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Now showing items 1 - 16 of 71

  • Direct observation of ligand migration within human hemoglobin at work

    Sato-Tomita, Ayana   Ohki, Mio   Ichiyanagi, Kouhei   Park, Sam-Yong  

    Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photo-dissociated CO molecules migrate along distinct pathways in the a and beta subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as alpha 14Trp(A12), alpha 105Leu(G12), beta 15Trp(A12), and beta 71Phe(E15). We also observe electron density evidence for the distal histidine [alpha 58/beta 63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in alpha subunits than in beta subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the alpha or beta subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.
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  • Seeing the light with BLUF proteins

    Park, Sam-Yong   Tame, Jeremy R. H.  

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  • Molecular mechanism of photoactivation of a light-regulated adenylate cyclase

    Ohki, Mio   Sato-Tomita, Ayana   Matsunaga, Shigeru   Iseki, Mineo   Tame, Jeremy R. H.   Shibayama, Naoya   Park, Sam-Yong  

    The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light-and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.
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  • Capturing the hemoglobin allosteric transition in a single crystal form.

    Shibayama, Naoya   Sugiyama, Kanako   Tame, Jeremy R H   Park, Sam-Yong  

    Allostery in many oligomeric proteins has been postulated to occur via a ligand-binding-driven conformational transition from the tense (T) to relaxed (R) state, largely on the basis of the knowledge of the structure and function of hemoglobin, the most thoroughly studied of all allosteric proteins. However, a growing body of evidence suggests that hemoglobin possesses a variety of intermediates between the two end states. As such intermediate forms coexist with the end states in dynamic equilibrium and cannot be individually characterized by conventional techniques, very little is known about their properties and functions. Here we present complete structural and functional snapshots of nine equilibrium conformers of human hemoglobin in the half-liganded and fully liganded states by using a novel combination of X-ray diffraction analysis and microspectrophotometric O2 equilibrium measurements on three isomorphous crystals, each capturing three distinct equilibrium conformers. Notably, the conformational set of this crystal form varies according to shifts in the allosteric equilibrium, reflecting the differences in hemoglobin ligation state and crystallization solution conditions. We find that nine snapshot structures cover the complete conformational space of hemoglobin, ranging from T to R2 (the second relaxed quaternary structure) through R, with various relaxed intermediate forms between R and R2. Moreover, we find a previously unidentified intermediate conformer, between T and R, with an intermediate O2 affinity, sought by many research groups over a period of decades. These findings reveal a comprehensive picture of the equilibrium conformers and transition pathway for human hemoglobin. =20
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  • Computational design of a self-assembling symmetrical beta-propeller protein.

    Voet, Arnout R D   Noguchi, Hiroki   Addy, Christine   Simoncini, David   Terada, Daiki   Unzai, Satoru   Park, Sam-Yong   Zhang, Kam Y J   Tame, Jeremy R H  

    The modular structure of many protein families, such as beta-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical beta-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry. =20
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  • Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

    Kato, Daiki   Osakabe, Akihisa   Arimura, Yasuhiro   Mizukami, Yuka   Horikoshi, Naoki   Saikusa, Kazumi   Akashi, Satoko   Nishimura, Yoshifumi   Park, Sam-Yong   Nogami, Jumpei   Maehara, Kazumitsu   Ohkawa, Yasuyuki   Matsumoto, Atsushi   Kono, Hidetoshi   Inoue, Rintaro   Sugiyama, Masaaki   Kurumizaka, Hitoshi  

    Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate" overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate. Consequently, about 250 base pairs of DNA are left-handedly wrapped in three turns, without a linker DNA segment between the hexasome and octasome moieties. The overlapping dinucleosome structure may provide important information to understand how nucleosome repositioning occurs during the chromatin remodeling process.
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  • Crystal structure of the human centromeric nucleosome containing CENP-A

    Tachiwana, Hiroaki   Kagawa, Wataru   Shiga, Tatsuya   Osakabe, Akihisa   Miya, Yuta   Saito, Kengo   Hayashi-Takanaka, Yoko   Oda, Takashi   Sato, Mamoru   Park, Sam-Yong   Kimura, Hiroshi  

    In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment(1,2). Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A(3-12). Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate alpha-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the alpha N helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome(13). A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg 80 and Gly 81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.
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  • Role of domains within the autotransporter Hbp/Tsh

    Nishimura, Kaoru   Yoon, Young-Ho   Kurihara, Atsushi   Unzai, Satoru   Luirink, Joen   Park, Sam-Yong   Tame, Jeremy R. H.  

    The autotransporter Tsh (temperature-sensitive haemagglutinin) secreted by avian pathogenic Escherichia coli was reported in 1994 and the almost identical Hbp (haemoglobin protease) was discovered some years later in isolates from patients suffering from peritoneal abscesses. However, the function of the protein remains uncertain. The crystal structure of Hbp shows that the protein carries a serine protease domain (domain 1) and a small domain of 75 residues called domain 2 which is inserted into the long beta-helix characteristic of autotransporter passenger proteins. In this paper, domain 1 is shown to bind calcium, although metal ions binding to this site do not seem to regulate protease activity. Tsh has been reported to bind red cells and components of the extracellular matrix, but it is demonstrated that these properties are not a consequence of the presence of domain 2.
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  • A Novel Intein-Like Autoproteolytic Mechanism in Autotransporter Proteins

    Tajima, Nami   Kawai, Fumihiro   Park, Sam-Yong   Tame, Jeremy R. H.  

    Many virulence factors secreted by pathogenic Gram-negative bacteria are found to be members of the autotransporter protein family. These proteins share a common mechanism by which they exit the periplasm, involving the formation of a 12-stranded beta-barrel domain in the outer membrane. The role of this barrel in the secretion of the N-terminal passenger domain is controversial, and no model currently explains satisfactorily the entire body of experimental data. After secretion, some autotransporter barrels autoproteolytically cleave away the passenger, and one crystal structure is known for a barrel of this type in the postcleavage state. Hbp is an autotransporter of the self-cleaving type, which cuts the polypeptide between two absolutely conserved asparagine residues buried within the barrel lumen. Mutation of the first asparagine residue to isosteric aspartic acid prevents proteolysis. Here we present the crystal structure of a truncated Hbp mutant carrying the C-terminal residues of the passenger domain attached to the barrel. This model mimics the state of the protein immediately prior to separation of the passenger and barrel domains, and shows the role of residues in the so-called "linker" between the passenger and beta domains. This high-resolution membrane protein crystal structure also reveals the sites of many water molecules within the barrel. The cleavage mechanism shows similarities to those of inteins and some viral proteins, but with a novel means of promoting nucleophilic attack. (C) 2010 Elsevier Ltd. All rights reserved.
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  • Development of an X-ray fluorescence holographic measurement system for protein crystals

    Sato-Tomita, Ayana   Shibayama, Naoya   Happo, Naohisa   Kimura, Koji   Okabe, Takahiro   Matsushita, Tomohiro   Park, Sam-Yong   Sasaki, Yuji C.   Hayashi, Kouichi  

    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metal-loprotein samples are described. Human hemoglobin, an alpha(2)beta(2) tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A chi-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 x 6 x 3 mm(3)) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0 degrees-70 degrees. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules. Published by AIP Publishing.
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  • The nature of the TRAP-Anti-TRAP complex

    Watanabe, Masahiro   Heddle, Jonathan G.   Kikuchi, Kenichi   Unzai, Satoru   Akashi, Satoko   Park, Sam-Yong  

    Tryptophan biosynthesis is subject to exquisite control in species of Bacillus and has become one of the best-studied model systems in gene regulation. The protein TRAP (trp RNA-binding attenuation protein) predominantly forms a ring-shaped 11-mer, which binds cognate RNA in the presence of tryptophan to suppress expression of the trp operon. TRAP is itself regulated by the protein Anti-TRAP, which binds to TRAP and prevents RNA binding. To date, the nature of this interaction has proved elusive. Here, we describe mass spectrometry and analytical centrifugation studies of the complex, and 2 crystal structures of the TRAP-Anti-TRAP complex. These crystal structures, both refined to 3.2-angstrom resolution, show that Anti-TRAP binds to TRAP as a trimer, sterically blocking RNA binding. Mass spectrometry shows that 11-mer TRAP may bind up to 5 AT trimers, and an artificial 12-mer TRAP may bind 6. Both forms of TRAP make the same interactions with Anti-TRAP. Crystallization of wild-type TRAP with Anti-TRAP selectively pulls the 12-mer TRAP form out of solution, so the crystal structure of wild-type TRAP-Anti-TRAP complex reflects a minor species from a mixed population.
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  • Autotransporter passenger proteins: virulence factors with common structural themes

    Nishimura, Kaoru   Tajima, Nami   Yoon, Young-Ho   Park, Sam-Yong   Tame, Jeremy R. H.  

    Autotransporter proteins are virulence factors associated with a wide variety of diseases caused by pathogenic Gram-negative bacteria, and they play a variety of roles in pathogenesis including disabling host defences and mediating colonization. Pertactin, a key component of the whooping cough vaccine, is an autotransporter protein. A large sub-family of the autotransporters carries a trypsin-like protease domain, but these enzymes have different substrates and functions. The unique export process which defines the autotransporter family involves the polypeptide chain C-terminus forming a barrel structure in the bacterial outer membrane, but the role of this barrel in secreting of the N-terminal 'passenger' domain remains very unclear. There are now four published crystal structures of passenger proteins or fragments of them. We have compared these models to catalogue common features and to help predict the structures and functions of other autotransporter proteins such as SepA, which is involved in the pathogenicity of Shigella.
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  • The structural basis for an essential subunit interaction in influenza virus RNA polymerase

    Park, Sam-Yong   Yoshida, Hisashi   Ohki, Mio   Sugiyama, Kanako  

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  • Crystal structures of penicillin-binding proteins 4 and 5 from Haemophilus influenzae.

    Kawai, Fumihiro   Clarke, Thomas B   Roper, David I   Han, Gab-Jo   Hwang, Kwang Yeon   Unzai, Satoru   Obayashi, Eiji   Park, Sam-Yong   Tame, Jeremy R H  

    We have determined high-resolution apo crystal structures of two low molecular weight penicillin-binding proteins (PBPs), PBP4 and PBP5, from Haemophilus influenzae, one of the most frequently found pathogens in the upper respiratory tract of children. Novel beta-lactams with notable antimicrobial activity have been designed, and crystal structures of PBP4 complexed with ampicillin and two of the novel molecules have also been determined. Comparing the apo form with those of the complexes, we find that the drugs disturb the PBP4 structure and weaken X-ray diffraction, to very different extents. PBP4 has recently been shown to act as a sensor of the presence of penicillins in Pseudomonas aeruginosa, and our models offer a clue to the structural basis for this effect. Covalently attached penicillins press against a phenylalanine residue near the active site and disturb the deacylation step. The ready inhibition of PBP4 by beta-lactams compared to PBP5 also appears to be related to the weaker interactions holding key residues in a catalytically competent position. Copyright (c) 2009. Elsevier Ltd. All rights reserved.
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  • Dynamic allostery in the ring protein TRAP

    Heddle, Jonathan G.   Okajima, Tomoyuki   Scott, David J.   Akashi, Satoko   Park, Sam-Yong   Tame, Jeremy R. H.  

    We have discovered distinct, characteristic differences in the thermodynamic signatures of tryptophan binding by trp RNA-binding attenuation protein (TRAP) from two different bacterial species. The TRAP 11mer ring binds 11 molecules of tryptophan at symmetry-related sites. Tryptophan binding to Bacillus stearothermophilus TRAP is not cooperative, but isothermal titration calorimetry shows that filling the first tryptophan binding sites of Bacillus subtilis TRAP has a marked effect on the thermodynamics of subsequent ligand binding. We have identified a single, conservative amino acid replacement (Ile to Leu) in B. subtilis TRAP that abolishes this effect, and suggest the initial ligand binding causes a change throughout the wildtype protein ring. (c) 2007 Elsevier Ltd. All rights reserved.
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  • Structural basis for protein recognition by B30.2/SPRY domains.

    Woo, Jae-Sung   Suh, Hye-Young   Park, Sam-Yong   Oh, Byung-Ha  

    B30.2/SPRY domains are found in numerous proteins that cover a wide spectrum of biological functions, including regulation of cytokine signaling and innate retroviral restriction. Herein, we report the crystal structure of the B30.2/SPRY domain of a SPRY domain-containing SOCS box (SSB) protein, GUSTAVUS, complexed with a 20 amino acid peptide derived from the RNA helicase VASA, revealing how these domains recognize target proteins. The peptide-binding site is conformationally rigid and has a preformed pocket. The interaction between the pocket and the Asp-Ile-Asn-Asn-Asn-Asn sequence within the peptide accounts for the high-affinity binding between GUSTAVUS and VASA. This observation led to a facile identification of the Glu-Leu-Asn-Asn-Asn-Leu sequence as the recognition motif in a proapoptotic protein Par-4 for its interaction with a GUSTAVUS homolog, SSB-1. Ensuing analyses indicated that many B30.2/SPRY domains have a similar preformed pocket, which would allow them to bind multiple targets.
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