structure determination by diffraction and scattering

... structure type It was found that for the IR data, combining the amide I and II bands substantially improved determinations of the a-helix and C + B + G + S structure assignments Combined IR and ... 2943 Table Comparison of determination accuracies for secondary structure assignment combinations and segregations The secondary structures determined by the DSSP program and combined or subdivided ... normalization of the band maximum to a constant intensity; normalization to a constant area; normalization of the combined amide I and II bands, with separate analyses of each band afterwards; and separate...

Ngày tải lên: 16/03/2014, 18:20

... number is increasing day by day Crystal structure determination is definitely the most popular and powerful method to solve a macromolecular structure 1.2 X-RAY SOURCES AND DIFFRACTION INSTRUMENTS ... branch – crystal structure determination One year later, W L Bragg determined the first structure From then on, crystal structure determination is broadly undertaken on inorganic and organic molecules ... SUMMARY X-ray crystal structure determination is one of the most powerful methods to determine the macromolecular structure and study the relationship between structure and function of macromolecules...

Ngày tải lên: 17/09/2015, 17:20

... al [15] determined the structures of E75Q and E75L mutants of rcSHMT and studied their properties However, the structures determined by them were not at high resolution and suffered from a lack ... Science, supported by the Department of Science and Technology and DBT We thank Babu and James for their help during data collection VR and BSB thank the Council for Scientific and Industrial Research, ... bsSHMT (Blue) Y51 and the Schiff base are in the same orientation in E53QbsSHMT and bsSHMT, whereas the orientations of E53, Y60 and Y61 have changed ˚ wild-type and mutant structures is 0.10...

Ngày tải lên: 18/02/2014, 16:20

... pattern, sequence, and partial linkages, and assign structural details of each branch (e.g the 3- and 6-branches) Blood group H, Lea/Lex and Leb/Ley determinants, together with type and type chains, ... present between 4.47 and 4.427 p.p.m., while those of GlcNAc are between 4.71 and 4.634 p.p.m The reducing terminal Glc I residue (see structure in Fig and below) is indicated by the respective ... characterized by rOes between Fuc IX H5 and Gal IV H2 and between Fuc IX CH3 and Gal IV H2 (see also TFiLNO above) Gal IV is substituted at the 3-position, as GlcNAc V H1 gives an rOe to Gal IV H3, and...

Ngày tải lên: 19/02/2014, 12:20

... complete amino acid sequence by a combination of Edman degradation and cDNA cloning, and report its biochemical characterization and the determination of its crystal structure Our results show ... mm NaOH) for followed by a linear gradient of 0–40% buffer B (100 mm NaOH and m sodium acetate) over 40 Crystallization and structure determination PPL2 was crystallized by the hanging drop vapor ... bond, and Asp125 and Tyr183 would contribute to the stabilization of the oxazolinium intermediate [45] In PPL2, these residues correspond to Asp125, Glu127 and Tyr182 (Figs and 4A) Asp125 and Glu127...

Ngày tải lên: 16/03/2014, 13:20

... may be influenced by a combination of heritable variation, random environmental effects, and individual choice Moreover, phenotypic traits may both influence and be influenced by reproductive time ... first individual) and reproductive lifespan (the length of time from the start of breeding by an individual until its death) Data are for female (lines and 2) and male (lines and 4) sockeye salmon ... higher survival) and the benefits of breeding late (more energy can be acquired by adults) The optimal breeding time for an individual is then determined by its condition and by proximity to the...

Ngày tải lên: 28/03/2014, 16:20

... structural elements, i.e a-helices and b-strands, are represented by cylinders and arrows, respectively The cysteines are shown in yellow and disulfide bridges are indicated by connecting links The regions ... flower showed an intense band for XAIP (as confirmed by N-terminal sequence determination) in the germinated bulb samples, but the corresponding band was absent in the leaf and flower samples, whereas, ... xylanase and a-amylase, the interactions between XAIP and a-amylase and between XAIP and GH11 xylanase were examined using docking procedures For this purpose, discovery Studio 2.0, insight ii and...

Ngày tải lên: 29/03/2014, 09:20

... MGAD improves by 9% over the MRAD, and the DMAD improves by almost 52% over the MGAD In terms of PSNR criterion, the MRAD improves by 0.0311 dB over the GRAD, the MGAD improves by 0.0995 dB over ... better match between the ideal and processed images PSNR cannot distinguish the bias errors and random errors In most cases, the bias errors are not as harmful as the random errors to the images, ... the proposed method gives the best result, which is better than the AWMF by 0.4325 dB and the GRAD by 0.4646 dB in the PSNR and 15% in the Q metric In the new technique, there are three innovative...

Ngày tải lên: 23/06/2014, 01:20

... isolates by multiplex PCR for Stx1, Stx2, eaeA, and hlyA genes, and by flagellar H7 PCR After identification by motility and agglutination tests Table The detection rates of E coli O157:H7 by three ... encoded by espA, espB and espD and the translocated intimin receptor encoded by tir [7] STEC infection has been often associated with the consumption of contaminated ground beef, raw milk, and other ... management and control unclear The objectives of this study are (i) to examine the prevalence of E coli O157:H7 in slaughterhouses and retail markets, (ii) to characterize the isolates by determination...

Ngày tải lên: 07/08/2014, 18:21

... ambient air were low during the daytime and high at night, and the lowest and the highest concentrations appeared at 16:00 and 7:00–8:00, respectively Fig 3(a) and (b) show the seasonally average ... 310 m and the average intensity of the urban heat island, as measured by the magnitude of the temperature difference between urban and rural sites, was 1:6  C Saitoh et al (1996) observed and ... Station A (a) and Station N (b) peak in the morning (7:00–9:00), and those in spring (March–May) and in autumn (September–October) showed transitional temporal variations between winter and summer...

Ngày tải lên: 26/11/2014, 14:57

... these are listed in Table PCB Standards All PCB internal standards, sample evaluation / preparation standards (SES/SPS), recovery determination standard (RDS) and retention time window PCBs were ... copyright legislation DEPARTMENT FOR ENVIRONMENT, FOOD AND RURAL AFFAIRS 2001 The Air Quality Strategy for England, Scotland, and Wales and Northern Ireland; A consultation document on proposals for air ... industries, landfill sites and scrap yards Over time these activities have resulted in varying levels of topsoil contamination by direct spillage and fall out With the expansion of conurbations and changes...

Ngày tải lên: 09/09/2015, 09:39

... oligomerisation and clusting of Eph receptors and ephrins are essential for their signalling function and might be regulated by localisation in membrane microdomains (Cowan and Henkemeyer, 2002; Kullanderand ... separated by one single carbon (Mayer, 2001) The recently published Hck SH3/Ligand complex structure suggests that the class I ligand consensus sequence +xφPxφP should be expanded by a ligand consensus ... state is characterised by little structure and few stabilising interactions with high energy and high entropy, whereas the folded state is characterised by highly structured and many stabilising...

Ngày tải lên: 14/09/2015, 14:09

... weight determination and further buffer exchange 2.2.4 Determination of Protein Concentration 49 The concentration of a protein solution is usually determined by measuring the absorbance at 280nm and ... parameters 2.5 NMR Experiments and Structure Determination The NMR samples were prepared by dissolving the lyophilised proteins into 0.4 ml of a 20 mM phosphate buffer, or by buffer exchange with a ... et al., 1993) program and analysed by MolMol graphic software (Koradi et al., 1996) 15 N T1 and T2 relaxation times and {1H}-15N steady-state NOEs of the wild type SH3- and SH3-3 were determined...

Ngày tải lên: 14/09/2015, 14:09

... angles Between β-strands and are the long RT loops arranged in an anti-parallel manner, and between β-strands and are the shorter n-Src loops (Figure 3.3A and D) Both RT and n-Src loops were ... chain connectivity, the NMR structures of the hNck2 SH3-2 and SH3-3 domains were calculated by CYANA and further refined by CNS Table 3.2 summarizes the constraints used and structural statistics ... electrostatic potential surface of SH3-2 and SH3-3, respectively P1 and P2 stand for Pocket and Pocket 2, which are labelled accordingly for SH3-2 and SH3-3 P3 stands for the specific pocket that normally...

Ngày tải lên: 14/09/2015, 14:09

... secondary -structure fractions are given in the analysis of CD spectra by different programs: 15% helix, 35% turn/strand, and 5% random coil by CONTINLL; 12% helix, 46% turn/strand, and 42% random ... turn/strand, and 42% random coil by SELCON3; and 5% helix, 59% turn/strand, and 36% random coil by 94 Figure 4.1 Bioinformatics analysis of secondary structures A) Secondary structure prediction of the ... the first hNck2 SH3 domain by computational programs GOR4, PHD, Predator, SIMPA96 and SOPMA “E” stands for the β-strand, “H” stands for helix and “C” stands for the random coil The four residues...

Ngày tải lên: 14/09/2015, 14:10

... β-strands, six between the second and third strands, seven between the third and fourth strands, and seven between the two RT-loop strands No long-range NOEs in the fifth β-strand were detected, probably ... of three seconds and a relaxation delay of five seconds at 800 MHz NMR data were first processed with an NMRPipe and subsequently analysed and fitted by NMRView The solution structure of the ... dimension and 18 ppm at 15 N dimension indicate that SH3-1-V22, -A22, -K22 and -D22 are in an unstructured state Meanwhile, these mutants and the wild type SH3-1 were also studied by CD, as shown...

Ngày tải lên: 14/09/2015, 14:10

... conducted on both ApLLP and its homologs, in this study we cloned and expressed the entire and the two dissected ApLLP forms and subsequently characterized their structural properties and binding interactions ... inclusion body and was pre-purified by Ni2+-affinity chromatography under a denatured condition The released ApLLP (120AA) and ApLLP fragments (87AA and 55AA) were further purified by HPLC on a ... three-dimensional structure in complex with the CRE DNA element by use of NMR spectroscopy Unexpectedly, both bioinformatics and experimental results reveal that no predominant secondary and tertiary structures...

Ngày tải lên: 14/09/2015, 14:10

... 7.2 Future work 1) Structure determinations and study of binding diversity are carried out for both SH3-2 and SH3-3 domain in this project However, whether the ... connected by poly-GS link region with N/C terminal of SH3 domain or the one in which no covalent bond exists between SH3 and proline-rich peptides The dynamic information of loops and 310-helix ... project However, whether the hydrogen bond network is involved in the binding between SH3 domains and proline-rich peptides is still need to be answered Specific NMR experiments can be done to investigate...

Ngày tải lên: 14/09/2015, 14:10

... disulfide-bonding pattern and a similar fold The structure of colipase fold is solved using X-ray crystallography and it consists of short β-strands connected by loops and stabilised by disulfide bonds, ... X-ray diffraction and Bragg’s law 23 1.7.4 Reciprocal space 24 1.7.5 The Ewald sphere 25 1.7.6 Fourier transformation and structure factor equation 25 1.7.7 Phase problem 26 STRUCTURE DETERMINATION ... Resonance (NMR) spectroscopy and cyro-electron microscopy Each technique has its own strengths and limitations and complements each other in structure determination 1.6.1 History and application of macromolecular...

Ngày tải lên: 04/10/2015, 10:23

... conformational space allowed by the constraints For this reason, a structure solved by NMR is in fact a bundle of structures rather than a unique one, and its quality is assessed by the root-mean-square ... is done by solving Newton’s equation of motion.51,52 In practice, a combination of DG and rMD is often adopted,53 in which initial conformations are generated by DG and used as starting structures ... understanding of the methods used for structure determination The key steps of spectral analysis and the challenges faced when dealing with large proteins are discussed The review ends by identifying...

Ngày tải lên: 04/10/2015, 15:45