The Experts below are selected from a list of 321 Experts worldwide ranked by ideXlab platform

Hitoshi Okazawa - One of the best experts on this subject based on the ideXlab platform.

  • polyglutamine tract binding protein 1 is an intrinsically unstructured protein
    Biochimica et Biophysica Acta, 2009
    Co-Authors: Masaki Takahashi, Hitoshi Okazawa, Mineyuki Mizuguchi, Hiroyuki Shinoda, Tomoyasu Aizawa, Makoto Demura, Keiichi Kawano
    Abstract:

    Polyglutamine tract binding protein-1 (PQBP-1) is a nuclear protein that interacts with disease proteins containing expanded polyglutamine repeats. PQBP-1 also interacts with RNA polymerase II and a spliceosomal protein U5-15kD. In the present study, we demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. Intriguingly, the large unstructured region encompasses two functional domains: a Polar Amino Acid rich domain and a C-terminal domain. These findings suggest that PQBP-1 belongs to the family of intrinsically unstructured/disordered proteins. Furthermore, the binding of the target molecule U5-15kD induces only minor conformational changes into PQBP-1. Our results suggest that PQBP-1 includes high content of unstructured regions in the C-terminal domain, in spite of the binding of U5-15kD.

  • pqbp 1 npw38 a nuclear protein binding to the polyglutamine tract interacts with u5 15kd dim1p via the carboxyl terminal domain
    Biochemical and Biophysical Research Communications, 2000
    Co-Authors: Masaaki Waragai, Sousuke Takeuchi, Ichiro Kanazawa, Maral M Mouradian, E Junn, Masunori Kajikawa, M Shibata, Hitoshi Okazawa
    Abstract:

    PQBP-1 was identified as a binding protein to the polyglutamine tract present in various transcription-related factors and causative genes for neurodegenerative disorders. This novel gene contains at least two functional domains, WW domain and carboxyl-terminal domain (CTD), strictly conserved beyond species. Although human PQBP-1 additionally contains the Polar Amino Acid-rich domain by which it binds to the polyglutamine tract, genuine physiological function(s) have not been clarified. In this study, we showed that U5-15kD, human homologue of fission yeast dim1p, is a partner molecule of PQBP-1 binding to CTD. This finding suggests physiological functions of PQBP-1 in splicing, cell cycle, and ubiquitination, through which we can speculate the pathological roles of PQBP-1 in triplet repeat diseases.

  • Polar Amino Acid-Rich Sequences Bind to Polyglutamine Tracts
    Biochemical and Biophysical Research Communications, 1998
    Co-Authors: Ichiro Imafuku, Masaaki Waragai, Ichiro Kanazawa, Masahiro Kawabata, Maral M Mouradian, Sosuke Takeuchi, Hitoshi Okazawa
    Abstract:

    Polyglutamine tracts are found in different proteins including transcription factors and cofactors as well as in triplet repeat disease gene products. To characterize the protein motif that binds to the polyglutamine tract, we screened a human embryonic brain cDNA library with the polyglutamine tract of Brn-2 as bait using the yeast two-hybrid method. All six isolated clones encoding polyglutamine tract binding proteins were rich in Polar Amino Acids. Three of these clones could form Polar helical structures. These observations suggest that Polar Amino Acid-rich sequences are essential for binding to the polyglutamine tract.

Philip S. Poole - One of the best experts on this subject based on the ideXlab platform.

  • Bacterial ABC transporters of Amino Acids.
    Research in microbiology, 2001
    Co-Authors: Arthur H.f. Hosie, Philip S. Poole
    Abstract:

    There are two subfamilies of ABC uptake systems for Amino Acids in bacteria, the Polar Amino Acid transport family and the hydrophobic Amino Acid transport family. We consider the general properties of these families and we examine the specific transporters. Focusing on some of the best-studied ATP binding cassette transporters we also examine the mechanism of Amino Acid uptake, paying particular attention to the question of bidirectionality of solute movement.

  • Distribution of a sub-class of bacterial ABC Polar Amino Acid transporter and identification of an N-terminal region involved in solute specificity
    FEBS letters, 1997
    Co-Authors: David L. Walshaw, Shaun Lowthorpe, Alison K. East, Philip S. Poole
    Abstract:

    A new sub-class of binding protein-dependent transporter with specificity for a broad range of Polar Amino Acids has been identified by sequence comparison, in Rhizobium leguminosarum, Rhodobacter capsulatus, Escherichia coli and Pseudomonas fluorescens. Southern blotting and PCR analysis has shown that transporters from this new sub-class are widely distributed in Gram-negative bacteria, including, in addition to the above, Citrobacter freundii, Erwinia carotovorum and Rhizobium meliloti. ABC transporters of Polar Amino Acids can be divided into two groups: those with narrow solute specificity and the newly identified sub-class with broad solute specificity. The binding and inner membrane proteins from transporters with a broad solute specificity are larger by approximately 30% than those with a narrow solute specificity. Multiple alignment of the inner membrane proteins from all sequenced Polar Amino Acid transporters indicates there is an N-terminal conserved region that may be involved in solute specificity. A conserved arginine or lysine at residue 30 of this region is changed to glutamate in arginine transporters. Residue 53 also has a strong correlation with the charge on the transported solute, with basic Amino Acid transporters replacing an aliphatic Amino Acid at this position with a negatively charged Amino Acid. The general Amino Acid permease from R. leguminosarum, which will transport aliphatic as well as basic and Acidic Amino Acids, juxtaposes two prolines at residues 52 and 53 of the N-terminal conserved region.

Shigenori Kanaya - One of the best experts on this subject based on the ideXlab platform.

  • increase in activation rate of pro tk subtilisin by a single nonPolar to Polar Amino Acid substitution at the hydrophobic core of the propeptide domain
    Protein Science, 2013
    Co-Authors: Kota Yuzaki, Yudai Sanda, Dong-ju You, Ryo Uehara, Yuichi Koga, Shigenori Kanaya
    Abstract:

    Tk-subtilisin (Gly70-Gly398) is a subtilisin homolog from Thermococcus kodakarensis. Active Tk-subtilisin is produced from its inactive precursor, Pro-Tk-subtilisin (Gly1-Gly398), by autoprocessing and degradation of the propeptide (Tk-propeptide, Gly1-Leu69). This activation process is extremely slow at moderate temperatures owing to high stability of Tk-propeptide. Tk-propeptide is stabilized by the hydrophobic core. To examine whether a single nonPolar-to-Polar Amino Acid substitution at this core affects the activation rate of Pro-Tk-subtilisin, the Pro-Tk-subtilisin derivative with the Phe17→His mutation (Pro-F17H), Tk-propeptide derivative with the same mutation (F17H-propeptide), and two active-site mutants of Pro-F17H (Pro-F17H/S324A and Pro-F17H/S324C) were constructed. The crystal structure of Pro-F17H/S324A was nearly identical to that of Pro-S324A, indicating that the mutation does not affect the structure of Pro-Tk-subtilisin. The refolding rate of Pro-F17H/S324A and autoprocessing rate of Pro-F17H/S324C were also nearly identical to those of their parent proteins (Pro-S324A and Pro-S324C). However, the activation rate of Pro-F17H greatly increased when compared with that of Pro-Tk-subtilisin, such that Pro-F17H is efficiently activated even at 40°C. The far-UV circular dichroism spectrum of F17H-propeptide did not exhibit a broad trough at 205–230 nm, which is observed in the spectrum of Tk-propeptide. F17H-propeptide is more susceptible to chymotryptic degradation than Tk-propeptide. These results suggest that F17H-propeptide is unfolded in an isolated form and is therefore rapidly degraded by Tk-subtilisin. Thus, destabilization of the hydrophobic core of Tk-propeptide by a nonPolar-to-Polar Amino Acid substitution is an effective way to increase the activation rate of Pro-Tk-subtilisin.

  • Increase in activation rate of Pro‐Tk‐subtilisin by a single nonPolar‐to‐Polar Amino Acid substitution at the hydrophobic core of the propeptide domain
    Protein science : a publication of the Protein Society, 2013
    Co-Authors: Kota Yuzaki, Yudai Sanda, Dong-ju You, Ryo Uehara, Yuichi Koga, Shigenori Kanaya
    Abstract:

    Tk-subtilisin (Gly70-Gly398) is a subtilisin homolog from Thermococcus kodakarensis. Active Tk-subtilisin is produced from its inactive precursor, Pro-Tk-subtilisin (Gly1-Gly398), by autoprocessing and degradation of the propeptide (Tk-propeptide, Gly1-Leu69). This activation process is extremely slow at moderate temperatures owing to high stability of Tk-propeptide. Tk-propeptide is stabilized by the hydrophobic core. To examine whether a single nonPolar-to-Polar Amino Acid substitution at this core affects the activation rate of Pro-Tk-subtilisin, the Pro-Tk-subtilisin derivative with the Phe17→His mutation (Pro-F17H), Tk-propeptide derivative with the same mutation (F17H-propeptide), and two active-site mutants of Pro-F17H (Pro-F17H/S324A and Pro-F17H/S324C) were constructed. The crystal structure of Pro-F17H/S324A was nearly identical to that of Pro-S324A, indicating that the mutation does not affect the structure of Pro-Tk-subtilisin. The refolding rate of Pro-F17H/S324A and autoprocessing rate of Pro-F17H/S324C were also nearly identical to those of their parent proteins (Pro-S324A and Pro-S324C). However, the activation rate of Pro-F17H greatly increased when compared with that of Pro-Tk-subtilisin, such that Pro-F17H is efficiently activated even at 40°C. The far-UV circular dichroism spectrum of F17H-propeptide did not exhibit a broad trough at 205–230 nm, which is observed in the spectrum of Tk-propeptide. F17H-propeptide is more susceptible to chymotryptic degradation than Tk-propeptide. These results suggest that F17H-propeptide is unfolded in an isolated form and is therefore rapidly degraded by Tk-subtilisin. Thus, destabilization of the hydrophobic core of Tk-propeptide by a nonPolar-to-Polar Amino Acid substitution is an effective way to increase the activation rate of Pro-Tk-subtilisin.

R Griffin - One of the best experts on this subject based on the ideXlab platform.

  • variant signal peptides of vaccine antigen fhbp impair processing affecting surface localization and antibody mediated killing in most meningococcal isolates
    Frontiers in Microbiology, 2019
    Co-Authors: Ronni Anderson Goncalves Da Silva, Av Karlyshev, A Ryan, Neil J Oldfield, Karl G Wooldridge, Christopher D Bayliss, R Griffin
    Abstract:

    Meningococcal lipoprotein, Factor H binding protein (FHbp), is the sole antigen of the Trumenba vaccine (Pfizer) and one of four antigens of the Bexsero vaccine (GSK) targeting Neisseria meningitidis serogroup B isolates. Lipidation of FHbp is assumed to occur for all isolates. We show in 91% of a collection of UK isolates (1742/1895) non-synonymous single nucleotide polymorphisms (SNPs) in the signal peptide of FHbp. A single SNP, common to all, alters a Polar Amino Acid that abolishes processing: lipidation and signal peptide cleavage. Whilst some of the FHbp precursor is retained in the cytoplasm due to reduced binding to SecA, remarkably some is translocated and further surface-localised by Slam. Thus we show Slam is not lipoprotein-specific. In a panel of isolates tested, the overall reduced surface localisation of the precursor FHbp, compared to isolates with an intact signal peptide, corresponded with decreased susceptibility to antibody-mediated killing. Our findings shed new light on the canonical pathway for lipoprotein processing and translocation of important relevance for lipoprotein-based vaccines in development and in particular for Trumenba.

  • Variant Signal Peptides of Vaccine Antigen, FHbp, Impair Processing Affecting Surface Localization and Antibody-Mediated Killing in Most Meningococcal Isolates
    2019
    Co-Authors: Rag Da Silva, Av Karlyshev, Nj Oldfield, Kg Wooldridge, Cd Bayliss, A Ryan, R Griffin
    Abstract:

    Meningococcal lipoprotein, Factor H binding protein (FHbp), is the sole antigen of the Trumenba vaccine (Pfizer) and one of four antigens of the Bexsero vaccine (GSK) targeting Neisseria meningitidis serogroup B isolates. Lipidation of FHbp is assumed to occur for all isolates. We show in the majority of a collection of United Kingdom isolates (1742/1895) non-synonymous single nucleotide polymorphisms (SNPs) in the signal peptide (SP) of FHbp. A single SNP, common to all, alters a Polar Amino Acid that abolishes processing: lipidation and SP cleavage. Whilst some of the FHbp precursor is retained in the cytoplasm due to reduced binding to SecA, remarkably some is translocated and further surface-localized by Slam. Thus we show Slam is not lipoprotein-specific. In a panel of isolates tested, the overall reduced surface localization of the precursor FHbp, compared to isolates with an intact SP, corresponded with decreased susceptibility to antibody-mediated killing. Our findings shed new light on the canonical pathway for lipoprotein processing and translocation of important relevance for lipoprotein-based vaccines in development and in particular for Trumenba

Srabani Taraphder - One of the best experts on this subject based on the ideXlab platform.

  • Free energies of proton transfer by Polar Amino Acid sidechain analogues anchored to the outer wall of single walled carbon nanotubes
    Computational and Theoretical Chemistry, 2014
    Co-Authors: T.g. Abi, Srabani Taraphder
    Abstract:

    Abstract Extensive empirical valence bond (EVB) simulation studies are reported on selected exohedrally functionalized derivatives of single walled carbon nanotube (SWCNT) in water. In each model studied, an analogue of a Polar Amino Acid sidechain (such as Asp, His and Ser) and one hydroxyl group are covalently linked to two carbon atoms in close proximity on the SWCNT wall. We have estimated the free energies of reaction and activation associated with proton transfer between the sidechain analogue (donor) and the hydroxyl group (acceptor). All the sidechain analogues are found to be spontaneous proton acceptors. We also compare these free energy values to those in model systems where the proton donor and acceptor groups are endohedrally linked to the wall and extend into the hydrophobic core of the nanotube. Our results clearly quantify the effect of hydrophobic confinement on the proton transfer reaction studied.

  • proton affinity of Polar Amino Acid sidechain analogues anchored to the outer wall of single walled carbon nanotubes
    Computational and Theoretical Chemistry, 2013
    Co-Authors: T.g. Abi, Tarak Karmakar, Srabani Taraphder
    Abstract:

    We investigate the proton affinity values of sidechain analogues of Ser, Asp, His and Tyr covalently attached to the the outer wall of single walled carbon nanotubes both in the gas phase and in the presence of a Polar solvent. The proton affinity values, estimated by B3LYP/SVP method, show marked sensitivity to the anchoring hydrophobic surface. His and Tyr-like sidechains exhibit high propensities towards accepting a proton from a neighboring –OH group similarly tethered to the carbon nanotube wall. Compared to Tyr sidechain in the gas phase, a marked increase in proton affinity values of Tyr-like sidechains is observed in functionalized systems if, in addition to the proton donor –OH group, an additional –OH group is present covalently attached to the wall within hydrogen bonding distance of the proton acceptor sidechain.

  • Proton transfer reactions in carbon nanotubes endohedrally functionalized with selected Polar Amino Acid sidechains
    Chemical Physics, 2012
    Co-Authors: T.g. Abi, Srabani Taraphder
    Abstract:

    Abstract We use the empirical-valence-bond (EVB) theory to investigate intramolecular proton transfer reactions between a selected set of Polar Amino Acid sidechains and hydroxyl groups suspended inside carbon nanotubes to model the effect of hydrophobic confinement on the energetics of proton transfer involving (i) translocation of an excess protonic charge (with protonated histidine sidechain as donor) and (ii) transformation of a neutral reactant state to a charge-separated product state (with sidechains of Asp, Glu, Ser and Thr as donor). In both the cases, confinement in hydrophobic medium is found to change the associated free energies compared to their respective values in the bulk solution phase. Presence of stable hydrogen bonding within the pore is found to have a significant effect on both free energies of reaction and activation and thus governs the thermodynamic and kinetic feasibilities of these intramolecular reactions in hydrophobic confinement.