1
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Boggiano-Ayo T, Palacios-Oliva J, Lozada-Chang S, Relova-Hernandez E, Gomez-Perez J, Oliva G, Hernandez L, Bueno-Soler A, Montes de Oca D, Mora O, Machado-Santisteban R, Perez-Martinez D, Perez-Masson B, Cabrera Infante Y, Calzadilla-Rosado L, Ramirez Y, Aymed-Garcia J, Ruiz-Ramirez I, Romero Y, Gomez T, Espinosa LA, Gonzalez LJ, Cabrales A, Guirola O, de la Luz KR, Pi-Estopiñan F, Sanchez-Ramirez B, Garcia-Rivera D, Valdes-Balbin Y, Rojas G, Leon-Monzon K, Ojito-Magaz E, Hardy E. Development of a scalable single process for producing SARS-CoV-2 RBD monomer and dimer vaccine antigens. Front Bioeng Biotechnol 2023; 11:1287551. [PMID: 38050488 PMCID: PMC10693982 DOI: 10.3389/fbioe.2023.1287551] [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: 09/01/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
We have developed a single process for producing two key COVID-19 vaccine antigens: SARS-CoV-2 receptor binding domain (RBD) monomer and dimer. These antigens are featured in various COVID-19 vaccine formats, including SOBERANA 01 and the licensed SOBERANA 02, and SOBERANA Plus. Our approach involves expressing RBD (319-541)-His6 in Chinese hamster ovary (CHO)-K1 cells, generating and characterizing oligoclones, and selecting the best RBD-producing clones. Critical parameters such as copper supplementation in the culture medium and cell viability influenced the yield of RBD dimer. The purification of RBD involved standard immobilized metal ion affinity chromatography (IMAC), ion exchange chromatography, and size exclusion chromatography. Our findings suggest that copper can improve IMAC performance. Efficient RBD production was achieved using small-scale bioreactor cell culture (2 L). The two RBD forms - monomeric and dimeric RBD - were also produced on a large scale (500 L). This study represents the first large-scale application of perfusion culture for the production of RBD antigens. We conducted a thorough analysis of the purified RBD antigens, which encompassed primary structure, protein integrity, N-glycosylation, size, purity, secondary and tertiary structures, isoform composition, hydrophobicity, and long-term stability. Additionally, we investigated RBD-ACE2 interactions, in vitro ACE2 recognition of RBD, and the immunogenicity of RBD antigens in mice. We have determined that both the monomeric and dimeric RBD antigens possess the necessary quality attributes for vaccine production. By enabling the customizable production of both RBD forms, this unified manufacturing process provides the required flexibility to adapt rapidly to the ever-changing demands of emerging SARS-CoV-2 variants and different COVID-19 vaccine platforms.
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Affiliation(s)
- Tammy Boggiano-Ayo
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | | | | | - Gonzalo Oliva
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Alexi Bueno-Soler
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Osvaldo Mora
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Dayana Perez-Martinez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Beatriz Perez-Masson
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Yaima Ramirez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Judey Aymed-Garcia
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Yamile Romero
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Tania Gomez
- Quality Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Annia Cabrales
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | | | | | | | | | | | - Gertrudis Rojas
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Kalet Leon-Monzon
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Eugenio Hardy
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
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2
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Rat C, Heindl C, Neuweiler H. Domain swap facilitates structural transitions of spider silk protein C-terminal domains. Protein Sci 2023; 32:e4783. [PMID: 37712205 PMCID: PMC10578117 DOI: 10.1002/pro.4783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/25/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Domain swap is a mechanism of protein dimerization where the two interacting domains exchange parts of their structure. Web spiders make use of the process in the connection of C-terminal domains (CTDs) of spidroins, the soluble protein building blocks that form tough silk fibers. Besides providing connectivity and solubility, spidroin CTDs are responsible for inducing structural transitions during passage through an acidified assembly zone within spinning ducts. The underlying molecular mechanisms are elusive. Here, we studied the folding of five homologous spidroin CTDs from different spider species or glands. Four of these are domain-swapped dimers formed by five-helix bundles from spidroins of major and minor ampullate glands. The fifth is a dimer that lacks domain swap, formed by four-helix bundles from a spidroin of a flagelliform gland. Spidroins from this gland do not undergo structural transitions whereas the others do. We found a three-state mechanism of folding and dimerization that was conserved across homologues. In chemical denaturation experiments the native CTD dimer unfolded to a dimeric, partially structured intermediate, followed by full unfolding to denatured monomers. The energetics of the individual folding steps varied between homologues. Contrary to the common belief that domain swap stabilizes protein assemblies, the non-swapped homologue was most stable and folded four orders of magnitude faster than a swapped variant. Domain swap of spidroin CTDs induces an entropic penalty to the folding of peripheral helices, thus unfastening them for acid-induced unfolding within a spinning duct, which primes them for refolding into alternative structures during silk formation.
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Affiliation(s)
- Charlotte Rat
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
| | - Cedric Heindl
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
| | - Hannes Neuweiler
- Department of Biotechnology & BiophysicsJulius‐Maximilians‐University WürzburgWürzburgGermany
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3
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Västberg A, Bolinsson H, Leeman M, Nilsson L, Nylander T, Sejwal K, Sintorn IM, Lidayova K, Sjögren H, Wahlgren M, Elofsson U. Investigating Thermally Induced Aggregation of Somatropin- New Insights Using Orthogonal Techniques. Int J Pharm 2023; 637:122829. [PMID: 36948472 DOI: 10.1016/j.ijpharm.2023.122829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023]
Abstract
Three orthogonal techniques were used to provide new insights into thermally induced aggregation of the therapeutic protein Somatropin at pH 5.8 and 7.0. The techniques were Dynamic Light Scattering (DLS), Asymmetric Flow-Field Flow-Fractionation (AF4), and the TEM-based analysis system MiniTEM™. In addition, Differential Scanning Calorimetry (DSC) was used to study the thermal unfolding and stability. DSC and DLS were used to explain the initial aggregation process and aggregation rate at the two pH values. The results suggest that electrostatic stabilization seems to be the main reason for the faster initial aggregation at pH 5.8, i.e., closer to the isoelectric point of Somatropin. AF4 and MiniTEM were used to investigate the aggregation pathway further. Combining the results allowed us to demonstrate Somatropin's thermal aggregation pathway at pH 7.0. The growth of the aggregates appears to follow two steps. Smaller elongated aggregates are formed in the first step, possibly initiated by partly unfolded species. In the second step, occurring during longer heating, the smaller aggregates assemble into larger aggregates with more complex structures.
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Affiliation(s)
- Amanda Västberg
- Research Institutes of Sweden, Drottning Kristinas väg 61B, 11428 Stockholm, Sweden; Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | | | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Ulla Elofsson
- Research Institutes of Sweden, Drottning Kristinas väg 61B, 11428 Stockholm, Sweden
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4
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Malik A, Khan JM, Alhomida AS, Ola MS. Modulation of the Structure and Stability of Novel Camel Lens Alpha-Crystallin by pH and Thermal Stress. Gels 2022; 8:gels8050273. [PMID: 35621572 PMCID: PMC9140948 DOI: 10.3390/gels8050273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
Alpha-crystallin protein performs structural and chaperone functions in the lens and comprises alphaA and alphaB subunits at a molar ratio of 3:1. The highly complex alpha-crystallin structure challenges structural biologists because of its large dynamic quaternary structure (300−1000 kDa). Camel lens alpha-crystallin is a poorly characterized molecular chaperone, and the alphaB subunit possesses a novel extension at the N-terminal domain. We purified camel lens alpha-crystallin using size exclusion chromatography, and the purity was analyzed by gradient (4−12%) sodium dodecyl sulfate−polyacrylamide gel electrophoresis. Alpha-crystallin was equilibrated in the pH range of 1.0 to 7.5. Subsequently, thermal stress (20−94 °C) was applied to the alpha-crystallin samples, and changes in the conformation and stability were recorded by dynamic multimode spectroscopy and intrinsic and extrinsic fluorescence spectroscopic methods. Camel lens alpha-crystallin formed a random coil-like structure without losing its native-like beta-sheeted structure under two conditions: >50 °C at pH 7.5 and all temperatures at pH 2.0. The calculated enthalpy of denaturation, as determined by dynamic multimode spectroscopy at pH 7.5, 4.0, 2.0, and 1.0 revealed that alpha-crystallin never completely denatures under acidic conditions or thermal denaturation. Alpha-crystallin undergoes a single, reversible thermal transition at pH 7.5. The thermodynamic data (unfolding enthalpy and heat capacity change) and chaperone activities indicated that alpha-crystallin does not completely unfold above the thermal transition. Camels adapted to live in hot desert climates naturally exhibit the abovementioned unique features.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.S.A.); (M.S.O.)
- Correspondence:
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Abdullah S. Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.S.A.); (M.S.O.)
| | - Mohammad Shamsul Ola
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.S.A.); (M.S.O.)
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5
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Jeje O, Maake R, van Deventer R, Esau V, Iwuchukwu EA, Meyer V, Khoza T, Achilonu I. Effect of Divalent Metal Ion on the Structure, Stability and Function of Klebsiella pneumoniae Nicotinate-Nucleotide Adenylyltransferase: Empirical and Computational Studies. Int J Mol Sci 2021; 23:116. [PMID: 35008542 PMCID: PMC8745210 DOI: 10.3390/ijms23010116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022] Open
Abstract
The continuous threat of drug-resistant Klebsiella pneumoniae justifies identifying novel targets and developing effective antibacterial agents. A potential target is nicotinate nucleotide adenylyltransferase (NNAT), an indispensable enzyme in the biosynthesis of the cell-dependent metabolite, NAD+. NNAT catalyses the adenylation of nicotinamide/nicotinate mononucleotide (NMN/NaMN), using ATP to form nicotinamide/nicotinate adenine dinucleotide (NAD+/NaAD). In addition, it employs divalent cations for co-substrate binding and catalysis and has a preference for different divalent cations. Here, the biophysical structure of NNAT from K. pneumoniae (KpNNAT) and the impact of divalent cations on its activity, conformational stability and substrate-binding are described using experimental and computational approaches. The experimental study was executed using an enzyme-coupled assay, far-UV circular dichroism, extrinsic fluorescence spectroscopy, and thermal shift assays, alongside homology modelling, molecular docking, and molecular dynamic simulation. The structure of KpNNAT revealed a predominately α-helical secondary structure content and a binding site that is partially hydrophobic. Its substrates ATP and NMN share the same binding pocket with similar affinity and exhibit an energetically favourable binding. KpNNAT showed maximum activity and minimal conformational changes with Mg2+ as a cofactor compared to Zn2+, Cu2+ and Ni2+. Overall, ATP binding affects KpNNAT dynamics, and the dynamics of ATP binding depend on the presence and type of divalent cation. The data obtained from this study would serve as a basis for further evaluation towards designing structure-based inhibitors with therapeutic potential.
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Affiliation(s)
- Olamide Jeje
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Reabetswe Maake
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Ruan van Deventer
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Veruschka Esau
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Emmanuel Amarachi Iwuchukwu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Vanessa Meyer
- Functional Genomics and Immunogenetics Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Thandeka Khoza
- Department of Biochemistry, School of Life Sciences, Pietermaritzburg Campus, University of KwaZulu-Natal, Pietermaritzburg 3209, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
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6
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Šulskis D, Thoma J, Burmann BM. Structural basis of DegP protease temperature-dependent activation. SCIENCE ADVANCES 2021; 7:eabj1816. [PMID: 34878848 PMCID: PMC8654288 DOI: 10.1126/sciadv.abj1816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/16/2021] [Indexed: 05/21/2023]
Abstract
Protein quality control is an essential cellular function mainly executed by a vast array of different proteases and molecular chaperones. One of the bacterial high temperature requirement A (HtrA) protein family members, the homo-oligomeric DegP protease, plays a crucial role in the Escherichia coli protein quality control machinery by removing unfolded proteins or preventing their aggregation and chaperoning them to their final folded state within the periplasm. DegP contains two regulatory PDZ domains, which play key roles in substrate recognition and in the transformation of DegP between inactive hexameric and proteolytic active cage-like structures. Here, we analyze the interaction and dynamics of the DegP PDZ domains underlying this transformation by high-resolution NMR spectroscopy complemented with biochemical cleavage assays. We identify an interdomain molecular lock, which controls the interactions between the two PDZ domains, regulated by fine-tuned temperature-dependent protein dynamics, and which is potentially conserved in proteins harboring tandem PDZ domains.
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Affiliation(s)
- Darius Šulskis
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Johannes Thoma
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
- Corresponding author.
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7
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Nonaka Y, Ogawa T, Shoji H, Nishi N, Kamitori S, Nakamura T. Crystal structure and conformational stability of a galectin-1 tandem-repeat mutant with a short linker. Glycobiology 2021; 32:251-259. [PMID: 34735570 DOI: 10.1093/glycob/cwab101] [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: 04/12/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 11/14/2022] Open
Abstract
Modification of the domain architecture of galectins has been attempted to analyze their biological functions and to develop medical applications. Several types of galectin-1 repeat mutants were previously reported but, however, it was not clear whether the native structure of the wild type was retained. In this study, we determined the crystal structure of a galectin-1 tandem-repeat mutant with a short linker peptide, and compared the unfolding profiles of the wild type and mutant by chemical denaturation. The structure of the mutant was consistent with that of the dimer of the wild type, and both carbohydrate-binding sites were retained. The unfolding curve of the wild type with lactose suggested that the dimer dissociation and the tertiary structure unfolding was concomitant at micromolar protein concentrations. The midpoint denaturant concentration of the wild type was dependent on the protein concentration and lower than that of the mutant. Linking the two subunits significantly stabilized the tertiary structure. The mutant exhibited higher T-cell growth-inhibition activity and comparable hemagglutinating activity. Structural stabilization may prevent the oxidation of the internal cysteine residue.
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Affiliation(s)
- Yasuhiro Nonaka
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Takashi Ogawa
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Hiroki Shoji
- Department of Biology, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0293, Japan
| | - Nozomu Nishi
- Life Science Research Center, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Shigehiro Kamitori
- Life Science Research Center, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Takanori Nakamura
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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8
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Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments. Methods Mol Biol 2021. [PMID: 33315219 DOI: 10.1007/978-1-0716-1154-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this paper we report a procedure to analyze protein homodimer interfaces.We approached the problem by means of a topological methodology. In particular, we analyzed the subunits interface of about 50 homodimers and we have defined a few parameters that allow to organize these proteins in six different classes. The main characteristics of each class of homodimers have been discussed also taking into account their stabilization energy, as reported in the literature from the experimental measurements. A paradigmatic example for each class has been reported and a graphical representation proposed in order to better explain the meaning of the parameters chosen.
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9
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Neira JL, Cámara-Artigas A, Hernández-Cifre JG, Ortore MG. The Histidine Phosphocarrier Kinase/Phosphorylase from Bacillus Subtilis Is an Oligomer in Solution with a High Thermal Stability. Int J Mol Sci 2021; 22:3231. [PMID: 33810099 PMCID: PMC8004850 DOI: 10.3390/ijms22063231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023] Open
Abstract
The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Alicante, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain;
| | - José Ginés Hernández-Cifre
- Departamento de Química Física, Facultad de Química, Campus de Espinardo, Universidad de Murcia, 30100 Murcia, Spain;
| | - María Grazia Ortore
- Dipartimento DiSVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
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10
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Klünemann T, Nimtz M, Jänsch L, Layer G, Blankenfeldt W. Crystal structure of NirF: insights into its role in heme
d
1
biosynthesis. FEBS J 2020; 288:244-261. [DOI: 10.1111/febs.15323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Klünemann
- Structure and Function of Proteins Helmholtz Centre for Infection Research Braunschweig Germany
| | - Manfred Nimtz
- Cellular Proteome Research Helmholtz Centre for Infection Research Braunschweig Germany
| | - Lothar Jänsch
- Cellular Proteome Research Helmholtz Centre for Infection Research Braunschweig Germany
| | - Gunhild Layer
- Institute of Pharmaceutical Sciences Pharmaceutical Biology Albert‐Ludwigs‐Universität Freiburg Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins Helmholtz Centre for Infection Research Braunschweig Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics Technische Universität Braunschweig Germany
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11
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Pacini L, Bourgeat L, Serghei A, Lesieur C. Analysis of Nanoconfined Protein Dielectric Signals Using Charged Amino Acid Network Models. Aust J Chem 2020. [DOI: 10.1071/ch19502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein slow motions involving collective molecular fluctuations on the timescale of microseconds to seconds are difficult to measure and not well understood despite being essential to sustain protein folding and protein function. Broadband dielectric spectroscopy (BDS) is one of the most powerful experimental techniques to monitor, over a broad frequency and temperature range, the molecular dynamics of soft matter through the orientational polarisation of permanent dipole moments that are generated by the chemical structure and morphological organisation of matter. Its typical frequency range goes from 107 Hz down to 10−3 Hz, being thus suitable for investigations on slow motions in proteins. Moreover, BDS has the advantage of providing direct experimental access to molecular fluctuations taking place on different length-scales, from local to cooperative dipolar motions. The unfolding of the cholera toxin B pentamer (CtxB5) after thermal treatment for 3h at 80°C is investigated by BDS under nanoconfined and dehydrated conditions. From the X-ray structure of the toxin pentamer, network-based models are used to infer the toxin dipoles present in the native state and to compute their stability and dielectric properties. Network analyses highlight three domains with distinct dielectric and stability properties that support a model where the toxin unfolds into three conformations after the treatment at 80°C. This novel integrative approach offers some perspective into the investigation of the relation between local perturbations (e.g. mutation, thermal treatment) and larger scale protein conformational changes. It might help ranking protein sequence variants according to their respective scale of dynamics perturbations.
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12
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Kim MH, Kim S. Structures and functions of multi-tRNA synthetase complexes. Enzymes 2020; 48:149-173. [PMID: 33837703 DOI: 10.1016/bs.enz.2020.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Human body is a finely-tuned machine that requires homeostatic balance based on systemically controlled biological processes involving DNA replication, transcription, translation, and energy metabolism. Ubiquitously expressed aminoacyl-tRNA synthetases have been investigated for many decades, and they act as cross-over mediators of important biological processes. In particular, a cytoplasmic multi-tRNA synthetase complex (MSC) appears to be a central machinery controlling the complexity of biological systems. The structural integrity of MSC determined by the associated components is correlated with increasing biological complexity that links to system development in higher organisms. Although the role of the MSCs is still unclear, this chapter describes the current knowledge on MSC components that are associated with and regulate functions beyond their catalytic activities with focus on human MSC.
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Affiliation(s)
- Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy & School of Medicine, Yonsei University, Incheon, South Korea.
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13
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Castro-Torres E, Jiménez-Sandoval P, Romero-Romero S, Fuentes-Pascacio A, López-Castillo LM, Díaz-Quezada C, Fernández-Velasco DA, Torres-Larios A, Brieba LG. Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:950-964. [PMID: 31034710 DOI: 10.1111/tpj.14375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Reactive oxidative species (ROS) and S-glutathionylation modulate the activity of plant cytosolic triosephosphate isomerases (cTPI). Arabidopsis thaliana cTPI (AtcTPI) is subject of redox regulation at two reactive cysteines that function as thiol switches. Here we investigate the role of these residues, AtcTPI-Cys13 and At-Cys218, by substituting them with aspartic acid that mimics the irreversible oxidation of cysteine to sulfinic acid and with amino acids that mimic thiol conjugation. Crystallographic studies show that mimicking AtcTPI-Cys13 oxidation promotes the formation of inactive monomers by reposition residue Phe75 of the neighboring subunit, into a conformation that destabilizes the dimer interface. Mutations in residue AtcTPI-Cys218 to Asp, Lys, or Tyr generate TPI variants with a decreased enzymatic activity by creating structural modifications in two loops (loop 7 and loop 6) whose integrity is necessary to assemble the active site. In contrast with mutations in residue AtcTPI-Cys13, mutations in AtcTPI-Cys218 do not alter the dimeric nature of AtcTPI. Therefore, modifications of residues AtcTPI-Cys13 and AtcTPI-Cys218 modulate AtcTPI activity by inducing the formation of inactive monomers and by altering the active site of the dimeric enzyme, respectively. The identity of residue AtcTPI-Cys218 is conserved in the majority of plant cytosolic TPIs, this conservation and its solvent-exposed localization make it the most probable target for TPI regulation upon oxidative damage by reactive oxygen species. Our data reveal the structural mechanisms by which S-glutathionylation protects AtcTPI from irreversible chemical modifications and re-routes carbon metabolism to the pentose phosphate pathway to decrease oxidative stress.
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Affiliation(s)
- Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Pedro Jiménez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Sergio Romero-Romero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alma Fuentes-Pascacio
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Laura M López-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
| | - D Alejandro Fernández-Velasco
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, México City, 04510, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, México, CP 36821, México
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14
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Faustino AF, Martins AS, Karguth N, Artilheiro V, Enguita FJ, Ricardo JC, Santos NC, Martins IC. Structural and Functional Properties of the Capsid Protein of Dengue and Related Flavivirus. Int J Mol Sci 2019; 20:E3870. [PMID: 31398956 PMCID: PMC6720645 DOI: 10.3390/ijms20163870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
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Affiliation(s)
- André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nina Karguth
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Vanessa Artilheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Joana C Ricardo
- Centro de Química-Física Molecular, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
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15
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Garton M, MacKinnon SS, Malevanets A, Wodak SJ. Interplay of self-association and conformational flexibility in regulating protein function. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0190. [PMID: 29735742 DOI: 10.1098/rstb.2017.0190] [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] [Accepted: 03/14/2018] [Indexed: 12/18/2022] Open
Abstract
Many functional roles have been attributed to homodimers, the most common mode of protein self-association, notably in the regulation of enzymes, ion channels, transporters and transcription factors. Here we review findings that offer new insights into the different roles conformational flexibility plays in regulating homodimer function. Intertwined homodimers of two-domain proteins and their related family members display significant conformational flexibility, which translates into concerted motion between structural domains. This flexibility enables the corresponding proteins to regulate function across family members by modulating the spatial positions of key recognition surfaces of individual domains, to either maintain subunit interfaces, alter them or break them altogether, leading to a variety of functional consequences. Many proteins may exist as monomers but carry out their biological function as homodimers or higher-order oligomers. We present early evidence that in such systems homodimer formation primes the protein for its functional role. It does so by inducing elevated mobility in protein regions corresponding to the binding epitopes of functionally important ligands. In some systems this process acts as an allosteric response elicited by the self-association reaction itself. Our analysis furthermore suggests that the induced extra mobility likely facilitates ligand binding through the mechanism of conformational selection.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Michael Garton
- Department of Molecular Genetics, University of Toronto, The Donnelly Centre, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Stephen S MacKinnon
- Cyclica Inc., 18 King Street East, Suite 810, Toronto, Ontario M5C 1C4, Canada
| | - Anatoly Malevanets
- Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | - Shoshana J Wodak
- VIB Structural Biology research Centre, VUB, Building E Pleinlaan 2, 1050 Brussels, Belgium
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16
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Romero-Romero S, Becerril-Sesín LA, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Structure and conformational stability of the triosephosphate isomerase from Zea mays. Comparison with the chemical unfolding pathways of other eukaryotic TIMs. Arch Biochem Biophys 2018; 658:66-76. [PMID: 30261166 DOI: 10.1016/j.abb.2018.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/18/2018] [Accepted: 09/23/2018] [Indexed: 12/16/2022]
Abstract
We studied the structure, function and thermodynamic properties for the unfolding of the Triosephosphate isomerase (TIM) from Zea mays (ZmTIM). ZmTIM shows a catalytic efficiency close to the diffusion limit. Native ZmTIM is a dimer that dissociates upon dilution into inactive and unfolded monomers. Its thermal unfolding is irreversible with a Tm of 61.6 ± 1.4 °C and an activation energy of 383.4 ± 11.5 kJ mol-1. The urea-induced unfolding of ZmTIM is reversible. Transitions followed by catalytic activity and spectroscopic properties are monophasic and superimposable, indicating that ZmTIM unfolds/refolds in a two-state behavior with an unfolding ΔG°(H20) = 99.8 ± 5.3 kJ mol-1. This contrasts with most other studied TIMs, where folding intermediates are common. The three-dimensional structure of ZmTIM was solved at 1.8 Å. A structural comparison with other eukaryotic TIMs shows a similar number of intramolecular and intermolecular interactions. Interestingly the number of interfacial water molecules found in ZmTIM is lower than those observed in most TIMs that show folding intermediates. Although with the available data, there is no clear correlation between structural properties and the number of equilibrium intermediates in the unfolding of TIM, the identification of such structural properties should increase our understanding of folding mechanisms.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Luis A Becerril-Sesín
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Adela Rodríguez-Romero
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico.
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17
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Lund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HKS. The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity. FEBS J 2018; 285:4214-4228. [PMID: 30153368 DOI: 10.1111/febs.14643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Abstract
Many class D β-lactamases form dimers in solution. The functional basis of the dimerization of OXA-48-like class D β-lactamases is not known, but in order to understand the structural requirements for dimerization of OXA-48, we have characterized the dimer interface. Size exclusion chromatography, small angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) were used to confirm the oligomeric state of OXA-48 in solution. X-ray crystallographic structures were used to elucidate the key interactions of dimerization. In silico residue scanning combined with site-directed mutagenesis was used to probe hot spots of dimerization. The affinity of dimerization was quantified using microscale thermophoresis, and the overall thermostability was investigated using differential scanning calorimetry. OXA-48 was consistently found to be a dimer in solution regardless of the method used, and the biological assembly found from the SAXS envelope is consistent with the dimer identified from the crystal structures. The buried chloride that interacts with Arg206 and Arg206' at the dimer interface was found to enhance the thermal stability by > 4 °C and crystal structures and mutations (R189A, R189A/R206A) identified several additional important ionic interactions. The affinity for OXA-48 R206A dimerization was in the picomolar range, thus revealing very high dimer affinity. In summary, OXA-48 has a very stable dimer interface, facilitated by noncovalent and predominantly charged interactions, which is stronger than the dimer interfaces previously described for other class D β-lactamases. PDB CODES: The oxacillinase-48 (OXA-48) R206A structure has PDB ID: 5OFT and OXA-48 R189A has PDB ID: 6GOA.
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Affiliation(s)
- Bjarte Aarmo Lund
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Ane Molden Thomassen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Birgit Helene Berg Nesheim
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Trine Josefine Olsen Carlsen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tony Christopeit
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
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18
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Biswas H, Chattopadhyaya R. Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from α 2β 2 to unfolded state. J Biomol Struct Dyn 2018. [DOI: 10.1080/07391102.2017.1345327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Himadri Biswas
- Department of Biochemistry, Bose Institute, Calcutta 700054, India
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19
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Chen S, Berglund P, Humble MS. The effect of phosphate group binding cup coordination on the stability of the amine transaminase from Chromobacterium violaceum. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2017.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Arai M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys Rev 2018; 10:163-181. [PMID: 29307002 PMCID: PMC5899706 DOI: 10.1007/s12551-017-0346-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022] Open
Abstract
Extensive experimental and theoretical studies have advanced our understanding of the mechanisms of folding and binding of globular proteins, and coupled folding and binding of intrinsically disordered proteins (IDPs). The forces responsible for conformational changes and binding are common in both proteins; however, these mechanisms have been separately discussed. Here, we attempt to integrate the mechanisms of coupled folding and binding of IDPs, folding of small and multi-subdomain proteins, folding of multimeric proteins, and ligand binding of globular proteins in terms of conformational selection and induced-fit mechanisms as well as the nucleation–condensation mechanism that is intermediate between them. Accumulating evidence has shown that both the rate of conformational change and apparent rate of binding between interacting elements can determine reaction mechanisms. Coupled folding and binding of IDPs occurs mainly by induced-fit because of the slow folding in the free form, while ligand binding of globular proteins occurs mainly by conformational selection because of rapid conformational change. Protein folding can be regarded as the binding of intramolecular segments accompanied by secondary structure formation. Multi-subdomain proteins fold mainly by the induced-fit (hydrophobic collapse) mechanism, as the connection of interacting segments enhances the binding (compaction) rate. Fewer hydrophobic residues in small proteins reduce the intramolecular binding rate, resulting in the nucleation–condensation mechanism. Thus, the folding and binding of globular proteins and IDPs obey the same general principle, suggesting that the coarse-grained, statistical mechanical model of protein folding is promising for a unified theoretical description of all mechanisms.
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Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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21
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Lund BA, Thomassen AM, Carlsen TJO, Leiros HKS. Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis. Acta Crystallogr F Struct Biol Commun 2017; 73:579-587. [PMID: 28994407 PMCID: PMC5633926 DOI: 10.1107/s2053230x17013838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 01/20/2023] Open
Abstract
The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinical Klebsiella pneumoniae strains and also from other human pathogens such as Pseudomonas aeruginosa and Escherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations. OXA-245 had the highest melting point (Tm = 55.8°C), as determined by differential scanning calorimetry, compared with OXA-163 (Tm = 49.4°C) and OXA-181 (Tm = 52.6°C). The differences could be explained by the loss of two salt bridges in OXA-163, and an overall decrease in the polarity of the surface of OXA-181 compared with OXA-245.
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Affiliation(s)
- Bjarte Aarmo Lund
- Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ane Molden Thomassen
- Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
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22
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Hjörleifsson JG, Ásgeirsson B. pH-Dependent Binding of Chloride to a Marine Alkaline Phosphatase Affects the Catalysis, Active Site Stability, and Dimer Equilibrium. Biochemistry 2017; 56:5075-5089. [DOI: 10.1021/acs.biochem.7b00690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens G. Hjörleifsson
- Department of Biochemistry,
Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry,
Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
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23
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Yageta S, Shibuya R, Imamura H, Honda S. Conformational and Colloidal Stabilities of Human Immunoglobulin G Fc and Its Cyclized Variant: Independent and Compensatory Participation of Domains in Aggregation of Multidomain Proteins. Mol Pharm 2017; 14:699-711. [DOI: 10.1021/acs.molpharmaceut.6b00983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seiki Yageta
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Risa Shibuya
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroshi Imamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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24
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Neira JL, Hornos F, Bacarizo J, Cámara-Artigás A, Gómez J. The Monomeric Species of the Regulatory Domain of Tyrosine Hydroxylase Has a Low Conformational Stability. Biochemistry 2016; 55:3418-31. [PMID: 27224548 DOI: 10.1021/acs.biochem.6b00135] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine, the first step in the synthesis of catecholamine neurotransmitters. The protein contains a 159-residue regulatory domain (RD) at its N-terminus that forms dimers in solution; the N-terminal region of RDTyrH (residues 1-71) is absent in the solution structure of the domain. We have characterized the conformational stability of two species of RDTyrH (one containing the N-terminal region and another lacking the first 64 residues) to clarify how that N-terminal region modulates the conformational stability of RD. Under the conditions used in this study, the RD species lacking the first 64 residues is a monomer at pH 7.0, with a small conformational stability at 25 °C (4.7 ± 0.8 kcal mol(-1)). On the other hand, the entire RDTyrH is dimeric at physiological pH, with an estimated dissociation constant of 1.6 μM, as determined by zonal gel filtration chromatography; dimer dissociation was spectroscopically silent to circular dichroism but not to fluoresecence. Both RD species were disordered below physiological pH, but the acquisition of secondary native-like structure occurs at pHs lower than those measured for the attainment of tertiary native- and compactness-like arrangements.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain.,Biocomputation and Complex Systems Physics Institute , 50009 Zaragoza, Spain
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
| | - Julio Bacarizo
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Ana Cámara-Artigás
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Javier Gómez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
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25
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Chen S, Land H, Berglund P, Humble MS. Stabilization of an amine transaminase for biocatalysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Mukherjee M, Ghosh R, Chattopadhyay K, Ghosh S. Stepwise unfolding of a multi-tryptophan protein MPT63 with immunoglobulin-like fold: detection of zone-wise perturbation during guanidine hydrochloride-induced unfolding using phosphorescence spectroscopy. RSC Adv 2016. [DOI: 10.1039/c6ra06545g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The present article highlights the simple inexpensive and rapid technique of phosphorescence spectroscopy at 77 K that reveals the environment of all the four tryptophan residues of a protein MPT63 during guanidine hydrochloride induced unfolding.
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Affiliation(s)
- Manini Mukherjee
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
| | - Ranendu Ghosh
- Structural Biology & Bio-Informatics Division
- Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | - Sanjib Ghosh
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
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27
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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28
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Ceccarelli A, Di Venere A, Nicolai E, De Luca A, Minicozzi V, Rosato N, Caccuri AM, Mei G. TNFR-Associated Factor-2 (TRAF2): Not Only a Trimer. Biochemistry 2015; 54:6153-61. [PMID: 26390021 DOI: 10.1021/acs.biochem.5b00674] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
TNF receptor-associated factors (TRAFs) are characterized by an oligomeric structure that plays a fundamental role in the binding process with membrane receptors. In this work, we studied the trimer-to-monomer (T ↔ 3M) equilibrium transition of the TRAF2 C-terminal domain using both chemical (dilution/guanidinium hydrochloride) and mechanical stress (high pressure) to induce the dissociation of the native protein into subunits. The experimental results and computer simulations indicate that stable monomers exist and that their population accounts for 15% of the total TRAF2 molecules already at a physiological intracellular concentration (≈1 μM), being instead the predominant species in the nanomolar concentration range. Because the total amount of TRAF2 changes during a cell cycle, the monomer-trimer equilibrium can be crucial for regulating the activities of TRAF2 in vivo.
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Affiliation(s)
- Arianna Ceccarelli
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy
| | - Almerinda Di Venere
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Eleonora Nicolai
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Anastasia De Luca
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Velia Minicozzi
- Physics Department, INFN University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Nicola Rosato
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Anna Maria Caccuri
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Giampiero Mei
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata , Via Montpellier 1, 00133 Rome, Italy.,The NAST Centre for Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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30
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Singh N, Kanthaje S, Bose K. Equilibrium dissociation and unfolding of human papillomavirus E2 transactivation domain. Biochem Biophys Res Commun 2015; 463:496-503. [PMID: 26091566 DOI: 10.1016/j.bbrc.2015.05.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/14/2015] [Indexed: 12/11/2022]
Abstract
Papillomavirus E2 protein that performs essential functions such as viral oncogene expression and replication represents specific target for therapeutic intervention. DNA-binding activity is associated with its C-terminal DNA-binding domain (DBD), while the N-terminal transactivation domain (TAD) is responsible for replication and transactivation functions. Although both demonstrate large dependence on dimerization for mediating their functions, KD for N-terminal dimerization is significantly high suggesting more dynamic role of this domain. However, unlike DBD, very little information is available on TAD dimerization, its folding and stability. Therefore, with an aim at delineating the regulatory switch of its dimerization, we have characterized high-risk HPV18 E2 TAD. Our studies demonstrate that E2 TAD is a weak but thermodynamically stable dimer (KD ∼ 1.8 μM, [Formula: see text] = 18.8 kcal mol(-1)) with α2-α3 helices forming the interface. It follows a three-state folding pathway, in which unfolding involves dissociation of a dimeric intermediate. Interestingly, 90% of the conformational free energy is associated with dimer dissociation (16.9 of 18.8 kcal mol(-1)) suggesting dimerization significantly contributes to its overall thermodynamic stability. These revelations might be important toward designing inhibitors for targeting dimerization or folding intermediates and hence multiple functions that E2 performs.
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Affiliation(s)
- Nitu Singh
- Integrated Biophysics and Structural Biology Lab, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Shruthi Kanthaje
- Integrated Biophysics and Structural Biology Lab, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India.
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31
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Thermal, chemical and pH induced unfolding of turmeric root lectin: modes of denaturation. PLoS One 2014; 9:e103579. [PMID: 25140525 PMCID: PMC4139268 DOI: 10.1371/journal.pone.0103579] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol−1 and 14.90 Kcal mol−1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp) is 3.42 Kcal mol−1 K−1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.
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33
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Cysteine residues impact the stability and micelle interaction dynamics of the human mitochondrial β-barrel anion channel hVDAC-2. PLoS One 2014; 9:e92183. [PMID: 24642864 PMCID: PMC3967697 DOI: 10.1371/journal.pone.0092183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/20/2014] [Indexed: 01/06/2023] Open
Abstract
The anti-apoptotic 19-stranded transmembrane human voltage dependent anion channel isoform 2 (hVDAC-2) β-barrel stability is crucial for anion transport in mitochondria. The role of the unusually high number of cysteine residues in this isoform is poorly understood. Using a Cys-less construct of hVDAC-2, we haveinvestigated the contribution of cysteines to channel function, barrel stability and its influence on the strength of protein-micelle interactions. We observe that despite the overall preservation in barrel structure upon cysteine mutation, subtle local variations in the mode of interaction of the barrel with its refolded micellar environment arise, which may manifest itself in the channel activity of both the proteins.Fluorescence measurements of the Trp residues in hVDAC-2 point to possible differences in the association of the barrel with lauryldimethylamine oxide (LDAO) micelles. Upon replacement of cysteines in hVDAC-2, our data suggests greater barrel rigidity by way of intra-protein interactions. This, in turn, lowers the equilibrium barrel thermodynamic parameters in LDAOby perturbingthe stability of the protein-micelle complex. In addition to this, we also find a difference in the cooperativity of unfolding upon increasing the LDAO concentration, implying the importance of micelle concentration and micelle-protein ratios on the stability of this barrel. Our results indicate that the nine cysteine residues of hVDAC-2 are the key in establishing strong(er) barrel interactions with its environment and also impart additional malleability to the barrel scaffold.
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Chen Z, Chang K, Capraro BR, Zhu C, Hsu CJ, Baumgart T. Intradimer/Intermolecular interactions suggest autoinhibition mechanism in endophilin A1. J Am Chem Soc 2014; 136:4557-64. [PMID: 24568626 PMCID: PMC3985530 DOI: 10.1021/ja411607b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Endophilin
A1 is a homodimeric membrane-binding endocytic accessory
protein with a high dimerization affinity. Its function has been hypothesized
to involve autoinhibition. However, the autoinhibition mechanism,
as well as the physicochemical basis for the high dimerization affinity
of endophilin in solution, have remained unclear. In this contribution,
we use a Förster resonance energy transfer (FRET) method to
investigate the homodimerization mechanism and intradimer molecular
interactions in endophilin. For the endophilin N-BAR domain (which
lacks the SH3 domain including a linker region of the full length
protein), we observe a large temperature dependence of the dimerization
affinity and dimer dissociation kinetics, implying large dimerization
enthalpy and dissociation activation enthalpy, respectively. Our evaluation
of the protein concentration dependence of dimer dissociation kinetics
implies that endophilin reversibly forms monomers via a dissociation/reassociation
mechanism. Furthermore, we use a kinetic method that allows us to
compare the dissociation kinetics of full-length endophilin to that
of truncated mutants. We find that mutants that lack either H0 helix
or SH3 domain show significantly faster dissociation kinetics relative
to full-length endophilin. This observation supports the presence
of an intradimer, intermonomer cross-interaction between H0 helix
and SH3 domain from different subunits within a homodimer. Because
the H0 helix is known to play a significant role in endophilin’s
membrane interactions, our measurements support a syngergistic model
where these interactions are inhibited in the absence of SH3 domain
binding ligands such as dynamin’s prolin rich domains, and
where the binding of these ligands may be suppressed for non-membrane-bound
endophilin.
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Affiliation(s)
- Zhiming Chen
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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35
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Banerjee B, Banerjee R. Guanidine Hydrochloride Mediated Denaturation of E. coli Alanyl-tRNA Synthetase: Identification of an Inactive Dimeric Intermediate. Protein J 2014; 33:119-27. [DOI: 10.1007/s10930-014-9544-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Kestler C, Knobloch G, Tessmer I, Jeanclos E, Schindelin H, Gohla A. Chronophin dimerization is required for proper positioning of its substrate specificity loop. J Biol Chem 2013; 289:3094-103. [PMID: 24338687 DOI: 10.1074/jbc.m113.536482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian phosphatases of the haloacid dehalogenase (HAD) superfamily have emerged as important regulators of physiology and disease. Many of these enzymes are stable homodimers; however, the role of their dimerization is largely unknown. Here, we explore the function of the obligatory homodimerization of chronophin, a mammalian HAD phosphatase known to dephosphorylate pyridoxal 5'-phosphate (PLP) and serine/threonine-phosphorylated proteins. The exchange of two residues in the murine chronophin homodimerization interface (chronophin(A194K,A195K)) yields a constitutive monomer both in vitro and in cells. The catalytic activity of monomeric chronophin toward PLP is strongly impaired. X-ray crystallographic studies of chronophin(A194K,A195K) revealed that dimer formation is essential for an intermolecular arginine-arginine-tryptophan stacking interaction that positions a critical histidine residue in the substrate specificity loop of chronophin for PLP coordination. Analysis of all available crystal structures of HAD hydrolases that are grouped together with chronophin in the C2a-type structural subfamily uncovered a highly conserved mode of dimerization that results in intermolecular contacts involving the substrate specificity loop. Our results explain how the dimerization of HAD hydrolases contributes to their catalytic efficiency and substrate specificity.
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Affiliation(s)
- Christian Kestler
- From the Institute for Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany and
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37
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Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein. Proc Natl Acad Sci U S A 2013; 110:E2782-91. [PMID: 23824290 DOI: 10.1073/pnas.1308846110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
HBc, the capsid-forming "core protein" of human hepatitis B virus (HBV), is a multidomain, α-helical homodimer that aggressively forms human HBV capsids. Structural plasticity has been proposed to be important to the myriad functions HBc mediates during viral replication. Here, we report detailed thermodynamic analyses of the folding of the dimeric HBc protomer under conditions that prevented capsid formation. Central to our success was the use of ion mobility spectrometry-mass spectrometry and microscale thermophoresis, which allowed folding mechanisms to be characterized using just micrograms of protein. HBc folds in a three-state transition with a stable, dimeric, α-helical intermediate. Extensive protein engineering showed thermodynamic linkage between different structural domains. Unusual effects associated with mutating some residues suggest structural strain, arising from frustrated contacts, is present in the native dimer. We found evidence of structural gatekeepers that, when mutated, alleviated native strain and prevented (or significantly attenuated) capsid formation by tuning the population of alternative native conformations. This strain is likely an evolved feature that helps HBc access the different structures associated with its diverse essential functions. The subtle balance between native and strained contacts may provide the means to tune conformational properties of HBc by molecular interactions or mutations, thereby conferring allosteric regulation of structure and function. The ability to trap HBc conformers thermodynamically by mutation, and thereby ablate HBV capsid formation, provides proof of principle for designing antivirals that elicit similar effects.
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38
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Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition. Proc Natl Acad Sci U S A 2013; 110:E2342-51. [PMID: 23754431 DOI: 10.1073/pnas.1220699110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding-folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative "coupled binding-folding" and three-state noncooperative "folding prior to binding" scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding-folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding-folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found "U-shape" temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments.
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39
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Wakankar MS, Krishnasastry MV, Jaokar TM, Patel KA, Gaikwad SM. Solution and in silico studies on the recombinant lectin from Cicer arietinum seeds. Int J Biol Macromol 2013; 56:149-55. [DOI: 10.1016/j.ijbiomac.2013.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
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40
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Georgescauld F, Moynié L, Habersetzer J, Cervoni L, Mocan I, Borza T, Harris P, Dautant A, Lascu I. Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of Mycobacterium tuberculosis. PLoS One 2013; 8:e57867. [PMID: 23526954 PMCID: PMC3589492 DOI: 10.1371/journal.pone.0057867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/27/2013] [Indexed: 01/10/2023] Open
Abstract
Most nucleoside diphosphate kinases (NDPKs) are hexamers. The C-terminal tail interacting with the neighboring subunits is crucial for hexamer stability. In the NDPK from Mycobacterium tuberculosis (Mt) this tail is missing. The quaternary structure of Mt-NDPK is essential for full enzymatic activity and for protein stability to thermal and chemical denaturation. We identified the intersubunit salt bridge Arg80-Asp93 as essential for hexamer stability, compensating for the decreased intersubunit contact area. Breaking the salt bridge by the mutation D93N dramatically decreased protein thermal stability. The mutation also decreased stability to denaturation by urea and guanidinium. The D93N mutant was still hexameric and retained full activity. When exposed to low concentrations of urea it dissociated into folded monomers followed by unfolding while dissociation and unfolding of the wild type simultaneously occur at higher urea concentrations. The dissociation step was not observed in guanidine hydrochloride, suggesting that low concentration of salt may stabilize the hexamer. Indeed, guanidinium and many other salts stabilized the hexamer with a half maximum effect of about 0.1 M, increasing protein thermostability. The crystal structure of the D93N mutant has been solved.
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Affiliation(s)
- Florian Georgescauld
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Lucile Moynié
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Johann Habersetzer
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Laura Cervoni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi “La Sapienza”, Roma, Italy
| | - Iulia Mocan
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Tudor Borza
- Laboratoire de Chimie Structurale des Macromolécules, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Pernile Harris
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alain Dautant
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
| | - Ioan Lascu
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
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41
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The stability of 2-state, 3-state and more-state proteins from simple spectroscopic techniques... plus the structure of the equilibrium intermediates at the same time. Arch Biochem Biophys 2013; 531:4-13. [DOI: 10.1016/j.abb.2012.10.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/22/2012] [Accepted: 10/28/2012] [Indexed: 11/20/2022]
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42
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Montecinos-Franjola F, Ross JA, Sánchez SA, Brunet JE, Lagos R, Jameson DM, Monasterio O. Studies on the dissociation and urea-induced unfolding of FtsZ support the dimer nucleus polymerization mechanism. Biophys J 2012; 102:2176-85. [PMID: 22824282 DOI: 10.1016/j.bpj.2012.03.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/31/2012] [Accepted: 03/12/2012] [Indexed: 01/23/2023] Open
Abstract
FtsZ is a major protein in bacterial cytokinesis that polymerizes into single filaments. A dimer has been proposed to be the nucleating species in FtsZ polymerization. To investigate the influence of the self-assembly of FtsZ on its unfolding pathway, we characterized its oligomerization and unfolding thermodynamics. We studied the assembly using size-exclusion chromatography and fluorescence spectroscopy, and the unfolding using circular dichroism and two-photon fluorescence correlation spectroscopy. The chromatographic analysis demonstrated the presence of monomers, dimers, and tetramers with populations dependent on protein concentration. Dilution experiments using fluorescent conjugates revealed dimer-to-monomer and tetramer-to-dimer dissociation constants in the micromolar range. Measurements of fluorescence lifetimes and rotational correlation times of the conjugates supported the presence of tetramers at high protein concentrations and monomers at low protein concentrations. The unfolding study demonstrated that the three-state unfolding of FtsZ was due to the mainly dimeric state of the protein, and that the monomer unfolds through a two-state mechanism. The monomer-to-dimer equilibrium characterized here (K(d) = 9 μM) indicates a significant fraction (~10%) of stable dimers at the critical concentration for polymerization, supporting a role of the dimeric species in the first steps of FtsZ polymerization.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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43
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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44
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Shu JY, Lund R, Xu T. Solution Structural Characterization of Coiled-Coil Peptide–Polymer Side-Conjugates. Biomacromolecules 2012; 13:1945-55. [DOI: 10.1021/bm300561y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Reidar Lund
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California,
United States
| | - Ting Xu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California,
United States
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45
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Merlino A, Russo Krauss I, Rossi B, Vergara A, De Vendittis A, Marco S, De Vendittis E, Sica F. Identification of an active dimeric intermediate populated during the unfolding process of the cambialistic superoxide dismutase from Streptococcus mutans. Biochimie 2012; 94:768-75. [DOI: 10.1016/j.biochi.2011.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/18/2011] [Indexed: 10/15/2022]
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46
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Jana B, Bandhu A, Mondal R, Biswas A, Sau K, Sau S. Domain Structure and Denaturation of a Dimeric Mip-like Peptidyl-Prolyl cis–trans Isomerase from Escherichia coli. Biochemistry 2012; 51:1223-37. [PMID: 22263615 DOI: 10.1021/bi2015037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Biswanath Jana
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054,
West Bengal, India
| | - Amitava Bandhu
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054,
West Bengal, India
| | - Rajkrishna Mondal
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054,
West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054,
West Bengal, India
| | - Keya Sau
- Department
of Biotechnology, Haldia Institute of Technology, PO-HIT, Dt-Purba Medinipur,
Pin 721657, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054,
West Bengal, India
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Lewis BC, Mackenzie PI, Miners JO. Homodimerization of UDP-glucuronosyltransferase 2B7 (UGT2B7) and identification of a putative dimerization domain by protein homology modeling. Biochem Pharmacol 2011; 82:2016-23. [DOI: 10.1016/j.bcp.2011.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 01/25/2023]
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Moreno-Vargas LM, Carrillo-Ibarra N, Arzeta-Pino L, Benítez-Cardoza CG. Thermal unfolding of apo- and holo-enolase from Saccharomyces cerevisiae: Different mechanisms, similar activation enthalpies. Int J Biol Macromol 2011; 49:871-8. [DOI: 10.1016/j.ijbiomac.2011.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/24/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
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Smith AG, Johnson CB, Vitha S, Holzenburg A. Oligomerization of plant FtsZ1 and FtsZ2 plastid division proteins. Arch Biochem Biophys 2011; 513:94-101. [PMID: 21781955 DOI: 10.1016/j.abb.2011.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/22/2011] [Accepted: 07/01/2011] [Indexed: 11/26/2022]
Abstract
FtsZ was identified in bacteria as the first protein to localize mid-cell prior to division and homologs have been found in many plant species. Bacterial studies demonstrated that FtsZ forms a ring structure that is dynamically exchanged with a soluble pool of FtsZ. Our previous work established that Arabidopsis FtsZ1 and FtsZ2-1 are capable of in vitro self-assembly into two distinct filament types, termed type-I and type-II and noted the presence of filament precursor molecules which prompted this investigation. Using a combination of electron microscopy, gel chromatography and native PAGE revealed that (i) prior to FtsZ assembly initiation the pool consists solely of dimers and (ii) during assembly of the Arabidopsis FtsZ type-II filaments the most common intermediate between the dimer and filament state is a tetramer. Three-dimensional reconstructions of the observed dimer and tetramer suggest these oligomeric forms may represent consecutive steps in type-II filament assembly and a mechanism is proposed, which is expanded to include FtsZ assembly into type-I filaments. Finally, the results permit a discussion of the oligomeric nature of the soluble pool in plants.
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Affiliation(s)
- Aaron G Smith
- Microscopy and Imaging Center, Texas A&M University, College Station, TX 77843-2257, USA
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Di Venere A, Nicolai E, Rosato N, Rossi A, Finazzi Agrò A, Mei G. Characterization of monomeric substates of ascorbate oxidase. FEBS J 2011; 278:1585-93. [DOI: 10.1111/j.1742-4658.2011.08084.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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