binding sites affinity and ensemble modulation

... conclude the precise location and the relative orientation of the binding sites in decorin and collagen are not yet known Our findings on multiple binding sites in collagen and on the relevance of Lys/Hyl ... decorins and decorin cores, respectively Left lane: standard protein markers and their molecular masses (in kDa) The core protein is present as two bands with apparent molecular masses of 47 and 42 ... interactions between type I and type II collagens, their peptides and decorin reveal the following (a) Type I and probably also type II collagen appear to have multiple binding sites for decorin, because...

Ngày tải lên: 21/02/2014, 15:20

... Ca2+ -binding sites is known to generate the J-band (610–650 nm) and ⁄ or the c-band (480–510 nm) Upon binding to Calnuc, the dye displayed prominent J-band and c-band in both absorption and CD ... the J-band and the c-band regions (Fig 6B) on binding to the protein CD results confirmed the absorbance data: Ca2+ binding is able to attenuate both the J-band and the c-band, whereas Mg2+ binding ... b-crystallin and d-crystallin behave similarly (show only one band), whereas calmodulin and troponin behave like each other On the other hand, Calnuc and parvalbumin generate both the J-band and the c-band,...

Ngày tải lên: 07/03/2014, 00:20

... was considered as 100%) was mutated and the activity of the mutant constructs was assessed Wild type and mutated GAGA and Adf-1 binding sites are shown by open and filled symbols, respectively (C) ... region of the a-F1-ATPase gene and found that the combination of GAF and Adf-1 binding sites is present both in other Drosophila species (D yakuba and D pseudoobscura) and in Anopheles gambiae (data ... singlestranded binding protein (mtSSB), and the catalytic (a) and accessory (b) subunits of the DNA polymerase c (Pol c) [24,25] Interestingly, the expression of the genes encoding mtSSB and Pol...

Ngày tải lên: 07/03/2014, 16:20

... from sugar binding at the +2 and +3 subsites FEBS Journal 277 (2010) 4549–4561 ª 2010 The Authors Journal compilation ª 2010 FEBS W M Patrick et al Carbohydrate binding sites in Candida exoglucanase ... of L3 binding in the active site pocket showing the Phe-Phe clamp and the F229A mutation Carbohydrate binding subsites are labelled )1, +1 and +2 Glycosidic bond cleavage occurs between )1 and ... Exg and a carbohydrate binding module CBM 4-2 from T maritima (PDB: 1gui) is shown with F144, F258 and F229 from Exg (cyan), and W51, W102 and W27 from CBM 4-2 (magenta) from the associated binding...

Ngày tải lên: 15/03/2014, 23:20

... contained multiple binding sites and its LPS binding manifested positive cooperativity Should a Ôtake-home messageÕ be needed from the present study, one might remember Gulliver and the Lilliputians ... to SMAP-29 [9–29] suggests that the Nterminal binding site has higher affinity for LPS than does the C-terminal one The presence of two binding sites and the sevenfold to 21-fold greater affinity ... therefore infer that cooperativity in LPS -binding is primarily intramolecular, whereas binding of one LPS -binding site in a SMAP-29 molecule facilitates binding by the other site The Hill coefficient...

Ngày tải lên: 17/03/2014, 23:20

... length and 14 A in length between subsites and and and 3, respectively An examination of these regions indicates that PheC175 protrudes into the substrate binding area between subsites and Thus, ... and 320–334 Ascorbic acid and lactose molecule binds at three subsites in the polysaccharide binding site of the TSbH domain of HylP2 The positions of ligands are indicated at the substrate binding ... between sub˚ between subsites and 3, respecsites and and 14 A tively The first molecule of ascorbic acid is held at the lower-most subsite consisting of residues LysC179 and GluB167 LysC179 forms...

Ngày tải lên: 23/03/2014, 04:21

... chimera mimicking the HIV-1 NF-kB binding sites Differential effects of the HIV-1 NF-kB PDP–PDP chimera on binding of NF-kB p52 and p50 to NF-kB binding sites of HIV-1 and IgK gene The experiment reported ... DNA and double stranded PDP –PDP chimeras mimicking the HIV-1 NF-kB binding sites, while effective inhibitors of binding of NF-kB p52 and p50 to HIV-1 LTR sequences, not efficiently inhibit the binding ... unlike symmetric NF-kB binding sites, possible problems related to self and/ or interstrand hybridization are expected to be minimal in the case of asymmetric NF-kB binding sites For these reasons,...

Ngày tải lên: 24/03/2014, 04:21

... putative binding sites relative to the ORF start position d A Sequences of putative binding sites e Changes in binding free energy and standard errors (DDGtotal Æ SE) Fig Confirmation of SYCRP1 binding ... al DG-based prediction of DNA binding sites by SYCRP1 Table Putative binding sites of SYCRP1 and the downstream genes The standard errors were calculated from standard errors of DDG No.a Locusb ... putative binding sites, we performed an EMSA to measure changes in binding free energy (observed DDGtotal) for the 11 binding sites with the lowest A DDGtotal values of the 23 putative binding sites...

Ngày tải lên: 30/03/2014, 10:20

... 1.5 lM, and another around 0.1 lM These transitions reflecting conformational changes correlate well with the two binding sites (IIG5 and IIG6, Kd ¼ and 0.2 lM, respectively) detected and measured ... hydrophobic and salt bridges between G2 helix a1 and the C-terminal helix of G6 It is proposed that binding of IIG6 disrupts the salt bridges between D669 and R168, and between D670 and R169 Cooperativity ... dissociation constant Kd and the maximal binding Amax) were determined by nonlinear fitting A ¼ Amax · [L]/(Kd + [L]) (relation 1) where A is the absorbance at 405 nm and [L] the ligand concentration,...

Ngày tải lên: 31/03/2014, 01:20

... potential sites Figure 10 shows these binding sites in detail and highlights the amino acids Tyr837, Phe834, Phe256 and Asn768 One potential site is located between the top of transmembrane helix M7 and ... spectrophotometer and the absorbance was monitored at 422 and 390 nm, and the difference taken Ca2+ -binding to the ATPase was measured using the dual labeling technique of Longland et al [13] ATPase ... catalytic and regulatory sites were unchanged (i.e 9.4 ± 2.8 and 1.3 ± 0.5 mM, respectively) The Vmax values, however, were reduced The catalytic and regulatory Vmax values were 2.5 ± 0.1 and 5.4...

Ngày tải lên: 31/03/2014, 23:20

... two tyrosine kinase sites (residues 227, 922), 30 protein kinase C phosphorylation sites and 26 casein kinase II phosphorylation sites were found The sites associated to PKC and CK2 phosphorylation ... potential N-glycosylation sites (outlined in Fig 1), and numerous putative consensus sites for various kinase related phosphorylations Two cAMP- and cGMP dependent protein kinase sites (residues 1089, ... 63 (exon 24) and 251 (exon 36) bp All exon-intron junctions conformed to the consensus splice donor (GT) and acceptor (AG) sites, except for the splice donor sites of intron (AT) and1 0 (GC) The...

Ngày tải lên: 11/08/2014, 08:20

... modifications in each arm gives the optimal binding affinity versus binding kinetic [30,31] Here we tested DNA and LNA (gap-mer) antisense oligos, DNA- and LNAzymes directed towards four highly ... targeting the selected DIS and PBS sites were synthesized both as DNA (DNAzymeDIS and DNAzymePBSD, respectively; Fig 1) and with two LNA modifications in each arm (LNAzymeDIS and LNAzymePBSD, respectively) ... were previously selected as optimal annealing sites in vitro, and we tested them as targets for DNA and LNA antisense oligonucleotides, and DNA- and LNA-zymes The antisense oligonucleotides were...

Ngày tải lên: 13/08/2014, 09:21

...  proteasomal binding sites,  having   been  successfully  used  to  identify binding sites  for  other  HbYX-­‐motif-­‐containing  proteins;   further  assay  optimization  should  yield  Pba1p and ...  University,  August  2012  Identification  of  the  Pba1   and  Pba2 Binding Sites  on  20S  Core  Particle  Intermediates  Major  Professor:  Andrew   Kusmierczyk       The  proteasome  is  responsible ... UNIVERSITY GRADUATE SCHOOL Research Integrity and Copyright Disclaimer Title of Thesis/Dissertation: Identification of the Pba1 and Pba2 Binding Sites on 20S Core Particle Intermediates For the...

Ngày tải lên: 24/08/2014, 13:48

... their tandemrepeated counterparts Third, binding sites from sigma factors were removed, as were binding sites from NarP, since all the latter are also binding sites for NarL Fourth, duplicate binding ... representing binding sites [Schneider and Stephens 1990] and in motif discovery [Hertz and Stormo 1999]; here, we apply it directly to the problem of searching for a transcription factor’s binding sites ... transcription factors and 410 binding sites, with an average of 11.7 ± 8.5 sites per transcription factor 2.2.2 Approaches for representing and searching for transcription factor binding sites Four basic...

Ngày tải lên: 13/11/2014, 09:10

... The and in ADSL, VDSL, and Multicarrier Modulation is not precise; the scope of the book is wider than the intersection (a logic designer's and ) but narrower than the union (a layperson's and ... Communications and particularly to its founder, John Ciof® John is a good friend, a brilliant engineer, and was a provocative and inspiring leader I thank him and everybody at Amati for the most exciting and ... Walling, Brian Wiese, Kate Wilson, and George Zimmerman for many helpful discussions ADSL, VDSL, and Multicarrier Modulation ADSL, VDSL, and Multicarrier Modulation John A C Bingham Copyright...

Ngày tải lên: 19/10/2013, 11:15

... NRE(A+B)); and in both Box A and B, NRE(A–B–) (C) Qualitative analysis of LacZ reporter activation in the interaction of APUM-2 and APUM-7 with NRE WT and NRE mutants The iron responsive element RNA and ... system (Figs 3D and 5E) The FAS-2 transcript used in the binding assay differs from that of WUS, CLV-1 and ZLL sequences in both APBE and flanking nucleotides (Fig 5C), whereas its binding core element ... human and mouse possess two; and Drosophila and Dyctiostelium have only one member [5] Recently, new studies have revealed the presence of ten, two and one homologs in Trypanosome, Plasmodium and...

Ngày tải lên: 18/02/2014, 06:20

... SAF34 and 8G8 for humans, SAF34, 8G8 and P4 for sheep, SAF34 and P4 for cattle, and SAF34 for mice; and for the C-terminal antibodies 6H4, SAF60 and SAF70 for humans, and mAbs 6H4, SAF60, SAF70 and ... SAF34 and P4 strongly stained the di-glycosylated band, and mAbs 6H4, SAF60, SAF70 and SAF84 showed the highest staining with the overlapping bands of nonglycosylated full-length PrPC and glycosylated ... While N-terminal binding antibodies as SAF34 detected only full-length PrPC, C-terminal binding antibodies recognized two bands comprising full-length PrPC and an 18–19 kDa protein band corresponding...

Ngày tải lên: 19/02/2014, 02:20

... cisplatin on p53(1–363) binding to various target sites: (A), natural p53 DNA -binding sites (p53DBSs) mdm2 and p21, and the synthetic PGM1 sequence; (B) mutated p53DBSs PGM4, p21a and p21b (Fig 1) The ... one strand and two AG steps in the other The mdm2 target, whose interaction with p53 was most strongly affected by DNA cis-platination, contains GG, GGG and AG motifs in one strand and GG and GTG ... showing retarded bands due to binding of p53(1–363) or p73d proteins to 50-mer target oligos containing PGM1, PGM4, mdm2, p21, p21a and p21b sites Other details as in (A), lanes and FEBS Journal...

Ngày tải lên: 19/02/2014, 05:20

... non-mutually exclusive inhibitor binding sites exist at the enzyme (Fig 1) [29] The inhibitor interacts with the enzyme both at the active site and at an additional binding site Binding of one inhibitor ... competitive binding of Tat(1–9) directly to the empty active site of DP IV [23], the docking studies demonstrate the possible binding of Tat(1–9) to two different binding sites, one binding site ... intersection For the calculation of the Ki value and the factors a, c and d the slopes and intercepts were replotted vs [I] according to Eqns (4) and (5), respectively Here, cÆKi represents the...

Ngày tải lên: 20/02/2014, 11:20

... showed maximum binding at 32 and 37 °C; OsHsfA9 showed efficient binding at 22, 32 and 37 °C; and OsHsfB4b showed maximum binding at 22 °C In contrast, the DNA affinity of OsHsfA7, OsHsfB4c and OsHsfC1b ... HSE oligonucleotides, i.e 4P-, 3P-, G- and S-types (Fig 3C) OsHsfA2c showed high affinity binding to 4P- and 3P-type HSEs and low affinity binding with G- and S-type HSEs A slowly migrating OsHsfA2c–HSE4P ... Hsf1 [19] OsHsfA9 showed binding to 4P- and 3Ptype HSEs but not to G- and S-type HSEs OsHsfB4b showed binding to 4P- and 3P-type HSEs with much higher affinity than the binding for G-type HSE Therefore,...

Ngày tải lên: 05/03/2014, 23:20