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Nakata N, Okamoto R, Sumi T, Koga K, Morita T, Imamura H. Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein. Protein Sci 2023; 32:e4763. [PMID: 37622187 PMCID: PMC10519159 DOI: 10.1002/pro.4763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.
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Affiliation(s)
- Noa Nakata
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
| | - Ryuichi Okamoto
- Graduate School of Information Science, University of HyogoKobeHyogoJapan
| | - Tomonari Sumi
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Kenichiro Koga
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Takeshi Morita
- Department of ChemistryGraduate School of Science, Chiba UniversityChibaJapan
| | - Hiroshi Imamura
- Department of Bio‐ScienceNagahama Institute of Bio‐Science and TechnologyNagahamaShigaJapan
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2
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Motov VV, Kot EF, Shabalkina AV, Goncharuk SA, Arseniev AS, Goncharuk MV, Mineev KS. Investigation of lipid/protein interactions in trifluoroethanol-water mixtures proposes the strategy for the refolding of helical transmembrane domains. JOURNAL OF BIOMOLECULAR NMR 2023; 77:15-24. [PMID: 36451032 DOI: 10.1007/s10858-022-00408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/22/2022] [Indexed: 05/03/2023]
Abstract
Membrane proteins are one of the keystone objects in molecular biology, but their structural studies often require an extensive search for an appropriate membrane-like environment and an efficient refolding protocol for a recombinant protein. Isotropic bicelles are a convenient membrane mimetic used in structural studies of membrane proteins. Helical membrane domains are often transferred into bicelles from trifluoroethanol-water mixtures. However, the protocols for such a refolding are empirical and the process itself is still not understood in detail. In search of the optimal refolding approaches for helical membrane proteins, we studied here how membrane proteins, lipids, and detergents interact with each other at various trifluoroethanol-water ratios. Using high-resolution NMR spectroscopy and dynamic light scattering, we determined the key states of the listed compounds in the trifluoroethanol/water mixture, found the factors that could be critical for the efficiency of refolding, and proposed several most optimal protocols. These protocols were developed on the transmembrane domain of neurotrophin receptor TrkA and tested on two model helical membrane domains-transmembrane of Toll-like receptor TLR9 and voltage-sensing domain of a potassium channel KvAP.
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Affiliation(s)
- Vladislav V Motov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Erik F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Alexandra V Shabalkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
| | - Marina V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Ulitsa Miklukho-Maklaya, 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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3
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Llontop EE, Cenens W, Favaro DC, Sgro GG, Salinas RK, Guzzo CR, Farah CS. The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri. PLoS Pathog 2021; 17:e1009808. [PMID: 34398935 PMCID: PMC8389850 DOI: 10.1371/journal.ppat.1009808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/26/2021] [Accepted: 07/17/2021] [Indexed: 11/19/2022] Open
Abstract
Type IV pili (T4P) are thin and flexible filaments found on the surface of a wide range of Gram-negative bacteria that undergo cycles of extension and retraction and participate in a variety of important functions related to lifestyle, defense and pathogenesis. During pilus extensions, the PilB ATPase energizes the polymerization of pilin monomers from the inner membrane. In Xanthomonas citri, two cytosolic proteins, PilZ and the c-di-GMP receptor FimX, are involved in the regulation of T4P biogenesis through interactions with PilB. In vivo fluorescence microscopy studies show that PilB, PilZ and FimX all colocalize to the leading poles of X. citri cells during twitching motility and that this colocalization is dependent on the presence of all three proteins. We demonstrate that full-length PilB, PilZ and FimX can interact to form a stable complex as can PilB N-terminal, PilZ and FimX C-terminal fragments. We present the crystal structures of two binary complexes: i) that of the PilB N-terminal domain, encompassing sub-domains ND0 and ND1, bound to PilZ and ii) PilZ bound to the FimX EAL domain within a larger fragment containing both GGDEF and EAL domains. Evaluation of PilZ interactions with PilB and the FimX EAL domain in these and previously published structures, in conjunction with mutagenesis studies and functional assays, allow us to propose an internally consistent model for the PilB-PilZ-FimX complex and its interactions with the PilM-PilN complex in the context of the inner membrane platform of the X. citri Type IV pilus.
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Affiliation(s)
- Edgar E. Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Denize C. Favaro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Química Orgânica, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Cristiane R. Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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4
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Msallam M, Sun H, Meledin R, Franz P, Brik A. Examining the role of phosphorylation of p19 INK4d in its stability and ubiquitination using chemical protein synthesis. Chem Sci 2020; 11:5526-5531. [PMID: 32874495 PMCID: PMC7446725 DOI: 10.1039/c9sc06300e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/12/2020] [Indexed: 11/21/2022] Open
Abstract
p19INK4d plays an important role in the regulation of the cell cycle by inhibiting the function of cyclin-dependent kinases 4/6 that is responsible for the phosphorylation and deactivation of the retinoblastoma protein (pRb) tumour suppressor. Recently, it was reported that phosphorylation of p19INK4d at Ser76 and Ser66 causes structural changes, which lead to its ubiquitination and degradation. Yet the exact contribution of each phosphorylation site remains unclear. To shed light on the role of these sites, we developed the chemical synthesis of unmodified, mono- and doubly phosphorylated p19INK4d using state of the art methods for chemical protein synthesis. The synthesized proteins were characterized by circular dichroism and biochemical methods to examine the effect of phosphorylation on the thermal stability and ubiquitination, respectively. Our results provide clear determination of p19INK4d stability upon phosphorylation at different sites and reveal that phosphorylation of both Ser residues might be necessary for promoting ubiquitination of p19INK4d.
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Affiliation(s)
- Muna Msallam
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Hao Sun
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Roman Meledin
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Pauline Franz
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Ashraf Brik
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
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5
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Liu Y, Zhang H, Han J, Jiang S, Geng X, Xue D, Chen Y, Zhang C, Zhou Z, Zhang W, Chen M, Lin M, Wang J. Functional assessment of hydrophilic domains of late embryogenesis abundant proteins from distant organisms. Microb Biotechnol 2019; 12:752-762. [PMID: 31012266 PMCID: PMC6559209 DOI: 10.1111/1751-7915.13416] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/06/2019] [Indexed: 01/03/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins play a protective role during desiccation and oxidation stresses. LEA3 proteins are a major group characterized by a hydrophilic domain (HD) with a highly conserved repeating 11-amino acid motif. We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into α-helical structures with the addition of glycerol or trifluoroethanol. Heterologous HD expression conferred enhanced desiccation and oxidation tolerance to Escherichia coli. These four HDs protected the enzymatic activities of lactate dehydrogenase (LDH) by preventing its aggregation under desiccation stress. The HDs also interacted with LDH, which was intensified by the addition of hydrogen peroxide (H2 O2 ), suggesting a protective role in a chaperone-like manner. Based on these results, the HDs of LEA3 proteins show promise as protectants for desiccation and oxidation stresses, especially DrHD, which is a potential ideal stress-response element that can be applied in synthetic biology due to its extraordinary protection and stress resistance ability.
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Affiliation(s)
- Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Heng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621000, China
| | - Xiuxiu Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621000, China
| | - Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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6
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Polyserine repeats promote coiled coil-mediated fibril formation and length-dependent protein aggregation. J Struct Biol 2018; 204:572-584. [PMID: 30194983 DOI: 10.1016/j.jsb.2018.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/06/2018] [Accepted: 09/01/2018] [Indexed: 12/13/2022]
Abstract
Short polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, together with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly understood. Early studies highlighted their structural versatility, similar to other homopolymers whose conformation is influenced by the surrounding protein context. As polyS stretches are frequently near polyQ and polyA repeats, which can be part of coiled coil (CC) structures, and the frameshift-derived polyS repeats in HD directly flank CC heptads important for aggregation, we investigate here the structural and aggregation properties of polyS in the context of CC structures. We have taken advantage of peptide models, previously used to study polyQ and polyA in CCs, in which we inserted polyS repeats of variable length and studied them in comparison with polyQ and polyA peptides. We found that polyS repeats promote CC-mediated polymerization and fibrillization as revealed by circular dichroism, chemical crosslinking, and atomic force microscopy. Furthermore, they promote CC-based, length-dependent intracellular aggregation, which is negligible with 7 and widespread with 49 serines. These findings show that polyS repeats can participate in the formation of CCs, as previously found for polyQ and polyA, conferring to peptides distinctive structural properties with aggregation kinetics that are intermediate between those of polyA and polyQ CCs, and contribute to an overall structural definition of the pathophysiogical roles of homopolymeric repeats in CC structures.
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7
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Gupte TM, Haque F, Gangadharan B, Sunitha MS, Mukherjee S, Anandhan S, Rani DS, Mukundan N, Jambekar A, Thangaraj K, Sowdhamini R, Sommese RF, Nag S, Spudich JA, Mercer JA. Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies. J Biol Chem 2014; 290:7003-15. [PMID: 25548289 DOI: 10.1074/jbc.m114.596676] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The most frequent known causes of primary cardiomyopathies are mutations in the genes encoding sarcomeric proteins. Among those are 30 single-residue mutations in TPM1, the gene encoding α-tropomyosin. We examined seven mutant tropomyosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutant proteins are altered, which in turn could provide a structural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca(2+) sensitivity of human β-cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca(2+) activation, and dilated cardiomyopathies are hyposensitive. We also report correlations between ATPase activity at maximum Ca(2+) concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computationally designed mutant, E181K, that is hypersensitive, confirming predictions derived from in silico structural analysis.
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Affiliation(s)
- Tejas M Gupte
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | - Farah Haque
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India, the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Binnu Gangadharan
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India, the Manipal University, Madhav Nagar, Manipal 576104, India
| | - Margaret S Sunitha
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India, the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Souhrid Mukherjee
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | - Swetha Anandhan
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | - Deepa Selvi Rani
- the Council for Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Namita Mukundan
- the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Amruta Jambekar
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | - Kumarasamy Thangaraj
- the Council for Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Ramanathan Sowdhamini
- the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ruth F Sommese
- the Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, and
| | - Suman Nag
- the Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, and
| | - James A Spudich
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India, the Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, and
| | - John A Mercer
- From the Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India, the McLaughlin Research Institute, Great Falls, Montana 59405
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8
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Shao Q, Fan Y, Yang L, Qin Gao Y. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 2012; 136:115101. [DOI: 10.1063/1.3692801] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Souza DP, Andrade MO, Alvarez-Martinez CE, Arantes GM, Farah CS, Salinas RK. A component of the Xanthomonadaceae type IV secretion system combines a VirB7 motif with a N0 domain found in outer membrane transport proteins. PLoS Pathog 2011; 7:e1002031. [PMID: 21589901 PMCID: PMC3093366 DOI: 10.1371/journal.ppat.1002031] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Accepted: 03/02/2011] [Indexed: 01/28/2023] Open
Abstract
Type IV secretion systems (T4SS) are used by Gram-negative bacteria to translocate protein and DNA substrates across the cell envelope and into target cells. Translocation across the outer membrane is achieved via a ringed tetradecameric outer membrane complex made up of a small VirB7 lipoprotein (normally 30 to 45 residues in the mature form) and the C-terminal domains of the VirB9 and VirB10 subunits. Several species from the genera of Xanthomonas phytopathogens possess an uncharacterized type IV secretion system with some distinguishing features, one of which is an unusually large VirB7 subunit (118 residues in the mature form). Here, we report the NMR and 1.0 Å X-ray structures of the VirB7 subunit from Xanthomonas citri subsp. citri (VirB7XAC2622) and its interaction with VirB9. NMR solution studies show that residues 27–41 of the disordered flexible N-terminal region of VirB7XAC2622 interact specifically with the VirB9 C-terminal domain, resulting in a significant reduction in the conformational freedom of both regions. VirB7XAC2622 has a unique C-terminal domain whose topology is strikingly similar to that of N0 domains found in proteins from different systems involved in transport across the bacterial outer membrane. We show that VirB7XAC2622 oligomerizes through interactions involving conserved residues in the N0 domain and residues 42–49 within the flexible N-terminal region and that these homotropic interactions can persist in the presence of heterotropic interactions with VirB9. Finally, we propose that VirB7XAC2622 oligomerization is compatible with the core complex structure in a manner such that the N0 domains form an extra layer on the perimeter of the tetradecameric ring. Many aspects of bacterial life require that they translocate proteins to the cell exterior. To do this, different macromolecular secretion systems of varying complexity have evolved (Type I–VI secretion systems). These secretion systems are often at the front lines of pathogen-host interactions and are important for the development of disease. In this work, we have determined the structure and studied the interactions of an unusually large VirB7 subunit (VirB7XAC2622) of the outer membrane pore of the Type IV secretion system found in the Xanthomonas genera of phytopathogens. Its mosaic structure combines a canonical VirB7 N-terminal region with a C-terminal globular domain whose topology is observed in a relatively limited set of proteins, all involved in molecular transport across outer membranes. Our results lead to the hypothesis that the VirB7XAC2622 globular domains can form an extra ring around the perimeter of the outer membrane pore and reveal deeper structural and evolutionary relationships among bacterial macromolecular secretion systems that have evolved to adopt a variety of functions, including structural modules in outer membrane pores (secretins from Type II, III and IV secretion systems, Type IV pili and filamentous phages), signal-transduction modules in TonB-dependent receptors and membrane-penetrating devices in T6SS and long-tailed bacteriophages.
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Affiliation(s)
- Diorge P. Souza
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Maxuel O. Andrade
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | - Guilherme M. Arantes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- * E-mail: (CSF); (RKS)
| | - Roberto K. Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- * E-mail: (CSF); (RKS)
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10
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Johnson ME, Malardier-Jugroot C, Head-Gordon T. Effects of co-solvents on peptide hydration water structure and dynamics. Phys Chem Chem Phys 2009; 12:393-405. [PMID: 20023817 DOI: 10.1039/b915888j] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluate the molecular response of hydration water as a function of temperature and proximity to the surface of the peptide N-acetyl-leucine-methylamide (NALMA) when in the presence of the kosmotrope co-solvent glycerol or the chaotrope co-solvent dimethyl sulfoxide (DMSO), using molecular dynamics simulation with a polarizable force field. These detailed microscopic studies complement established thermodynamic analysis on the role of co-solvents in shifting the equilibrium for proteins away from or towards the native folded state. We find that the structure of the water at the peptide interfaces reflects an increase in hydration number in the glycerol solution and a decrease in hydration numbers in the DMSO solution. While the water dynamics around NALMA in the presence of both co-solvents is slower than that observed with the water solvent alone, in the DMSO mixture we no longer measure a separation in water motion time scales at low temperatures as is seen in the pure water solvent, but rather one single relaxation time. In the glycerol, however, we do observe a separation of time scales at low temperatures, supporting the hypothesis that hydration water near a hydrophobic solute evolves on a separate time scale than the extensive hydrogen-bonding network of more bulk-like water. Our simulation studies highlight the differences in the two co-solvent solutions due to the relative frequency of water contacts with the hydrophobic vs. hydrophilic peptide surface, and direct water interactions with the co-solvents.
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Affiliation(s)
- Margaret E Johnson
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, CA 94720, USA.
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11
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Cho KJ, Kim JK, Lee JH, Shin HJ, Park SS, Kim KH. Structural features of cephalosporin acylase reveal the basis of autocatalytic activation. Biochem Biophys Res Commun 2009; 390:342-8. [PMID: 19800869 DOI: 10.1016/j.bbrc.2009.09.134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 09/30/2009] [Indexed: 10/20/2022]
Abstract
Cephalosporin acylase (CA), a member of the N-terminal nucleophile hydrolase family, is activated through two steps of intramolecular autoproteolysis, the first mediated by a serine residue, and the second by a glutamate, which releases the pro-segment and produces an active enzyme. In this study, we have determined the crystal structures of mutants which could affect primary or secondary auto-cleavage and of sequential intermediates of a slow-processing mutant at 2.0-2.5A resolutions. The pro-segments of the mutants undergo dynamic conformational changes during activation and adopt surprisingly different loop conformations from one another. However, the autoproteolytic site was found to form a catalytically competent conformation with a solvent water molecule, which was essentially conserved in the CA mutants.
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Affiliation(s)
- Ki Joon Cho
- Department of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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12
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Corrêa F, Farah CS, Salinas RK. Mg2+ ions bind at the C-terminal region of skeletal muscle alpha-tropomyosin. Biopolymers 2009; 91:583-90. [PMID: 19280641 DOI: 10.1002/bip.21185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tropomyosin (Tm) is a dimeric coiled-coil protein that polymerizes through head-to-tail interactions. These polymers bind along actin filaments and play an important role in the regulation of muscle contraction. Analysis of its primary structure shows that Tm is rich in acidic residues, which are clustered along the molecule and may form sites for divalent cation binding. In a previous study, we showed that the Mg(2+)-induced increase in stability of the C-terminal half of Tm is sensitive to mutations near the C-terminus. In the present report, we study the interaction between Mg(2+) and full-length Tm and smaller fragments corresponding to the last 65 and 26 Tm residues. Although the smaller Tm peptide (Tm(259-284(W269))) is flexible and to large extent unstructured, the larger Tm(220-284(W269)) fragment forms a coiled coil in solution whose stability increases significantly in the presence of Mg(2+). NMR analysis shows that Mg(2+) induces chemical shift perturbations in both Tm(220-284(W269)) and Tm(259-284(W269)) in the vicinity of His276, in which are located several negatively charged residues.
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Affiliation(s)
- Fernando Corrêa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Nayak A, Sorci M, Krueger S, Belfort G. A universal pathway for amyloid nucleus and precursor formation for insulin. Proteins 2009; 74:556-65. [PMID: 18655073 DOI: 10.1002/prot.22169] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To help identify the etiological agents for amyloid-related diseases, attention is focused here on the fibrillar precursors, also called oligomers and protofibrils, and on modeling the reaction kinetics of the formation of the amyloid nucleus. Insulin is a favored model for amyloid formation, not only because amyloidosis can be a problem in diabetes, but also because aggregation and fibrillation causes problems during production, storage, and delivery. Small angle neutron scattering (SANS) is used to measure the temporal formation of insulin oligomers in H(2)O- and D(2)O-based solvents and obtain consistent evidence of the composition of the insulin nucleus that comprised three dimers or six monomers similar to that recently proposed in the literature. A simple molecular structural model that describes the growth of oligomers under a wide range of environmental conditions is proposed. The model first involves lengthening or end-on-end association of dimers to form three-dimer nuclei, and then exhibits broadening or side-on-side association of nuclei. Using different additives to demonstrate their influence on the kinetics of oligomer formation, we showed that, although the time required to form the nucleus was dependent on a specific system, they all followed a universal pathway for nucleus and precursor formation. The methods and analyses presented here provide the first experimental molecular size description of the details of amyloid nucleus formation and subsequent propagation to fibril precursors independent of kinetics.
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Affiliation(s)
- Arpan Nayak
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Corrêa F, Salinas RK, Bonvin AMJJ, Farah CS. Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex. Proteins 2008; 73:902-17. [PMID: 18536019 DOI: 10.1002/prot.22116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Skeletal alpha-tropomyosin (Tm) is a dimeric coiled-coil protein that forms linear assemblies under low ionic strength conditions in vitro through head-to-tail interactions. A previously published NMR structure of the Tm head-to-tail complex revealed that it is formed by the insertion of the N-terminal coiled-coil of one molecule into a cleft formed by the separation of the helices at the C-terminus of a second molecule. To evaluate the contribution of charged residues to complex stability, we employed single and double-mutant Tm fragments in which specific charged residues were changed to alanine in head-to-tail binding assays, and the effects of the mutations were analyzed by thermodynamic double-mutant cycles and protein-protein docking. The results show that residues K5, K7, and D280 are essential to the stability of the complex. Though D2, K6, D275, and H276 are exposed to the solvent and do not participate in intermolecular contacts in the NMR structure, they may contribute to head-to-tail complex stability by modulating the stability of the helices at the Tm termini.
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Affiliation(s)
- Fernando Corrêa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Wu LZ, Ma BL, Sheng YB, Wang W. Equilibrium and kinetic analysis on the folding of hen egg lysozyme in the aqueous-glycerol solution. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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