a crystal structure of l14

... library is based on the concept of combinatorial chemistry.138-143 Lehn has stated the meaning of a dynamic combinatorial library as follows: "Dynamic combinatorial libraries are designed as mixtures ... given great support for my research work Thanks for the help and friendship from all my colleagues: Tao, Pan, Valerie J, Ayten, Robyn, Azad, Chris, Annette, Amar, Barbara, Deborah, Sebastien, ... complexes and dynamic combinatorial libraries 1.1 Supramolecular chemistry Supramolecular chemistry has become an active research area over the past 25 years.16 Lehn and Vögtle have defined supramolecular...

Ngày tải lên: 02/07/2014, 13:33

... a- amino-b-carboxymuconate-e-semialdehyde decarboxylase J Am Chem Soc 129, 9278–9279 Fukuoka SI, Ishiguro K, Yanagihara K, Tanabe A, Egashira Y, Sanada H & Shibata K (2002) Identification and expression of a cDNA encoding human 6622 ... a- amino-b-carboxymuconate-e-semialdehyde decarboxylase (ACMSD) J Biol Chem 277, 35162–35167 Tanabe A, Egashira Y, Fukuoka SI, Shibata K & Sanada H (2002) Expression of rat hepatic 2-amino3-carboxymuconate-6-semialdehyde ... T, Yang K, Liu A & Zhang H (2006) Crystal structure of a- amino-b-carboxymuconic-e-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylase reaction...

Ngày tải lên: 18/02/2014, 06:20

... were amplified by PCR using pairs of primers 5¢-CATATGCAACAGACAACCCAAATTCAGCCC-3¢ and 5¢-AGATCTTATCACTCCCTTACTAAGTCGATG-3¢ for the b subunit and 5¢-CATATGAGCGAGAAAACCA TGCGCGTGCAG-3¢ and 5¢-AGATCTTAGCTTCCTTT ... DNA polymerase (Stratagene) and pairs of primers 5¢-TCTGAGTGCGGTGGAAGAGATG ATGAAGCG-3¢ and 5¢-AGATCTTATTCAATGGTGT CGGGCTGAACC-3¢ and digested with EcoRV and BglII Resulting 210-bp fragment was ... Materials Crystalline AdoCbl was a gift from Eizai, Tokyo, Japan DEAE-cellulose was purchased from Wako, Osaka, Japan The other chemicals were analytical grade reagents Preparation of expression plasmids...

Ngày tải lên: 21/02/2014, 03:20

... The DASA of the AB dimer is defined as [(ASA of A) + (ASA of B) ) (ASA of AB dimer)] ⁄ The number of water molecules in the dimer interface was detected with ASV CALCULATOR [34] ASA was calculated ... was calculated (Table 1) It is conceivable that a dimer with larger DASA is more plausible We found that the DASAs of the AB and DA dimers were comparable Although the DASA of the CD dimer was ... beamline staff of PF and SPring-8 for data collection We also acknowledge the kind support of M Maeda (National Institute of Agrobiological Sciences, Japan) for calculation of DASA This work was...

Ngày tải lên: 14/03/2014, 23:20

... precipitant Prior to data collection, a crystal was transferred into Analysis of substrate specificity Substrate specificity was analyzed using xyloglucan tetradecasaccharide, XXXGXXXG, prepared as ... crystallography Acta Crystallogr D 50, 760–763 18 Navaza J (1994) AMoRe: an automated package for molecular replacement Acta Crystallogr A 50, 157–163 19 Brunger AT, Adams PD, Clore GM, DeLano WL, ¨ Gros ... at various concentrations of the substrate, tamarind seed xyloglucan (Dainippon Sumitomo Pharma, Osaka, Japan), in 50 mm sodium acetate buffer (pH 5.5) at 45 °C for 15 The bicinchoninate assay...

Ngày tải lên: 23/03/2014, 05:22

... Glu272–Arg148 21 19 14 092 8248 5844 –1 6.5 No of hydrogen bonds (side chain–side chain) Aromatic stacking ˚ ASA total (A2 ) ˚ ASA apolar (A2 ) ˚ ASA polar (A2 ) Formal global charge Theoretical pIb ... activity: crystallographic structure at 2 -A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase Proc Natl Acad Sci USA 90, 11257–11261 ... hydrophobic contacts and aromatic interactions are similar in all enzymes Frequently, alterations of the accessible surface of nonpolar side chains and of the accessible charged surfaces are observed...

Ngày tải lên: 23/03/2014, 07:20

... present in the crystal and no part of it has got cleaved off during the crystallization process 4.5.2 Data collection and analysis The native and selenomethionylated crystal data sets for all the five ... oscillation one degree for the respective crystals The crystal parameters and data collection statistics are given in Table below Table Crystal parameters and data-collection statistics for wt AtCyP38 ... obtained by vapor batch method in a condition having PEG6000 and t-butanol as precipitants Crystals of selenomethionylated AtCyP38 protein was obtained in the same condition as that of native AtCyP38...

Ngày tải lên: 14/09/2015, 17:50

... report, partially purified AmyA that contained the signal peptide with a His-tag was used for the activity assay From the crystal structure of AmyA it appears that the His-tag and Nterminal signal ... N-terminal signal peptide cleaved AmyA The primary amino acid sequence of AmyA was analyzed by using the SignalP V 2.0 (Henrik et al, 1997) server and we have found that AmyA has a signal peptide at ... crystallographic statistics are summarized in Table 2.1 40 Figure 2.5 lAmyA crystal picture Crystals of AmyA, with maximum dimensions of 0.1 x 0.1 x 0.6 mm Table 2.1 Crystal parameters and data...

Ngày tải lên: 16/09/2015, 08:31

... in the most favourable region of the Ramachandran plot (Table 2) Crystal structure of a Thielavia arenaria laccase Kinetic data Kinetic constants (Km and Vmax) for rMaL, TaLcc1 and ThL were determined ... Journal compilation ª 2011 FEBS 2293 Crystal structure of a Thielavia arenaria laccase J P Kallio et al 15 Lyashenko AV, Zhukova Y, Zhukhlistova N, Zaitsev V, Stepanova E, Kachalova G, Koroleva ... Journal 278 (2011) 2283–2295 ª 2011 The Authors Journal compilation ª 2011 FEBS J P Kallio et al Crystal structure of a Thielavia arenaria laccase Fig (A) The crystal structure of TaLcc1 as a surface...

Ngày tải lên: 14/02/2014, 18:20

... (excluding water molecules and peptide atoms) and rj is the standard deviation of B factors The normalized B factors have a zero mean and unit variance All atoms that satisfy Bz ‡ are treated as outliers ... protein crystallography Acta Crystallogr D: Biol Crystallogr 50, 760–763 37 Evans P (2006) Scaling and assessment of data quality Acta Crystallogr D: Biol Crystallogr 62, 72–82 38 McCoy AJ, Grosse-Kunstleve ... with a contact area ˚ of 13.5 A2 and the Lys residue at P3 with a contact ˚ area of 10.2 A2 Residues outside the central binding area have significantly lower values These results are summarized...

Ngày tải lên: 14/02/2014, 19:20

... Academia Sinica and National Synchrotron Radiation Research Center (Taiwan, ROC) We thank Ms M.Sakai (Osaka University) for performing ultracentrifugation analysis and Mr K Mieda and M Sakata ... hyperthermophilic archaeon growing at temperatures up to 100°C Int J Syst Bacteriol 46, 1070–1077 10 Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A ... 14 Mizohata E, Sakai H, Fusatomi E, Terada T, Murayama K, Shirouzu M & Yokoyama S (2005) Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum...

Ngày tải lên: 14/02/2014, 22:20

... values increase from G1P over PhyK to AppA by a factor of  2200 The conformational changes of AppA upon substrate binding facilitate a faster turnover of phytate and are in line with a higher specificity ... site-directed mutagenesis kit (Stratagene, La Jolla, CA, USA) Plasmid pET-1TK was used as template and Kleb(HtoA)fw (5¢-GCTTAGCCGCGCCGGCATTCG) and Kleb(HtoA)rv (5¢-CGAATGCCGGCGCGGCTAAGC) as primers ... conserved active-site motifs, RHGXRXP and HD, and hydrolyze metal-free phytate with pH optima in the acidic range They consist of two domains, a large a ⁄ b domain and a small a domain with the catalytic...

Ngày tải lên: 16/02/2014, 09:20

... growth factors and proteinase inhibitors Biol Chem 380, 473–483 Kataoka H, Uchino H, Asada Y, Hatakeyama K, Nabeshima K, Sumiyoshi A & Koono M (1997) Analy- Crystal structure of the catalytic domain ... Shimomura T, Denda K, Kitamura A, Kawaguchi T, Kito M, Kondo J, Kagaya S, Qin L, Takata H, Miyazawa K et al (1997) Hepatocyte growth factor activator inhibitor, a novel Kunitz-type serine protease ... al Crystal structure of the catalytic domain of DESC1 Fig Structure- based sequence alignment of the human DESC1 catalytic domain with human DESC2 [2], human DESC3 [2], HAT, HAT-like [6], human...

Ngày tải lên: 19/02/2014, 00:20

... References Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A et al (2003) Genome sequence of Bacillus cereus and comparative analysis ... consisting of two hydrogen-bonded antiparallel b-strands (b6–b7), an a- helical hairpin (helices a5 , a6 ) and a C-terminal strand (b8) Helix a5 and strand b7 partially cover one side of the Rossmann fold ... Tanaka T, Fukui T, Atomi H & Imanaka T (2003) Characterization of an exo-b-D-glucosaminidase involved in a novel chitinolytic pathway from the hyperthermophilic archaeon Thermococcus kodakaraensis...

Ngày tải lên: 19/02/2014, 00:20

... atoms of Asp11 and Asn23 (Fig 3) in an arrangement similar to what is observed in VPRK Both PRK and VPRK have calcium bound at Ca3 SPRK also has an aspartic acid residue at position at 200, and ... initial comparative studies showed that the catalytic turnover was at least twice that of PRK, but substrate affinity was reduced SPRK was compared with PRK and was found to be remarkable stable against ... program for molecular replacement J Appl Crystallogr 30, 1022–1025 Perrakis A, Harkiolaki M, Wilson KS & Lamzin VS (2001) ARP ⁄ wARP and molecular replacement Acta Crystallogr Sect D Biol Crystallogr...

Ngày tải lên: 19/02/2014, 07:20

... Number of ion pairsa Number of hydrogen bonds Main chain–main chain Main chain–side chain Side chain–side chain Total ˚ Exposed surface areab (A2 ) ˚ Apolarc (A2 ) ˚ Buried surface areab (A2 ) ˚ Apolarc ... uracil–DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features Acta Crystallogr Sect D 59, 1357–1365 10 Aghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser ... whereas the overall exposed surface areas of the psychro- and the mesophilic enzymes are larger than for the thermophile enzyme, mainly as a result of larger area of apolar atoms, the meso- and...

Ngày tải lên: 19/02/2014, 16:20

... oligonucleotides: a sense primer 5¢-CAACAAATTTGCATATGACTATT AAAG-3¢ containing an NdeI site (underlined) next to the start codon of the T brucei gGAPDH gene; an antisense primer 5¢-CAGCCAAGCGCCTAGGGAGCGAGA AC-3¢, ... Castellano, E.E., Garratt, R.C & Craivich, A (1998) Set-up and experimental parameters of the protein crystallography beamline at the Brazilian National Synchrotron Laboratory J Synchr Rad 5, ... oscillation mode Methods Enzymol 276, 307–326 Navaza, J (1994) AMoRe: an automated package for molecular replacement Acta Crystallogr A 50, 157–163 Brunger, A. T., Adams, P.D., Clore, G.M., Delano,...

Ngày tải lên: 20/02/2014, 02:21

... PATTERN: a precession simulation programme for displaying reciprocal-space diffraction data J Appl Crystallogr 32, 375–376 Navaza, J (1994) AMoRe: an automated package for molecular replacement Acta Crystallogr ... intermediate in enzymatic thiamin catalysis: Crystal structure of the a- carbanion of (a, b-dihydroxyethyl) -thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae Proc Natl ... S., Marion-Poll, A. , Caboche, M., Kamiya, Y & Koshiba, T (1998) Molecular cloning and characterization of aldehyde oxidases in Arabidopsis thaliana Plant Cell Physiol 39, 433–442 Koga, J., Adachi,...

Ngày tải lên: 20/02/2014, 11:20

... asparaginase of Erwinia carotovora LGlutamate (cylinder) on the surfaces of the structures of TG (A) and asparaginase of E carotovora (B) are shown Putative inter˚ actions (atom distance less than ... salt-tolerant glutaminase K Yoshimune et al 32 Chantawannakul P, Yoshimune K, Shirakihara Y, Shiratori A, Wakayama M & Moriguchi M (2003) Crystallization and preliminary X-ray crystallographic studies ... Kravchenko OV, Kislitsin YA, Popov AN, Nikonov SV & Kuranova IP (2008) Three-dimensional structures of l-asparaginase from Erwinia carotovora complexed with aspartate and glutamate Acta Crystallogr...

Ngày tải lên: 06/03/2014, 09:22

... 5¢-aataatccatggggagtaatacttcctggcgta aaagtgaagtcc-3¢ and 5¢-attattggatccctattgctggtccgattctgccag-3¢ 3-TPR NlpI primers (residues 62–197) were 5¢-aataatccatgg gggcacagcttttatatgagcgcggag-3¢ and ... hydrodynamic radius than a globular molecule of similar polypeptide length However, calculation of the Matthews coefficient from initial crystallographic data indicated that a dimer was most compatible ... (Finland) Data for this study were measured at beamline X12C of the National Synchrotron Light Source We are grateful for the assistance of Dr Anand Saxena in the use of this beamline The National...

Ngày tải lên: 07/03/2014, 16:20