31261636 PMCID: PMC6651367 DOI: 10.3390/ijms20133155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Protein-ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein-ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant in binding affinity and ligand selectivity. In this paper, a novel piece of open-source software to approach this problem is presented, called GPathFinder. It is built as an extension of the modular GaudiMM platform and is able to simulate ligand diffusion pathways at atomistic level. The method has been benchmarked on a set of 20 systems whose ligand-binding routes were studied by other computational tools or suggested from experimental "snapshots". In all of this set, GPathFinder identifies those channels that were already reported in the literature. Interestingly, the low-energy pathways in some cases indicate novel possible binding routes. To show the usefulness of GPathFinder, the analysis of three case systems is reported. We believe that GPathFinder is a software solution with a good balance between accuracy and computational cost, and represents a step forward in extending protein-ligand docking capacities, with implications in several fields such as drug or enzyme design.
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Affiliation(s)
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | | | - Pablo Orenes Chueca
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | | | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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30
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Dulcey CE, López de Los Santos Y, Létourneau M, Déziel E, Doucet N. Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. FEBS J 2019; 286:4036-4059. [PMID: 31177633 DOI: 10.1111/febs.14954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
The 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA is an essential enzyme involved in the biosynthesis of HAAs in Pseudomonas and Burkholderia species. RhlA modulates the aliphatic chain length in rhamnolipids, conferring distinct physicochemical properties to these biosurfactants exhibiting promising industrial and pharmaceutical value. A detailed molecular understanding of substrate specificity and catalytic performance in RhlA could offer protein engineering tools to develop designer variants involved in the synthesis of novel rhamnolipid mixtures for tailored eco-friendly products. However, current directed evolution progress remains limited due to the absence of high-throughput screening methodologies and lack of an experimentally resolved RhlA structure. In the present work, we used comparative modeling and chimeric-based approaches to perform a comprehensive semi-rational mutagenesis of RhlA from Pseudomonas aeruginosa. Our extensive RhlA mutational variants and chimeric hybrids between the Pseudomonas and Burkholderia homologs illustrate selective modulation of rhamnolipid alkyl chain length in both Pseudomonas aeruginosa and Burkholderia glumae. Our results also demonstrate the implication of a putative cap-domain motif that covers the catalytic site of the enzyme and provides substrate specificity to RhlA. This semi-rational mutant-based survey reveals promising 'hot-spots' for the modulation of RL congener patterns and potential control of enzyme activity, in addition to uncovering residue positions that modulate substrate selectivity between the Pseudomonas and Burkholderia functional homologs. DATABASE: Model data are available in the PMDB database under the accession number PM0081867.
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Affiliation(s)
- Carlos Eduardo Dulcey
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Canada
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31
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Aguayo-Ortiz R, Dominguez L. APH-1A Component of γ-Secretase Forms an Internal Water and Ion-Containing Cavity. ACS Chem Neurosci 2019; 10:2931-2938. [PMID: 30979338 DOI: 10.1021/acschemneuro.9b00150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Anterior pharynx-defective 1A (APH-1A) is a seven transmembrane component of γ-secretase (GS), an aspartyl protease enzyme involved in the production of toxic amyloid-β peptides in Alzheimer's disease patients. Cryo-electron microscopy structures of the enzyme complex revealed a central cavity in its APH-1A component, similar to water-containing cavities in G-protein coupled receptors (GPCRs). In this work, we performed molecular dynamics and umbrella sampling simulations to understand the role of the APH-1A cavity in the GS complex. Our results suggest that APH-1A is able to store water molecules in its inner cavity and transport some of them between cell spaces. Additionally, APH-1A allows the influx of extracellular cations into a central hydrophilic cavity but cannot transport them into the intracellular space. Overall, this study seeks to describe an alternative APH-1A function in GS besides its complex stabilization role and provide novel approaches to understand the functioning of the GS enzyme.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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32
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Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J. Engineering enzyme access tunnels. Biotechnol Adv 2019; 37:107386. [PMID: 31026496 DOI: 10.1016/j.biotechadv.2019.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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33
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Fang L, Geng M, Liu C, Wang J, Min W, Liu J. Structural and molecular basis of angiotensin-converting enzyme by computational modeling: Insights into the mechanisms of different inhibitors. PLoS One 2019; 14:e0215609. [PMID: 30998765 PMCID: PMC6472769 DOI: 10.1371/journal.pone.0215609] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 11/18/2022] Open
Abstract
Angiotensin-I converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase involved in regulating blood pressure via the kallikrein-kininand renin-angiotensin-aldosterone complex. Therefore, ACE is a key drug target for the treatment of cardiovascular system diseases. At present many works are focus on searching for new inhibitory peptides of ACE to control the blood pressure. In order to exploit the interactions between ACE and its inhibitors, molecular dynamics simulations were used. The results showed that (a) the secondary structures of the three inhibitor-protein complexes did not change significantly; (b) root-mean-square deviation (RMSD), radius of gyration (Rg), and solvent-accessible surface area (SASA) values of Leu-Ile-Val-Thr (LIVT)-ACE complexes were significantly higher than that of other systems; (c) the backbone movement of LIVT was vigorous in Asp300-Val350, compared with that in Tyr-Leu-Val-Pro-His (YLVPH) and Tyr-Leu-Val-Arg(YLVR), as shown by the center-of-mass distance; and (d) the backbone movement of Asp300-Val350 may contribute to the interaction between ACE and its inhibitors. Our theoretical results will be helpful to further the design of specific inhibitors of ACE.
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Affiliation(s)
- Li Fang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
| | - Mingxian Geng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
- Changchun Vocational Institute of Technology, Changchun, China
| | - Chunlei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
| | - Ji Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
| | - Weihong Min
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
- * E-mail:
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- National Engineering Laboratory of Wheat and Corn Deep Processing, Changchun, China
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34
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Gatsogiannis C, Merino F, Roderer D, Balchin D, Schubert E, Kuhlee A, Hayer-Hartl M, Raunser S. Tc toxin activation requires unfolding and refolding of a β-propeller. Nature 2018; 563:209-213. [DOI: 10.1038/s41586-018-0556-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022]
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35
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Tian W, Chen C, Lei X, Zhao J, Liang J. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 2018; 46:W363-W367. [PMID: 29860391 PMCID: PMC6031066 DOI: 10.1093/nar/gky473] [Citation(s) in RCA: 1102] [Impact Index Per Article: 183.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/04/2018] [Accepted: 05/17/2018] [Indexed: 12/23/2022] Open
Abstract
Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.
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Affiliation(s)
- Wei Tian
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chang Chen
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xue Lei
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jieling Zhao
- Institut National de Recherche en Informatique et en Automatique, Paris 75012, France
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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36
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Liu Y, Yu Z, Zhu J, Wang S, Xu D, Han W. Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study. Front Chem 2018; 6:223. [PMID: 29967763 PMCID: PMC6016274 DOI: 10.3389/fchem.2018.00223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
Thermus thermophiles Argonaute (TtAgo) is a complex, which is consisted of 5′-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507–509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.
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Affiliation(s)
- Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Dong Xu
- Department of Electric Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,College of Computer Science and Technology, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
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37
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Lee GY, You DG, Lee HR, Hwang SW, Lee CJ, Yoo YD. Romo1 is a mitochondrial nonselective cation channel with viroporin-like characteristics. J Cell Biol 2018; 217:2059-2071. [PMID: 29545371 PMCID: PMC5987721 DOI: 10.1083/jcb.201709001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/22/2018] [Accepted: 02/28/2018] [Indexed: 11/22/2022] Open
Abstract
Romo1 regulates mitochondrial reactive oxygen species production and acts as an essential redox sensor in mitochondrial dynamics. Lee et al. demonstrate that Romo1 is a unique mitochondrial ion channel with viroporin-like characteristics that distinguish Romo1 from other known eukaryotic ion channels. Reactive oxygen species (ROS) modulator 1 (Romo1) is a nuclear-encoded mitochondrial inner membrane protein known to regulate mitochondrial ROS production and to act as an essential redox sensor in mitochondrial dynamics. Although its physiological roles have been studied for a decade, the biophysical mechanisms that explain these activities of Romo1 are unclear. In this study, we report that Romo1 is a unique mitochondrial ion channel that differs from currently identified eukaryotic ion channels. Romo1 is a highly conserved protein with structural features of class II viroporins, which are virus-encoded nonselective cation channels. Indeed, Romo1 forms a nonselective cation channel with its amphipathic helical transmembrane domain necessary for pore-forming activity. Notably, channel activity was specifically inhibited by Fe2+ ions, an essential transition metal ion in ROS metabolism. Using structural bioinformatics, we designed an experimental data–guided structural model of Romo1 with a rational hexameric structure. We propose that Romo1 establishes a new category of viroporin-like nonselective cation channel in eukaryotes.
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Affiliation(s)
- Gi Young Lee
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul, Republic of Korea
| | - Deok-Gyun You
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hye-Ra Lee
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul, Republic of Korea.,Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sun Wook Hwang
- Department of Biomedical Sciences, Korea University College of Medicine, Korea University, Seoul, Republic of Korea
| | - C Justin Lee
- Center for Neuroscience and Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Korea University-Korea Institute of Science and Technology Graduate School of Convergence Technology, Korea University, Seoul, Republic of Korea
| | - Young Do Yoo
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul, Republic of Korea
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38
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Tian W, Liang J. On quantification of geometry and topology of protein pockets and channels for assessing mutation effects. ... IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS. IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS 2018; 2018:263-266. [PMID: 30272056 PMCID: PMC6157619 DOI: 10.1109/bhi.2018.8333419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Geometric and topological features of proteins such as voids, pockets and channels are important for protein functions. We discuss a method for visualizing protein pockets and channels based on orthogonal spheres computed from alpha shapes of the protein structures, and how metric properties of channel surfaces can be mapped. In addition, we discuss how structurally prominent sites, such as constriction sties in channels, can be computed, which may help to understand protein functions and mutation effects, with implications in developing novel therapeutic interventions.
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Affiliation(s)
- Wei Tian
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jie Liang
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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39
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Barletta GP, Fernandez-Alberti S. Protein Fluctuations and Cavity Changes Relationship. J Chem Theory Comput 2018; 14:998-1008. [PMID: 29262685 DOI: 10.1021/acs.jctc.7b00744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein cavities and tunnels are critical for function. Ligand recognition and binding, transport, and enzyme catalysis require cavities rearrangements. Therefore, the flexibility of cavities should be guaranteed by protein vibrational dynamics. Molecular dynamics simulations provide a framework to explore conformational plasticity of protein cavities. Herein, we present a novel procedure to characterize the dynamics of protein cavities in terms of their volume gradient vector. For this purpose, we make use of algorithms for calculation of the cavity volume that result robust for numerical differentiations. Volume gradient vector is expressed in terms of principal component analysis obtained from equilibrated molecular dynamics simulations. We analyze contributions of principal component modes to the volume gradient vector according to their frequency and degree of delocalization. In all our test cases, we find that low frequency modes play a critical role together with minor contributions of high frequency modes. These modes involve concerted motions of significant fractions of the total residues lining the cavities. We make use of variations of the potential energy of a protein in the direction of the volume gradient vector as a measure of flexibility of the cavity. We show that proteins whose collective low frequency fluctuations contribute the most to changes of cavity volume exhibit more flexible cavities.
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Affiliation(s)
- German P Barletta
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352, B1876BXD Bernal, Argentina
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40
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Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study. Biophys Chem 2018; 233:47-54. [DOI: 10.1016/j.bpc.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022]
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41
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Abstract
Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability.
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Affiliation(s)
- Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Barbora Kozlikova
- Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
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42
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Hernandez CC, Zhang Y, Hu N, Shen D, Shen W, Liu X, Kong W, Jiang Y, Macdonald RL. GABA A Receptor Coupling Junction and Pore GABRB3 Mutations are Linked to Early-Onset Epileptic Encephalopathy. Sci Rep 2017; 7:15903. [PMID: 29162865 PMCID: PMC5698489 DOI: 10.1038/s41598-017-16010-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
GABAA receptors are brain inhibitory chloride ion channels. Here we show functional analyses and structural simulations for three de novo missense mutations in the GABAA receptor β3 subunit gene (GABRB3) identified in patients with early-onset epileptic encephalopathy (EOEE) and profound developmental delay. We sought to obtain insights into the molecular mechanisms that might link defects in GABAA receptor biophysics and biogenesis to patients with EOEE. The mutant residues are part of conserved structural domains such as the Cys-loop (L170R) and M2-M3 loop (A305V) that form the GABA binding/channel gating coupling junction and the channel pore (T288N), which are functionally coupled during receptor activation. The mutant coupling junction residues caused rearrangements and formation of new hydrogen bonds in the open state, while the mutant pore residue reshaped the pore cavity. Whereas mutant coupling junction residues uncoupled during activation and caused gain of function, the mutant pore residue favoured low conductance receptors and differential sensitivity to diazepam and loss of function. These data reveal novel molecular mechanisms by which EOEE-linked mutations affect GABAA receptor function.
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Affiliation(s)
- Ciria C Hernandez
- Department of Neurology, Vanderbilt University, Nashville, TN., 37240-7915., USA. .,University of Michigan, Life Sciences Institute, 210 Washtenaw Ave., Room 6115, Ann Arbor, MI, 48109-2216, USA.
| | - Yujia Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University, Nashville, TN., 37240-7915., USA
| | - Dingding Shen
- The Graduate Program of Neuroscience, Vanderbilt University, Nashville, 37240-7915., TN, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University, Nashville, TN., 37240-7915., USA
| | - Xiaoyan Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Weijing Kong
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
| | - Robert L Macdonald
- Department of Neurology, Vanderbilt University, Nashville, TN., 37240-7915., USA.
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43
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Bartolami E, Knoops J, Bessin Y, Fossépré M, Chamieh J, Dumy P, Surin M, Ulrich S. One-Pot Self-Assembly of Peptide-Based Cage-Type Nanostructures Using Orthogonal Ligations. Chemistry 2017; 23:14323-14331. [DOI: 10.1002/chem.201702974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
- Present address: Department of Organic Chemistry; University of Geneva; 30 Quai Ernest Ansermet 1211 Geneva 4 Switzerland
| | - Jérémie Knoops
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Yannick Bessin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Joseph Chamieh
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
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44
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Xenon for tunnelling analysis of the efflux pump component OprN. PLoS One 2017; 12:e0184045. [PMID: 28886086 PMCID: PMC5590881 DOI: 10.1371/journal.pone.0184045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.
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45
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Lind U, Järvå M, Alm Rosenblad M, Pingitore P, Karlsson E, Wrange AL, Kamdal E, Sundell K, André C, Jonsson PR, Havenhand J, Eriksson LA, Hedfalk K, Blomberg A. Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity. PLoS One 2017; 12:e0181192. [PMID: 28715506 PMCID: PMC5513457 DOI: 10.1371/journal.pone.0181192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.
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Affiliation(s)
- Ulrika Lind
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Michael Järvå
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Alm Rosenblad
- Department of Marine Sciences, National Infrastructure of Bioinformatics (NBIS), Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Piero Pingitore
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emil Karlsson
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Anna-Lisa Wrange
- RISE Research Institute of Sweden, Section for Chemistry and Materials, Borås, Sweden
| | - Emelie Kamdal
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Kristina Sundell
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Per R. Jonsson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Jon Havenhand
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Leif A. Eriksson
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Kristina Hedfalk
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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46
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Altered Channel Conductance States and Gating of GABA A Receptors by a Pore Mutation Linked to Dravet Syndrome. eNeuro 2017; 4:eN-NWR-0251-16. [PMID: 28197552 PMCID: PMC5301078 DOI: 10.1523/eneuro.0251-16.2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 11/21/2022] Open
Abstract
We identified a de novo missense mutation, P302L, in the γ-aminobutyric acid type A (GABAA) receptor γ2 subunit gene GABRG2 in a patient with Dravet syndrome using targeted next-generation sequencing. The mutation was in the cytoplasmic portion of the transmembrane segment M2 of the γ2 subunit that faces the pore lumen. GABAA receptor α1 and β3 subunits were coexpressed with wild-type (wt) γ2L or mutant γ2L(P302L) subunits in HEK 293T cells and cultured mouse cortical neurons. We measured currents using whole-cell and single-channel patch clamp techniques, surface and total expression levels using surface biotinylation and Western blotting, and potential structural perturbations in mutant GABAA receptors using structural modeling. The γ2(P302L) subunit mutation produced an ∼90% reduction of whole-cell current by increasing macroscopic desensitization and reducing GABA potency, which resulted in a profound reduction of GABAA receptor-mediated miniature IPSCs (mIPSCs). The conductance of the receptor channel was reduced to 24% of control conductance by shifting the relative contribution of the conductance states from high- to low-conductance levels with only slight changes in receptor surface expression. Structural modeling of the GABAA receptor in the closed, open, and desensitized states showed that the mutation was positioned to slow activation, enhance desensitization, and shift channels to a low-conductance state by reshaping the hour-glass-like pore cavity during transitions between closed, open, and desensitized states. Our study revealed a novel γ2 subunit missense mutation (P302L) that has a novel pathogenic mechanism to cause defects in the conductance and gating of GABAA receptors, which results in hyperexcitability and contributes to the pathogenesis of the genetic epilepsy Dravet syndrome.
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47
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Behmard E, Abdolmaleki P, Taghdir M. Molecular dynamics investigation on structural and transport properties of p7 ion channel. J Biomol Struct Dyn 2016; 35:2725-2735. [PMID: 27668345 DOI: 10.1080/07391102.2016.1230519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Esmaeil Behmard
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
| | - Parviz Abdolmaleki
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
| | - Majid Taghdir
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
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48
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Hanukoglu I. ASIC and ENaC type sodium channels: conformational states and the structures of the ion selectivity filters. FEBS J 2016; 284:525-545. [DOI: 10.1111/febs.13840] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/04/2016] [Accepted: 08/26/2016] [Indexed: 12/18/2022]
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49
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Gatsogiannis C, Merino F, Prumbaum D, Roderer D, Leidreiter F, Meusch D, Raunser S. Membrane insertion of a Tc toxin in near-atomic detail. Nat Struct Mol Biol 2016; 23:884-890. [PMID: 27571177 DOI: 10.1038/nsmb.3281] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022]
Abstract
Tc toxins from pathogenic bacteria use a special syringe-like mechanism to perforate the host cell membrane and inject a deadly enzyme into the host cytosol. The molecular mechanism of this unusual injection system is poorly understood. Using electron cryomicroscopy, we determined the structure of TcdA1 from Photorhabdus luminescens embedded in lipid nanodiscs. In our structure, compared with the previous structure of TcdA1 in the prepore state, the transmembrane helices rearrange in the membrane and open the initially closed pore. However, the helices do not span the complete membrane; instead, the loops connecting the helices form the rim of the funnel. Lipid head groups reach into the space between the loops and consequently stabilize the pore conformation. The linker domain is folded and packed into a pocket formed by the other domains of the toxin, thereby considerably contributing to stabilization of the pore state.
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Affiliation(s)
- Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Franziska Leidreiter
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dominic Meusch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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50
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Hassani S, Haghbeen K, Fazli M. Non-specific binding sites help to explain mixed inhibition in mushroom tyrosinase activities. Eur J Med Chem 2016; 122:138-148. [PMID: 27344491 DOI: 10.1016/j.ejmech.2016.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022]
Abstract
Inhibition and activation studies of tyrosinase could prove beneficial to agricultural, food, cosmetic, and pharmaceutical industries. Although non-competitive and mixed-inhibition are frequent modes observed in kinetics studies on mushroom tyrosinase (MT) activities, the phenomena are left unexplained. In this study, dual effects of phthalic acid (PA) and cinnamic acid (CA) on MT during mono-phenolase activity were demonstrated. PA activated and inhibited MT at concentrations lower and higher than 150 μM, respectively. In contrast, CA inhibited and activated MT at concentrations lower and higher than 5 μM. The mode of inhibition for both effectors was mixed-type. Complex kinetics of MT in the presence of a modulator could partly be ascribed to its mixed-cooperativity. However, to explain mixed-inhibition mode, it is necessary to demonstrate how the ternary complex of substrate/enzyme/effector is formed. Therefore, we looked for possible non-specific binding sites using MT tropolone-bound PDB (2Y9X) in the computational studies. When tropolone was in MTPa (active site), PA and CA occupied different pockets (named MTPb and MTPc, respectively). The close Moldock scores of PA binding posed in MTPb and MTPa suggested that MTPb could be a secondary binding site for PA. Similar results were obtained for CA. Ensuing results from 10 ns molecular dynamics simulations for 2Y9X-effector complexes indicated that the structures were gradually stabilized during simulation. Tunnel analysis by using CAVER Analyst and CHEXVIS resulted in identifying two distinct channels that assumingly participate in exchanging the effectors when the direct channel to MTPa is not accessible.
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Affiliation(s)
- Sorour Hassani
- Department of Chemistry, Faculty of Science, Semnan University, Semnan, Iran
| | - Kamahldin Haghbeen
- Department of Plant Bioproducts, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.
| | - Mostafa Fazli
- Department of Chemistry, Faculty of Science, Semnan University, Semnan, Iran
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