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Understanding the mechanism of the interaction between inorganic materials and peptides is important for the development of organic/inorganic hybrid materials. The titanium-binding peptide (TBP; Arg1-Lys2-Leu3-Pro4-Asp5-Ala6) has been reported to possess a high binding affinity to SiO2 as well as TiO2 surfaces. Here, we report the binding modes and mechanism of the TBP to SiO2 nanoparticles. To accomplish this objective, we analyzed the binding sites of the TBP to a SiO2 surface and the structure of the TBP bound to the SiO2 using solution NMR spectroscopy. Saturation transfer difference (STD) NMR analysis was performed to identify the TBP sites that interact with the SiO2 surface, and then Arg1 and Asp5 were identified to be in close contact with the SiO2 surface. The structure of the TBP bound to SiO2 was well defined, and the Arg1 and Asp5 side chains face in the same direction. The combination of these results validates that the guanidyl group of Arg1 and the carboxyl group of Asp5 interact electrostatically with the silanol groups SiO− and SiOH2+ on the SiO2 surface, respectively. The binding mode of TBP/SiO2 was found to be different from that of the TBP/TiO2 system, which has been previously reported. Saturation transfer difference (STD) NMR analysis was performed to identify the titanium-binding peptide (TBP) sites that interact with the SiO2 nanoparticle surface, and then Arg1 and Asp5 were identified to be in close contact with the surface. The structure of the TBP bound to SiO2 determined by the NOESY measurement was well defined, and the Arg1 and Asp5 side chains face in the same direction. These results validates that the NH2+ of Arg1 and the COO− of Asp5 interact electrostatically with the SiO− and SiOH2+ on the SiO2 surface, respectively.

The silk fibroin stored in the silk gland of the Bombyx mori silkworm, called "liquid silk", is spun out and converted into the silk fiber with extremely high strength and high toughness. Therefore it is important to determine the silk structure before spinning called Silk I at an atomic level to clarify the fiber formation mechanism. We proposed the repeated type II β-turn structure as Silk I in the solid state with the model peptide (AG)15 and several solid state NMR techniques previously. In this paper, the solution structure of native "liquid silk" was determined with solution NMR, especially for tandem repeated sequences with (GAGXGA)n (X = S, Y, V) and GAASGA motifs in the B. mori silk fibroin. The assignment of the (13)C, (15)N, and (1)H solution NMR spectra for the repetitive sequence motifs was achieved, and the chemical shifts were obtained. The program, TALOS-N, to predict the backbone torsion angles from the chemical shifts of proteins was applied to these motifs with (13)Cα, (13)Cβ, (13)CO, (1)Hα, (1)HN, and (15)N chemical shifts. The twenty-five best matches of torsion angles (ϕ, φ) were well populated and mainly fell into the regions for typical type II β-turn structures in the (ϕ, φ) map for the GAGXGA (X = S, Y, V) motifs. In contrast, (ϕ, φ) plots for motif GAASGA were scattered, indicating that the motif is in a disordered structure. Furthermore, inter-residue HN-Hα NOE cross peaks between i-th and (i+2)th residues in GAGXGA (X = S, Y, V) motifs were observed, supporting the repeated type II β-turn structure. Thus, we could show the presence of the repeated type II β-turn structure in "liquid silk".

Saturation transfer difference (STD) NMR spectroscopy is a powerful method for detecting and characterizing ligand-receptor interactions. In this study, the STD method was used to characterize the interactions of a Ti-binding peptide (TBP:RKLPDA) with TiO2 nanoparticles. The water peak in the NMR spectrum was selectively saturated, and the STD amplitudes for TBP were observed in the presence of TiO2, demonstrating that the side chains of the N-terminal residues Arg1 and Lys2 exhibit the strongest saturation transfer effect from water molecules; i.e., the two N-terminal residues are in contact with the TiO2 surface. The relaxation rate in the rotating frame, R1ρ, was observed to be high at the N-terminal residues; R1ρ decelerated toward the C-terminus, indicating that the N-terminal residues serve as anchors on the TiO2 surface and that the TBP motion bound to TiO2 particles is modeled as a wobble-in-cone with a fairly flexible C-terminus. The dissociation constant Kd of the TBP-TiO2 nanoparticle complex was 4.9 ± 1.8 mM, as estimated from the STD experiments and R1ρ measurements. The combination of these results and the negative zeta potential of the TiO2 surface validate that both the positively charged guanidyl group of Arg1 and amino group of Lys2 play key roles in interaction with the TiO2 surface by electrostatic force.

We determined the three-dimensional structure of the PHD finger of the rice Siz/PIAS-type SUMO ligase, OsSiz1, by NMR spectroscopy and investigated binding ability for a variety of methylated histone H3 tails, showing that OsSiz1–PHD primarily recognizes dimethylated Arg2 of the histone H3 and that methylations at Arg2 and Lys4 reveal synergy effect on binding to OsSiz1–PHD. The K4 cage of OsSiz1–PHD for trimethylated Lys4 of H3K4me3 was similar to that of the BPTF–PHD finger, while the R2 pocket for Arg2 was different. It is intriguing that the PHD module of Siz/PIAS plays an important role, with collaboration with the DNA binding domain SAP, in gene regulation through SUMOylation of a variety of effectors associated with the methylated arginine-riched chromatin domains.

The small ubiquitin-related modifier (SUMO) is a ubiquitin-like post-translational modifier that alters the localization, activity, or stability of many proteins. In the sumoylation process, an activated SUMO is transferred from SUMO-activating enzyme E1 complex (SAE1/SAE2) to SUMO-conjugating enzyme E2 (Ubc9). Among the multiple domains in E1, a C-terminal ubiquitin fold domain (UFD) of SAE2 shows high affinity for Ubc9, implying that UFD will be functionally important. We report NMR chemical shift assignments of UFD in SAE2 from rice. Almost all the resonances of UFD were assigned uniquely, representing a single conformation of UFD in solution. This is a contrast to the previous report for the corresponding UFD of human SAE2 which shows two conformational states. The secondary structure prediction of UFD in rice SAE2 shows the similar overall structure to the crystal structures of UFD in other E1 proteins such as SAE2 of human and yeast, ubiquitin-activating enzyme of yeast, and NEDD8-activating enzyme E1 catalytic subunit of human. Concomitantly, differences in the length of helices, strands, and loops are observed, particularly in the binding region to E2, supposing the variation in the UFD-E2 binding mode which may play a critical role in determining E1-E2 specificity.

The monomeric Alzheimer's beta amyloid peptide, Abeta, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary-structure contents for the disordered state: 70% random, 25% beta-structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25-residue segment (residues 12-36) of Abeta in explicit water and obtained the conformational ensemble over a wide temperature range. The secondary-structure contents calculated from the conformational ensemble at 300 degrees K reproduced the experimental secondary-structure contents. The constructed free-energy landscape at 300 degrees K was not plain but rugged with five clearly distinguishable clusters, and each cluster had its own characteristic tertiary structure: a helix-structural cluster, two beta-structural clusters, and two random-structural clusters. This indicates that the contribution from the five individual clusters determines the secondary-structure contents experimentally measured. The helical cluster had a similarity with a stable helical structure for monomeric Abeta in 2,2,2-trifluoroethanol (TFE)/water determined by an NMR experiment: The positions of helices in the helical cluster were the same as those in the NMR structure, and the residue-residue contact patterns were also similar with those of the NMR structure. The cluster-cluster separation in the conformational space indicates that free-energy barriers separate the clusters at 300 degrees K. The two beta-structural clusters were characterized by different strand-strand hydrogen-bond (H-bond) patterns, suggesting that the free-energy barrier between the two clusters is due to the H-bond rearrangements.

Multicanonical molecular dynamics (McMD) simulations were performed for a 40-residue protein, the C-terminal domain of H-NS, having α and β secondary-structure elements, starting the simulation from a disordered structure, and free-energy landscapes were obtained from 280 K to 700 K. Cooperative formation of α and β structures provided native-topology structures with the smallest backbone rmsd, 3.27 A, to the NMR structure, although such structures were minority even when a knowledge-based force field was applied to the backbone dihedral potentials. Current study suggests that our McMD simulation could sample many different structures including the native-topology ones, and that the force field issue should be critical.

High-speed counter-current chromatography (HSCCC) using the three-phase solvent system n-hexane-methyl acetate-acetonitrile-water at a volume ratio of 4:4:3:4 was applied to the comprehensive separation of secondary metabolites in several natural product extracts. A wide variety of secondary metabolites in each natural product was effectively extracted with the three-phase solvent system, and the filtered extract was directly submitted to the HSCCC separation using the same three-phase system. In the HSCCC profiles of crude natural drugs listed in the Japanese Pharmacopoeia, several physiologically active compounds were clearly separated from other components in the extracts. The HSCCC profiles of several tea products, each manufactured by a different process, clearly showed their compositional difference in main compounds such as catechins, caffeine, and pigments. These HSCCC profiles also provide useful information about hydrophobic diversity of whole components present in each natural product.

Aqueous–aqueous two-phase (AATP) systems composed of polyethylene glycol (PEG) (molecular mass, Mr:1000–8000) and dextran (Mr:40,000) were evaluated for purification of maltose binding protein tagged-histone deacetylase (MBP-HDAC) by counter-current chromatography (CCC). CCC purification of an MBP-HDAC from Escherichia coli cell-lysate was successfully demonstrated with a 7.0% PEG 3350–10% dextran T40 system containing 10 mM potassium phosphate buffer at pH 9.0. After CCC purification, both polymers in the CCC fractions were easily removed by ultrafiltration in a short period of time. The collected fractions containing target protein were analyzed by an HPLC-based in vitro assay as well as sodium dodecyl sulfate polyacrylamide gel electrophoresis. MBP tag was digested from fusion HDAC during the CCC separation and native HDAC was purified by one-step operation with well preserved deacetyl enzyme activity.

New aqueous–aqueous two-phase systems composed of relatively low molecular weight polymers such as polyethylene glycol (PEG) (Mr: 1000–4000) and dextran (Mr: 10,000 and 40,000) were evaluated for purification of proteins by counter-current chromatography (CCC). The compositions of aqueous two-phase systems were optimized by measuring parameters such as viscosity and volume ratio between the two phases. CCC purification of a glucosyltransferase (GTF) from Streptococcus mutans (SM) cell-lysate was successfully demonstrated with a 7.5% PEG 3350–10% dextran T40 system containing 10 mM potassium phosphate buffer at pH 9.0. After CCC purification, both PEG and dextran contained in the CCC fractions were easily removed by ultrafiltration in a short period of time. The fractionated column contents containing GTF were analyzed by enzymatic activity as well as sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. The recovery of the enzyme from CCC fraction was over 95% as estimated by enzymatic activities.

In Saccharomyces cerevisiae , a-cell-specific genes are repressed in MAT α cells by α2/Mcm1, acting in concert with the Ssn6-Tup1 corepressors and the Isw2 chromatin remodeling complex, and nucleosome positioning has been proposed as one mechanism of repression. However, prior studies showed that nucleosome positioning is not essential for repression by α2/Mcm1 in artificial reporter plasmids, and the importance of the nucleosome positioning remains questionable. We have tested the function of positioned nucleosomes through alteration of genomic chromatin at the a -cell-specific gene BAR1 . We report here that a positioned nucleosome in the BAR1 promoter is disrupted in cis by the insertion of diverse DNA sequences such as poly(dA) · poly(dT) and poly(dC-dG) · poly(dC-dG), leading to inappropriate partial derepression of BAR1 . Also, we show that isw2 mutation causes loss of nucleosome positioning in BAR1 in MAT α cells as well as partial disruption of repression. Thus, nucleosome positioning is required for full repression, but loss of nucleosome positioning is not sufficient to relieve repression completely. Even though disruption of nucleosome positioning by the cis - and trans -acting modulators of chromatin has a modest effect on the level of transcription, it causes significant degradation of the α-mating pheromone in MAT α cells, thereby affecting its cell type identity. Our results illustrate a useful paradigm for analysis of chromatin structural effects at genomic loci.

High-speed counter-current chromatography (HSCCC) using the type-J coil planet centrifuge was applied to compositional analysis of tea catechins and separation of other food-related polyphenols. The HSCCC separation of nine different standard compounds and those from extracts of commercial tea leaves was performed with a two-phase solvent system composed of tert-butyl methyl ether-acetonitrile-0.1% aqueous trifluoroacetic acid (TFA) (2:2:3, v/v/v) by eluting the upper organic phase at a flow rate of 2 ml/min. The main compounds in the extract of non-fermented green tea were found to be monomeric catechins, their galloylated esters and caffeine. In addition to these compounds, oxidized pigments, such as hydrophobic theaflavins (TFs) and polar thearubigins (TRs) were also separated and detected from the extracts of semi-fermented oolong tea and fermented black tea. Furthermore, several food-related polyphenols, such as condensed catechin oligomers (procyanidins), phenolic acids and flavonol glycosides were clearly separated under the same HSCCC condition. These separation profiles of HSCCC provide useful information about the hydrophobic diversity of these bioactive polyphenols present in various types of teas and food products.

Four decades have passed since linker histone H1 was discovered. In spite of many efforts, structural and functional roles of linker histone in the chromatin formation still remain to be elucidated. Notable studies related to linker histones have been reported recently, such as findings of specific roles in cell division, interaction modes of its globular domain with DNA and higher order structure of chromatin. The recent advance will be reviewed.

A new technique, stationary phase volume controlled high‐speed counter‐current chromatography (HSCCC), was used to determine the octanol‐water partition coefficients (P o/w) of catechins and their isomers, oligomers, and other organic compounds. The stationary phase volume in the CCC column was effectively controlled under hydrodynamic equilibrium system. The log P o/w values ranging from −1.35 to +3.60 were measured within 21 min using this new HSCCC technology. The linear relationship (correlation coefficient value, r=0.993) was observed between log P o/w values obtained by the shake‐flask method and those values by the HSCCC method. In this technique, it is possible to inject multiple samples successively into the CCC column at short intervals to measure their retention times without renewing the stationary phase volume.

Polyphenols derived from hop (Humulus lupulus L.) bract region (HBP) can be used as food materials, thereby preventing dental caries. Chemical details of the active substances need to be elucidated. The polyphenols from hop bract (HBP) region were purified by countercurrent chromatography (CCC). The fractions were analyzed by high‐performance size‐exclusion chromatography (HPSEC) and reversed phase high‐performance liquid chromatography (RP‐HPLC). From HBP fractions by HPSEC, some low‐molecular‐ weight polyphenols (glycosides of flavonoids, catechins, and proanthocyanidins) were identified by RP‐HPLC. However, a very hydrophilic fraction was found to have the most potent cavity‐preventive activity, but it showed no peak in its RP‐HPLC chromatogram (absence of small polyphenols). HPSEC analysis showed that the major components of this fraction were high‐molecular weight substances, which were supposed to be proanthocyanidins, consisting of approximately 22 catechin units in its structure.

Two new triterpenes named 7-oxodihydrokarounitriol (1) and 7,11-dioxodihydrokarounidiol (2), and one known triterpene, 7-oxodihydrokarounidiol (3), were isolated from the unsaponifiable matter of the seeds of Trichosanthes cucumeroides. The structures of 1 and 2 were elucidated as (3alpha, 11beta, 13alpha, 14beta, 20alpha)-3,11,29-trihydroxy-13-methyl-26-norolean-8-ene-7-one, and (3alpha,13alpha,14beta,20alpha)-3,29-dihydroxy-13-methyl-26-norolean-8-ene-7,11-dione on the basis of extensive NMR (1H, 13C, 1H-1H COSY, DEPT, HMQC, HMBC and NOESY) and MS studies.

A liquid chromatographic method with fluorescence detection coupled with a solid-phase extraction was applied to the rapid determination of epoxyeicosatrienoic acids (EETs) in the rabbit renal artery. The EETs were extracted with an acetonitrile from renal artery homogenate and concentrated by a solid-phase extraction method. The concentrated EETs were reacted directly with a 6, 7-dimethoxy-1-methyl-2 (1H)-quinoxalinone-3-propionyl-carboxylic acid (DMEQ) hydrazide and separated by a reversed-phase HPLC with eluting a combination of a step-wise and a gradient of a mixture of methanol and water. The content of EETs in the renal arteries was significantly greater in the 0.5% cholesterol fed rabbits than in control rabbits. It is suggested that hyperchlesterolemia increases the production of EETs in the rabbit renal artery.

Human mitochondrial (mt) tRNALys has a taurine-containing modified uridine, 5-taurinomethyl-2-thiouridine (τm5s2U), at its anticodon wobble position. We previously found that the mt tRNALys, carrying the A8344G mutation from cells of patients with myoclonus epilepsy associated with ragged-red fibers (MERRF), lacks the τm5s2U modification. Here we describe the identification and characterization of a tRNA-modifying enzyme MTU1 (mitochondrial tRNA-specific 2-thiouridylase 1) that is responsible for the 2-thiolation of the wobble position in human and yeast mt tRNAs. Disruption of the yeast MTU1 gene eliminated the 2-thio modification of mt tRNAs and impaired mitochondrial protein synthesis, which led to reduced respiratory activity. Furthermore, when MTO1 or MSS1, which are responsible for the C5 substituent of the modified uridine, was disrupted along with MTU1, a much more severe reduction in mitochondrial activity was observed. Thus, the C5 and 2-thio modifications act synergistically in promoting efficient cognate codon decoding. Partial inactivation of MTU1 in HeLa cells by small interference RNA also reduced their oxygen consumption and resulted in mitochondria with defective membrane potentials, which are similar phenotypic features observed in MERRF., This work was supported by grants-in-aid for scientific research on priority areas from the Ministry of Education, Science, Sports, and Culture of Japan, and by a grant from the New Energy and Industrial Technology Development Organization (to T. S.).

高速向流クロマトグラフィー（HSCCC）により，鶏卵卵黄中のホスファチジルコリン（PC），ホスファチジルエタノールアミン（PE）の大量分離を行った．各種有機溶媒と水系とから構成される34種類の二相，三相系について，各相の比を求めるとともに，二相系では上層と下層間，三相系では上層と中間層間におけるPC，PEのミセルの形成状態や分配係数を求めた．その結果，酢酸メチル，n -ヘキサン，アセトニトリル，水から構成される二相又は三相系では，PEはミセルを形成した．クロロホルム : n -ヘプタン : n -ブタノール : メタノール : 60％ 酢酸＝2 : 3 : 2 : 3 : 5 の二相系の上層を固定相，下層を移動相に用いて（流量: 1 ml/min），鶏卵卵黄の高速向流クロマトグラフィー（HSCCC）分離を試みた．PC，PEのリン脂質は，単純脂質から完全に相互分離が可能であった．HSCCC画分中のPC，PE，単純脂質は薄層クロマトグラフィーにより確認した．

A member of the PIAS (protein inhibitor of activated STAT) family of proteins, PIAS1, have been reported to serve as an E3-type SUMO ligase for tumor suppressor p53 and its own. It also was proposed that the N-terminal domain of PIAS1 interacts with DNA as well as p53. Extensive biochemical studies have been devoted recently to understand sumoylations and its biological implications, whereas the structural aspects of the PIAS family and the mechanism of its interactions with various factors are less well known to date. In this study, the three-dimensional structure of the N-terminal domain (residues 1-65) of SUMO ligase PIAS1 was determined by NMR spectroscopy. The structure revealed a unique four-helix bundle with a topology of an up-down-extended loop-down-up, a part of which the helix-extended loop-helix represented the SAP (SAF-A/B, Acinus, and PIAS) motif. Thus, this N-terminal domain may be referred to as a four-helix SAP domain. The glutathione S-transferase pull-down assay demonstrated that this domain possesses a binding ability to tumor suppressor p53, a target protein for sumoylation by PIAS1, whereas gel mobility assays showed that it has a strong affinity toward A/T-rich DNA. An NMR analysis of the four-helix SAP domain complexed with the 16-bp-long DNA demonstrated that one end of the four-helix bundle is the binding site and may fit into the minor groove of DNA. The three-dimensional structure and its binding duality are discussed in conjunction with the biological functions of PIAS1 as a SUMO ligase.

Glucosyltransferase (GTF), a cariogenic factor of Streptococcus sobrinus (SS), was extracted from a large quantity of cell culture medium by batch extraction with aqueous polymer two‐phase systems (APTPs). The small quantity of the extract was further purified by countercurrent chromatography (CCC) using polyethylene glycol (PEG) 8000‐dextran T500 system at pH 9.2, by eluting the impurities with the upper mobile phase at 1.0 mL/min. After the elution, the GTF still remaining in the dextran‐rich lower stationary phase was collected. The GTF fractions were subjected to hydroxyapatite chromatography to eliminate polymers, such as PEG 8000 and dextran T500. Purified fractions were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) and GTF enzyme activity, which rose over 270 fold from that in the original culture medium.

Alcohol dehydrogenase (ADH) was extracted from a crude bovine liver homogenate by dye-ligand affinity counter-current chromatography (CCC) using a cross-axis coil planet centrifuge (x-axis CPC). The purification was performed using two types of polymer phase systems composed of 4.4% polyethylene glycol (PEG) 8000-7.0% dextran T500-0.1 M potassium phosphate buffers and 16% PEG 1000-12.5% potassium phosphate buffers, both containing a procion red dye as an affinity ligand at various pH values. The best purification was achieved using the PEG 1000-potassium phosphate system at pH 7.3 containing 0.05% procion red as a ligand. The upper PEG-rich phase containing procion red was used as the stationary phase and a crude bovine liver homogenate was eluted with the potassium phosphate-rich lower phase at 0.5 ml/min. After elution of bovine liver proteins in the homogenate, ADH still retained in the stationary phase was collected from the column by eluting with the PEG 1000-rich upper phase. Collected fractions were analyzed by ADH enzymatic activity and by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) to detect contaminant proteins in the ADH fractions. The ADH was purified directly from crude bovine liver extract within 6h with minimum loss of its enzymatic activity.

向流クロマトグラフィー（CCC）によるタンパク質の分離用の新規水性二相溶媒系を探索した．卵白中からovomucinの選択的分離が15％ ポリエチレングリコール（PEG）1540-15％dextran T10-100 mMリン酸カリウム緩衝液（pH 7.0）二相系の上層を固定相，下層を移動相とする向流クロマトグラフィーにより達成された．分配係数の小さなovalbumin，conalbumin，lysozymeはdextran-richな下層の移動相によりカラムから溶出された．分配係数の大きなovomucinはPEG-richな上層の固定相に親和性が高いのでカラムから溶出されなかった．他の3種類のタンパク質を溶出後，固定相液体を押し出すことによってovomucinをカラムから回収できた．精製後，PEG 1540，dextran T10は限外ろ過によって容易に短時間で除去できた．また，CCCにより精製されたタンパク質はドデシル硫酸ナトリウム（SDS）-PAGEによって確認した．

11種類のカテキン類について，オクタデシルシリル化シリカ（ODS）モノリスカラムを用いる高速液体クロマトグラフィー（HPLC）と，t -ブチルメチルエーテル/アセトニトリル/0.1％ トリフルオロ酢酸（2 : 2 : 3）の二相溶媒系を用いる高速向流クロマトグラフィー（HSCCC）による逆相分配クロマトグラフィー分離をそれぞれ行った．実験に供したカテキン類の中でも，エピカテキンの三量体であるプロシアニジンC1（PC1）は，オクタノール/水二相溶媒系における分配係数P 及びlog P 値が最も小さな親水性化合物であるにもかかわらず，逆相HPLCのODSカラムに強く保持された．一方，逆相HSCCCにおけるカテキン類の溶出順序は，各化合物のlog P 値によく対応し，log P 値が減少するほどクロマトグラム上の保持時間も短くなった．すなわち，PC1のような最も親水的なオリゴマー成分は，逆相HSCCCのカラムから一番最初に溶出することが確認できた．

Hho1p is assumed to serve as a linker histone in Saccharomyces cerevisiae and, notably, it possesses two putative globular domains, designated HD1 (residues 41-118) and HD2 (residues 171-252), that are homologous to histone H5 from chicken erythrocytes. We have determined the three-dimensional structure of globular domain HD1 with high precision by heteronuclear magnetic resonance spectroscopy. The structure had a winged helix-turn-helix motif composed of an alphabetaalphaalphabetabeta fold and closely resembled the structure of the globular domain of histone H5. Interestingly, the second globular domain, HD2, in Hho1p was unstructured under physiological conditions. Gel mobility assay demonstrated that Hho1p preferentially binds to supercoiled DNA over linearized DNA. Furthermore, NMR analysis of the complex of a deletion mutant protein (residues 1-118) of Hho1p with a linear DNA duplex revealed that four regions within the globular domain HD1 are involved in the DNA binding. The above results suggested that Hho1p possesses properties similar to those of linker histones in higher eukaryotes in terms of the structure and binding preference towards supercoiled DNA.

Single-strand DNA binding protein (SSB) from Escherichia coli lysate was purified by counter-current chromatography (CCC) using the ammonium sulfate precipitation method in a coiled column. About 5 ml of E. coli lysate was separated by CCC using a polymer phase system composed of 16% (w/w) polyethylene glycol (PEG) 1000 and 17% (w/w) ammonium sulfate aqueous polymer two-phase solvent system. The precipitation of proteins in the lysate took place in the CCC column, and the SSB protein was eluted in the fraction 51-56. Many other impurities were either eluted immediately after the solvent front or precipitated in the column. The identities of the proteins in the fractions and in the precipitate were confirmed by SDS-polyacrylamide gel electrophoresis with Coomassie Brilliant Blue staining.

Catechin oligomers with different degrees of polymerization were separated from apple condensed tannins (ACTs) by countercurrent chromatography using a type‐J multilayer coil planet centrifuge. Partition coefficient values for oligomers up to pentamers of catechin and/or epicatechin were determined on hydrophilic two‐ or three‐phase solvent systems. The best separation was achieved using a three‐phase solvent system composed of hexane/methyl acetate/acetonitrile/water at a volume ratio of 1/1/1/1, which formed three layers. After the elution of monomers, dimers, trimers, and a part of tetramers using the middle phase, methyl acetate was used as a mobile phase to facilitate elution of the oligomers from tetramers to decamers. These oligomers eluted from the column according to their degree of polymerization. The higher polymerized oligomers over 11‐mers were collected from the column with the elution by the lower phase. The masses of the fractionated oligomers were determined by matrix‐assisted la...

Polysaccharides were purified from a high molecular weight complex of Achyranthes bidentata Bl. (Fam. Amaranthaceae) root by high speed countercurrent chromatography (HSCCC) using a cross‐axis coil planet centrifuge (X‐axis CPC). The purification was performed with an aqueous polymer two‐phase system composed of 12.5% (w/w) polyethylene glycol (PEG) 1000, 8% (w/w) potassium dihydrogen phosphate, and 8% (w/w) dipotassium hydrogen phosphate buffer at pH 6.8. The preparative separation of the crude sample (2 g) was successfully performed, yielding 1.1 g of polysaccharides at high purity.

pH-peak focusing counter-current chromatography (CCC) was applied to the purification of lactic acid dehydrogenase (LDH) from a crude bovine heart extract using a cross-axis coil planet centrifuge (CPC). The experiment was performed with two sets of polymer phase systems composed of 16% (w/w) polyethylene glycol (PEG) 1000-12.5% (w/w) potassium phosphate buffer and 15% (w/w) PEG 1540-15% (w/w) ammonium sulfate each at various pH values. The best result was achieved from the PEG 1540-ammonium sulfate polymer phase system by adding a retainer (10 mM acetic acid) to the upper stationary phase and an eluter (100 mM sodium hydroxide) to the lower mobile phase. At a flow-rate of 0.5 ml/min, LDH was eluted as a sharp peak which was well resolved from other proteins. Collected fractions were analyzed by the LDH enzymatic activity and by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis to detect contaminated proteins. LDH was purified directly from crude bovine heart extract in a concentrated state.

Novel pulse sequences incorporating the double pulsed field gradient spin-echo technique are presented that have particular use in identifying macromolecular bound water. The use of these sequences is illustrated using ribonuclease T1. Five amide protons cross-relaxing with bound water protons were observed. Examination of the crystal structure revealed that all of these amide protons donate hydrogen bonds or are in close proximity to water molecules with very low temperature factors, indicating that these amide protons are highly correlated with the bound water molecules. This method rapidly provides reliable information for characterizing macromolecular bound water molecules. Copyright © 2002 John Wiley & Sons, Ltd.

Chicken egg white proteins were fractionated by high-speed counter-current chromatography (HSCCC) using a cross-axis coil planet centrifuge (X-axis CPC). The separation was performed with an aqueous polymer two-phase system composed of 16% polyethylene glycol (PEG) 1000 and 12.5% potassium phosphate buffer at different pH of 6.8, 8.0, and 9.2. From 20 g of the crude egg white solution, the best separation was achieved with a polymer phase system at pH 8.0 by eluting the lower phase at 1.0 mL/min. After the sequential elution of ovotransferrin, ovalbumin, and lysozyme from the column, ovomucin still retained in the column was eluted in the reverse direction with upper PEG-rich phase. All four proteins in the CCC fractions were identified by SDS gel electrophoresis with Coomassie brilliant blue staining.

The type XL cross-axis coil planet centrifuge (CPC) was successfully utilized for purification of cholinesterase (ChE) from human serum by countercurrent chromatography (CCC). Aqueous-aqueous polymer phase systems composed of polyethylene glycol-potassium phosphate buffers were tested at various pHs, ranging from 6.8 to 9.2 for the distribution ratios (D) of ChE, human serum albumin, α- and γ-globulins. The CCC separation was performed with optimized polymer phase systems in two different coiled columns. The best purification was achieved with 16.0% PEG 600–12.5% potassium phosphate at pH 9.2, by eluting the lower phase at 0.5 mL/min through the small capacity column in which ChE was purified directly from human serum within 2h. The ChE fractions confirmed by the enzymatic activity were free of serum proteins by SDS PAGE analysis.

l-Histidine Cu(II) complex bound to DNA showed broad EPR signals characteristic of the aggregated Cu(II) species, which could be observed even when the molar ratio of l-histidine to Cu(II) ion was smaller than unity. The signal for the DNA fibers changed with the orientation of the fibers in the static magnetic field. Based on these results, the signal was assigned to a mono-histidine Cu(II) complex stereospecifically aggregated in a groove or along a phosphodiester chain of the double helical DNA. In contrast to the l-histidine complex, the d-histidine complex bound to DNA did not show such broad signals and the observed spectra for the complex on B-form DNA fibers at −150 °C were simulated assuming that the g‖ axis of the mono-d-histidine complex tilts by about 55° from the DNA-fiber axis. Addition of some deoxy-nucleotides, but not deoxy-nucleosides, to a solution of a mono-histidine complex resulted in the formation of a dinuclear ternary complex with different structures for l- or d-histidine, suggesting the possibility that the stereospecific aggregation of the l-histidine complex on a double helical DNA was mediated by the phosphodiester backbones.

The Escherichia coli yhhP gene was predicted to encode a small hypothetical protein of 81 amino acids, the cellular function of which is not known. To gain insight into the function of this uncharacterized YhhP protein, genetic and biochemical studies were done. We first tried to express and purify the YhhP protein to prepare an anti-YhhP antiserum. Western blotting showed that the hypothetical yhhP gene is indeed transcribed and translated as a minor cytoplasmic protein. YhhP-deficient (delta yhhP) cells formed colonies poorly on a rich medium (e.g., Luria-Bertani medium) containing a relatively low concentration of NaCl, while they can grow normally either in LB containing 3% NaCl or in a synthetic medium (e.g., M9-glucose). During exponential growth in rich medium, an early step of cell division was inhibited in delta yhhP cells, forming filaments. For the YhhP-deficient filamentous cells, the FtsZ-ring formation was analyzed with immunofluorescence microscopy. The FtsZ-ring formation did not occur normally in the delta yhhP filaments, although the filamentous cells contained the FtsZ protein at a certain level comparable to that in the wild-type cells. The ftsZ gene was found to function as a multicopy suppressor of the delta yhhP mutant. Another multicopy suppressor gene was identified as the dksA gene. Provided that either the ftsZ or dksA gene was introduced into the mutant cells with its multicopy state, the resulting transformants were capable of growing in rich medium, formed wild-type short rods. These results are discussed with regard to the presumed function of this ubiquitous protein.

The DNA binding domain of H-NS protein was studied with various N-terminal deletion mutant proteins and identified by gel retardation assay and heteronuclear 2D- and 3D-NMR spectroscopies. It was shown from gel retardation assay that DNA binding affinity of the mutant proteins relative to that of native H-NS falls in the range from 1/6 to 1/25 for H-NS(60-137), H-NS(70-137) and H-NS(80-137), whereas it was much weaker for H-NS(91-137). Thus, the DNA binding domain was defined to be the region from residue A80 to the C-terminus. Sequential nuclear Overhauser effect (NOE) connectivities and those of medium ranges revealed that the region of residues Q60-R93 in mutant protein H-NS(60-137) forms a long stretch of disordered, flexible chain, and also showed that the structure of the C-terminal region (residues A95-Q137) in mutant H-NS(60-137) was nearly identical to that of H-NS(91-137). 1H and 15N chemical shift perturbations induced by complex formation of H-NS(60-137) with an oligonucleotide duplex 14-mer demonstrated that two loop regions, i.e. residues A80-K96 and T110-A117, play an essential role in DNA binding.

The zinc finger protein Rme1p is a negative regulator of the meiotic activator IME1 in Saccharomyces cerevisiae . Prior studies have shown that Rme1p binds in vitro to a site near nt -2030 in the IME1 upstream region, but a genomic mutation in that site has little effect on repression of IME1 . To identify Rme1p binding sites in vivo , we have examined the binding of Rme1p to genomic sites through in vivo footprinting. We show that Rme1p binds to two sites in the IME1 upstream region, near nt -1950 and -2030. Mutations in both binding sites abolish repression of chromosomal IME1 by Rme1p, whereas a mutation in either single site causes partial derepression. Therefore, both Rme1p binding sites are essential for repression of IME1 . Prior studies have shown that repression by Rme1p depends upon RGR1 and SIN4 , which specify RNA polymerase II mediator subunits that are required for normal nucleosome density. We find that RGR1 and SIN4 are not simply required for Rme1p to bind to DNA in vivo . These results suggest that Rme1p functions directly as a repressor of IME1 and that Rgr1p and Sin4p are required for DNA-bound Rme1p to exert repression.

The yeast repressor Rme1p acts from distant binding sites to block transcription of the chromosomal IME1 gene. Rme1p can also repress the heterologous CYC1 promoter when Rme1p binding sites are placed 250–300 bp upstream of CYC1 transcriptional activator binding sites (UAS1 and UAS2). Here, in vivo footprinting studies indicate that Rme1p acts over this distance by preventing the binding of the CYC1 transcriptional activators to UAS1 and UAS2. Inhibition of activator binding by Rme1p has the same genetic requirements as repression: both depend upon sequences flanking the Rme1p binding sites and upon Rgr1p and Sin4p, two subunits of the RNA polymerase II-associated Mediator complex that are required for normal nucleosome density. Thus Rme1p may alter chromatin to prevent binding of transcriptional activators to distant DNA sequences.

ESR data have been obtained on some hydrated copper(I)) and copper(II) amino acid complexes bound to highly oriented DNA fibers. The complexes bind with random orientation on A-form DNA, while some of them bind stereospecifically on B-form DNA. The hydrated copper(II) ions bind to at least two different sites on B-form DNA at room temperature; one site is so mobile that the orientations of the complex fluctuate dynamically, while the other site fixes the orientation of the bound ions such that the angle between the g axis and the DNA helical axes becomes ca. 55°. The g axis of glycine complex on B-form DNA at room temperature is aligned parallel to the fiber axis with large fluctuations in the orientation. L-serine and L-threonine fix the g axes of some of the complexes parallel to the fiber axes, indicating that the hydroxyl groups work as linkers to bind the complexes stereospecifically to B-form DNA. The hydroxyl groups in D-isomers do not work as L-isomers.

We have investigated the thermodynamics and specificity of DNA triplex formation with isothermal titration calorimetry (ITC). The triplex formation between a 23-mer double-stranded homopurine−homopyrimidine and a 15-mer single-stranded homopyrimidine oligonucleotide forming T·AT and C+·GC triads at pH 4.8 is driven by a large negative calorimetric enthalpy change, ΔHcal, of the order of −80 kcal/mol. ΔHcal is strongly temperature dependent, yielding a heat capacity change, ΔCp, of about −1 (kcal/mol)K-1. The equilibrium association constant, K, obtained from the titration curve is about 9 × 107 M-1 at 25 °C (binding free energy change, ΔG, is about −11 kcal/mol). Thus, the triplex formation is accompanied by a negative entropy change (ΔS = −245 (cal/mol)K-1 at 25 °C). We found that K is insensitive to temperature near room temperature, leading to an apparently small van't Hoff enthalpy change (ΔHvH), in sharp contrast with the large negative ΔHcal. Together, the analyses of the observed temperature depend...

To understand the roles of the 5'-flanking region of the recognition sites in binding specificity and the affinity of integration host factor (IHF), a variety of DNA fragments with a 13-bp consensus sequence, 5'-WATCAAN4TTR-3'[Friedman, Cell, 55, 545 (1988)], but with different 5'-flanking sequences were investigated by gel retardation and methylation interference assays. It has been well-established that the putative A/T rich element distal from the 5'-end of the consensus made a significant contributions to the binding of IHF. However, many of the DNA fragments used here revealed specific binding to IHF without such an A/T element. Several bases neighboring to the 5'-end of the consensus sequence had significant effects on the binding specificity as well as its affinity, and these results indicate that the sequence-directed bendability of the flanking region plays an important role in the specific recognition by IHF.

The effect of base composition in the central region of polypurine.polypyrimidine (Pur.Pyr) tracts on the formation of intramolecular DNA triplexes in plasmids was examined using chemical probes (diethyl pyrocarbonate and OsO4), and two-dimensional (2-D) agarose gel electrophoresis. Two isomers exist for an intramolecular triplex: one with the 3'-half of the Pyr strand as the third strand (H-y3) and the other with the 5'-half of the Pyr strand as the third strand (H-y5). It was shown that the content and position of G + C residues in the triplex loop region (the center of Pur.Pyr tracts) are primary determinants for the isomerization between the H-y3 and H-y5 triplexes. Divalent metal ions such as Mg2+ and negative supercoiling also modulate the isomerization: the H-y5 conformation is stabilized by the divalent metal ions and/or under relatively lower negative supercoiling. 2-D gel analyses revealed that two isomers, H-y3 and H-y5, are topologically non-equivalent: the H-y3 formation relaxes one more supercoil turn than H-y5. As the G + C content in the center of Pur.Pyr tracts increases, the triplex requires more supercoil energy for formation. Therefore, the base-pair opening in the center of Pur.Pyr tracts is the initial and critical step in the pathway for the formation of triplex as well as the isomerization. The role of the triplex loop sequence is explained by a model in which the nucleation process of H-y3 formation requires a wide range of base-pair opening compared to that of H-y5: such unwinding would not be favored for the central region of the duplex with high G + C content and so it would be in the presence of Mg2+, and thereby the H-y5 formation is promoted.

Binding specificity of integration host factor (IHF) to oligo DNAs has been studied by circular dichroism (CD) spectroscopy and filter binding experiment. CD difference spectra of IHF-DNA complexes demonstrated that a conformational change in DNA was induced by binding of IHF when DNA had a consensus sequence for the binding sites of IHF, but that such conformational change was not observed for consensus DNA 20 mer as well as nonconsensus DNA 45 mer. Dissociation constants for IHF-DNA complexes determined by filter binding assay showed that IHF has indeed stronger affinity to DNA with the consensus binding site than to nonconsensus DNA, but the difference in its affinity between consensus and nonconsensus DNAs was rather small, 3.4-fold. It was, therefore, concluded that the flanking regions of the consensus sequence are important for the specific binding of IHF and that its binding specificity is well characterized by the induced conformational change in DNA rather than by dissociation constants for IHF-DNA complexes.

Binding specificity of histone-like HU alpha protein to supercoiled DNA was examined by gel retardation assay and chemical probing with OsO4. The latter method was proved to be a unique means for detecting torsional tension restrained in supercoiled plasmid in the presence of HU alpha. It was shown that HU alpha protein has preferential affinity to negatively supercoiled DNA relative to relaxed, nicked and linearized DNAs. There were two modes for binding of HU alpha to the supercoiled DNA: one was the binding associated with topological changes in DNA and the other was relatively strong binding, probably specific to certain particular structures of DNA. It was suggested that HU in vivo interacts preferentially with the regions deformed under torsional stress or with the metabolically active regions along DNA.

The solution structures of HUα and its complex with oligo DNA were studied by proton NMR spectroscopy. It was confirmed that the arm region of HU forms antiparallel β-sheet and that all of the residues of phenylalanines together with some of leucines and/or valines form a hydrophobic core within the dimer of HU protein. Upon complex formation of HUα with DNA, several resonances from both HU and DNA were perturbed and the intermolecuar NOEs between HU and DNA were observed, suggesting that HU binds primarily to the minor groove of DNA.

SUMO E3 ligase of the Siz/PIAS family that promotes sumoylation of target proteins contains SAP motif in its N-terminal region. The SAP motif with a consensus sequence of 35 residues was first proposed to be as a new DNA binding motif found in diverse nuclear proteins involved in chromosomal organization. We have determined solution structures of the SAP domains of SUMO ligases Siz1 from yeast and rice by NMR spectroscopy, showing that the structure of the SAP domain (residues 2–105) of rice Siz1 is a four-helix bundle with an up-down-extended loop-down-up topology, whereas the SAP domain (residues 1–111) of yeast Siz1 is comprised of five helices where the fifth helix α5 causes a significant change in the alignment of the four-helix bundle characteristic to the SAP domains of the Siz/PIAS family. We have also demonstrated that both SAP domains have binding ability to an A/T-rich DNA, but that binding affinity of yeast Siz1 SAP is at least by an order of magnitude higher than that of rice Siz1 SAP. Our NMR titration experiments clearly showed that yeast Siz1 SAP uses α2-helix for DNA binding more effectively than rice Siz1 SAP, which would result from the dislocation of this helix due to the existence of the extra helix α5. In addition, based on the structures of the SAP domains determined here and registered in Protein Data Bank, general features of structures of the SAP domains are discussed in conjunction with equivocal nature of their DNA binding. Proteins 2009. © 2008 Wiley-Liss, Inc.