fi cation by searching protein sequence databases

... F-actin filaments; (d) proteins that nucleate actin polymerization [29,30]; (e) proteins that bundle F-actin filaments; (f) proteins that stabilize filament networks; (g) proteins that sever F-actin filaments; ... controlled and modified by several regulatory proteins Of special importance are the plus end binding proteins EB1 (end binding protein 1) and CLIP-170 (cytoplasmic linker protein 170), which ... studies clarified that in fact TccC3 modifies Thr148 (marked in Fig 1) So far, threonine residues were not known to be acceptor amino acids for modi cation by ADP-ribosylation The finding of a different...

Ngày tải lên: 14/03/2014, 22:20

... grade commercially available Protein expression and puri cation GRK2 was overexpressed in and purified from Sf9 insect cells as described previously with some modifications [10] The infected Sf9 ... dephosphorylation, tubulin was first phosphorylated in the presence of [c-32P]ATP by GRK2 and then subjected to dephosphorylation by PP2A, followed by SDS/PAGE and quanti cation of the radioactivity ... GST fusion proteins were purified using glutathione-Sepharose by the procedure recommended by the manufacturer, as described previously [10] Dephosphorylation of tubulin Tubulin purified from porcine...

Ngày tải lên: 17/03/2014, 09:20

... hydropathy profile from an aminoacid sequence, but in general they only permit one or a few profiles to be generated at a time The resulting hydropathy profiles are typically examined by eye for significant ... false-positives The first goal is achieved by applying the algorithm to a sequence database containing all proteins that belong to the family of interest The parameters are refined by trial and error ... membrane proteins that are related to AChRs only by function Candidate LGICs retrieved by the search strategy Fig Hydropathy profiles of four proteins that were retrieved from the human proteome by...

Ngày tải lên: 17/03/2014, 23:20

... from protein binding to the same but unmodified p53DBS Effects of cisplatin DNA modi cation on sequence- specific binding of the p53 protein Previously, it has been shown [31,32] that DNA modi cation ... suppressor protein p53 with DNA are influenced by covalent modi cation of the DNA by antitumor platinum complexes [31–36] Sequence- nonspecific DNA binding (in the absence of the p53DBS) of the p53 protein ... of target recognition by the protein) DNA binding of the C-terminally truncated p53(1–363) protein Fig The effects of DNA modi cation with cisplatin on binding of the p73 proteins to the p21 and...

Ngày tải lên: 19/02/2014, 05:20

... puri cation of recombinant human protein C Recombinant protein C variants K37S/K38Q/K39Q (37-loop mutant), K62N/K63D (60-loop mutant), K37S/K38Q/K39Q/K62N/K63D (37+60-loop mutant) were created by ... structure of heparin (file 1hpn [35]) The X-ray crystal structure of APC (with modifications in loop 148, see below) and a model structure for the three A domains of FVa (with some modifications at the ... stimulation of the rate of inactivation (k¢306) by heparin was calculated (Fig 1C) by fitting to a single exponential Table summarizes all rate constants obtained by fitting all time courses to the random-order...

Ngày tải lên: 19/02/2014, 13:20

... significantly differently from state-ofthe-art sentence simpli cation systems in terms of human-judged Simpli cation In terms of Fluency and Adequacy our system is judged to perform significantly ... select the most appropriate simpli cation by using integer linear programming We follow Zhu et al (2010) and Coster and Kauchak (2011) in proposing that sentence simpli cation can be approached as ... to build the sentence simpli cation model GIZA++ utilizes IBM Models to and an HMM word alignment model to find statistically motivated alignments between words We first tokenize and lowercase...

Ngày tải lên: 07/03/2014, 18:20

... procedures Peptide synthesis Peptides were made by manual solid-phase peptide synthesis using the tBoc method [11], purified by RP-HPLC, and analysed by MS The following peptides were synthesized ... 267 nm using molar absorption coefficients of 652 M)1Æcm)1 for phosphotyrosine [14] and 1427 M)1Æcm)1 for tyrosine [15] Gene cloning, protein expression, and puri cation of glutathione S -transferase ... p56Lck (amino acids 1–509) was placed in-frame with the coding sequence of GST from Gene cloning, protein expression, and puri cation of His-cTCRf The cytosolic portion of human TCRf was cloned...

Ngày tải lên: 08/03/2014, 02:20

... presence of GF 109203X, whereas GF 109203X alone did not result in any significant morphological modi cation of the cells Quanti cation of this experiment indicated that whereas a 24 h cadmium treatment ... performed ZIP8 knockdown by siRNA transfection Our ZIP8 siRNA mix was first validated on cells transiently expressing a bicistronic RNA encoding ZIP8 on the first cistron, followed by GFP on the second ... the phorbol ester PMA that is efficiently abrogated by the specific broad-spectrum PKC inhibitor GF 109203X This corresponds to the conventional mitogen-activated protein kinase cascade observed,...

Ngày tải lên: 23/03/2014, 06:20

... the protein databases to find more sequences, which are validated before being added to the family The WWW site provides keyword searching and classi cation of protein sequences by PSSM (HMM) searching ... to these databases, as well as to the protein sequence databases The WWW site shows interrelationships between the various family classifications graphically Classi cation of new protein sequences ... represented by a simple pattern and sequences can belong to more than one family A few families are also represented by profiles The WWW site provides keyword searching and classi cation of protein sequences...

Ngày tải lên: 23/03/2014, 12:20

... N-terminal sequence and internal fragments near the C terminus were translated into degenerate primers for PCR Extension by 3¢-RACE led to identi cation of the entire sequence This new sequence ... series of [Glu1]fibrinopeptide B Fragment spectra were finally processed manually by using BioLynx Peptide sequencing software (Waters-Micromass) Sequence alignments were performed by using the multalin ... (WWYTYQDKE), had the sequences 5¢-TCYTTRTCYTG RTANGTGTACCACC-3¢ and 5¢-CYTTRTCYTGRTANG TATACCACC-3¢ The PCR fragments obtained were purified by using the DNA and Gel puri cation kit from Amersham...

Ngày tải lên: 23/03/2014, 15:20

... automatically extracted by finding duration below a certain amplitude level which lasts more than one second Topic Identi cation based on HMMs We employ HMMs for topic identi cation, where a hidden ... information they utilized was just keywords Features for Topic Identi cation First, we’ll describe the features that we use for topic identi cation, which are listed in Table They consist of three modalities: ... Discussion We conducted the experiment of the topic identi cation We first trained HMM parameters for each program, and then applied the trained model to five videos each, in which, we manually assigned...

Ngày tải lên: 31/03/2014, 01:20

... known The viral proteins most directly involved in RNA replication include protein 3AB, the precursor of 3A, which is a small membrane binding and RNA binding protein, the terminal protein VPg, ... fold by and by 3CDpro(3CproH40G, 3CDpro(3CproH40A) polR455A/R456A) but not by 3CDpro(3Cpro R84S/ 3D I86A) The formation of 155S particles is enhanced about 3–7 fold by 3CDpro(3CproH40A) but not by ... translation-RNA replication system by viral protein 3CDpro J Virol 2005, 79(10):6358-6367 Verlinden Y, Cuconati A, Wimmer E, Rombaut B: The viral protein 3CD induces an equilibrium between the viral protein...

Ngày tải lên: 19/06/2014, 08:20

... Duong 25* Note: * Fruits were coved by plastic bag 3.4 Control fruit fly by using protein bait 3.4.1 Control fruit fly by protein bait for small area The use of protein bait sprays on peach, citrus, ... 17/7 100 4.00 100 100 3.4.4 Control fruit fly by using protein bait for large area in some provinces After some experiment to control fruit fly by using protein bait for large area of apple and peach ... measure the impact of protein bait In the late season, only 5% of peaches were damaged by fruit fly in these orchards At the same time, on the orchards, that were not applying protein bait, almost...

Ngày tải lên: 21/06/2014, 05:20

... non-rRNA sequences were characterized by BLASTX searches against NCBI-nr, KEGG, and assembled protein sequences taken from the GOS database Protein- coding sequences were identified as the top ... number of protein- coding genes in the sequenced reference genome of each taxon cSister taxon used for identification of core genome (see main text) dPercentage of core is the percentage of protein- coding ... expression level is still debated Sequence conservation in highly expressed proteins has been hypothesized to be driven by selection acting to minimize the costs of protein misfolding, which should...

Ngày tải lên: 09/08/2014, 22:24

... expression by more than 15-fold, IL-11 expression by more than eight-fold, IL-8 gene by four-fold and IL-6 by two-fold, respectively (Figure 2A) Likewise, when endogenous OP-1 was inhibited by OP1AS, ... inhibited by rhOP-1 by 1.6-fold (P < 0.001) along with tissue inhibitor of metalloproteinases (TIMP)-3 (2.06-fold, P < 0.001) At the same time, expression of MMP-2 (gelatinase A), which is activated by ... stimulated by rhOP-1 Table 8) Matrix proteins and their receptors Cartilage-specific matrix genes were found to be modulated by rhOP-1 treatment Expression of the 1.50↓ 1.52↓ Capillary morphogenesis protein...

Ngày tải lên: 12/08/2014, 15:22

... a pure sequence classification, struct frag: fragments from a pure structural classification; seq+struct frag: fragments from a combined sequence and structure classification protein sequence ... proteins Using the sequence of 1fa4 as a query, a sequence profile was built using the non-redundant protein sequence database and used to search against protein data bank sequences [58] This ... substitution matrices from protein blocks Proc Natl Acad Sci USA 1992, 89:10915-10919 Jung J, Lee B: Use of residue pairs in protein sequencesequence and sequence- structure alignments Protein Sci 2000,...

Ngày tải lên: 12/08/2014, 17:20

... actions • A path in the state space is a sequence of states connected by a sequence of actions • The solution of the problem is part of the map formed by the state space Problem solution • A ... through a city sequence? More concrete problem definition A state space An initial state A goal state A function defining state transitions A function defining the “cost” of a state sequence Choose ... space by generating successors of already explored states (AKA expanding states) Sweep out from start (breadth) Tree search algorithms • Basic idea: – Simulated exploration of state space by generating...

Ngày tải lên: 18/04/2015, 10:32

... kg/con/ngy), th p nh t lụ khụng b sung protein thoỏt qua cng ủ t 0,732 kg/con/ngy Tuy nhiờn m t nh ng ủi u khú lý gi i thay th protein thoỏt qua ủõy l m c 20 v 30% protein c a kh u ph n thỡ tng tr ... 10% protein thoỏt qua, m c dự tng tr ng cng ủ t 0,744-0,705 kg/con/ngy Cú th thnh ph n dinh d ng kh u ph n cõn ủ i hn so v i cỏc kh u ph n khỏc, ủ c bi t t l gi a protein thoỏt qua v nit phi protein ... 1.4 1.2 Nng l ng (MJ/kg CK) 12.0 12.05 12.08 12.09 Protein thụ 176.4 178.8 176 178.1 T l VCK (%) 79.6 79.47 79.32 79.2 (Lụ 2, v ủ c thay th t ng protein c a kh u ph n b ng 10; 20 v 30% b t cỏ) X...

Ngày tải lên: 17/05/2015, 23:37

... columns indicate protein colocalization 27 Chapter Results 3.1 Expression and purification of 6b proteins Before protein expression, a sequence comparison between the three 6b protein (AK6b, AB6b ... List of Figures FIG SEQUENCE ALIGNMENT OF 6B GENES WITH ROLB .28 FIG EXPRESSION AND PURIFICATION OF AK6B PROTEIN 29 FIG EXPRESSION AND PURIFICATION OF NHIS-AB6B PROTEIN 30 FIG ... were harvested by centrifugation at 4,000 rpm for 15 min, and the pellet was stored at -20°C for further purification 16 2.7.2 Protein purification His tag or His-SUMO tag fusion proteins included...

Ngày tải lên: 13/10/2015, 16:50