Ebook Organic structure determination using 2D NMR spectroscopy Part 2

Báo cáo khoa học: Solution structure of long neurotoxin NTX-1 from the venom of Naja naja oxiana by 2D-NMR spectroscopy pot

... the length of loop I is longer in short neurotoxins The NMR structure of NTX-1 is closest to that of the a-cobratoxin crystal The superposition of these two ˚ structures shows an RMSD value of ... similar They all show a conformational variability at the tip portion of loop II, with the difference being that the length of the b-strands in NTX-1 is longer than in the others These neurotoxins ... neurotoxin- 1 from Naja ˚ naja oxiana venom at 1.9 A resolution FEBS Lett 320, 111–117 Connolly, P.J., Stern, A.S & Hoch, J.C (1996) solution structure of LSIII, a long neurotoxin from venom of Laticauda...

facilitation of protein three-dimensional structure determination using enhanced peptide amide deuterium exchange mass spectrometry (dxms)

... by Enhanced Amide Hydrogen -Deuterium Exchange Mass Spectrometry (DXMS) Blood 100:259a xviii xix ABSTRACT OF THE DISSERTATION FACILITATION OF PROTEIN 3-D STRUCTURE DETERMINATION USING ENHANCED PEPTIDE ... labeling of proteins via amide hydrogen /deuterium exchange followed by proteolytic fragmentation of labeled protein and analysis by mass spectrometry Hydrogen /deuterium exchange mass spectrometry ... Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry J Mass Spectrometry 1997;32:135-146 14 Thomas, Jr GJ Raman spectroscopy of protein and nucleic acid...

Báo cáo khoa học: Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination potx

... been developed with the goal of obtaining structural and Macromolecular NMR for the non-spectroscopist II dynamic information from such systems [79–83] As for solution- state NMR, the development ... even though no information can be obtained about the site on the protein receptor to which the ligand binds In STD -NMR, the interaction is monitored by observing the NMR spectrum of the ligand, following ... move beyond mapping of binding surfaces to the determination of a high-resolution structure of a complex using experiments based on the NOE (see the accompanying review [1] for an explanation) For...

DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY

... DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY ZHANG LEI B.SC (HONS.), NUS A THESIS SUBMITTED FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE ... cycle of refinement may go on several times before a high resolution structure can be determined Figure 1.5: Outline of the procedure for protein structure determination by NMR For the context of ... representation of pulse sequences used in multidimensional NMR experiments Figure 1.5: Outline of the procedure for protein structure determination by NMR 15 Figure 1.6: Effects of protein size on NMR signals...

Tài liệu Báo cáo khóa học: Determination by electrospray mass spectrometry and 1H-NMR spectroscopy of primary structures of variously fucosylated neutral oligosaccharides based on the iso-lacto-N-octaose core doc

... produced by cone voltage fragmentation [14] The fragment ions of m/z 729 and m/z 544 are both from the monofucosylated D2b-5 ion m/z 1037 and not from the difucosylated D2b-5 ion m/z 1183 Thus the ... iLNO core structures and its variously fucosylated analogues, and to determine their anomeric configurations and linkages The proton chemical shifts of Ó FEBS 2004 Sequence determination of oligosaccharides ... previously as a core type [24] based on the identification of its fucosylated derivatives The monofucosylated iso-lacto-N-octaose, containing a Fuc at the first GlcNAc residue of the 6-branch forming...

Mapping the binding site of ligands to proteins using chemical exchange parameters by NMR spectroscopy

... design The TRAIL agonist (TNF related apoptosis inducing ligand receptors) Inhibitors of Bcl-2 family proteins [57, 58] Inhibitors of IAP proteins (inhibitors of apoptosis) Inhibitors of MDM2 ... at the protein to ligand ratio of 1:1, whereas saturation could not be reached for G94 3.3.4.3 Binding site analysis using NMR based parameters The mapping of binding site was carried out using ... characteristic selectivity towards the target protein are chosen for further study into the nature of the interaction[14] The identiﬁcation of the binding pocket for these molecules is the subsequent stage...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 1

... properties of the hNck2 SH3 domains 1. 5.2 Secondary structure transition study of hNck2 SH3- 1 domain The unfolding of SH3- 1 induced by the pH change and transition from the β-sheet dominant to the helical ... main binding region of DOCK180 was located at region 18 19 -18 36 In addition, two of the other weak binding sites were pinpointed at the region of 17 93 -18 10 and 18 35 -18 52 respectively Finally, these ... that Wrch1 is one of the binding partners of Nck2 The interaction was shown to be mediated via PxxP motifs in the N-terminal of Wrch1 to the second and third SH3 domains of Nck2 Wrch1, which...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 2

... relaxation delays of 10, 30, 45, 60, 75, 90 and 150ms 15 N T1 and T2 relaxation times and {1H}-15N steady-state NOEs of SH3- 1-V 22 52 (insertion of Val at 22 nd) were determined at 20 °C 15 N T1 values ... delays of 10, 500, 50, 300, 100, 400 and 20 0ms 15 N T2 values were determined with relaxation delays of 10, 50, 80, 120 , 150, 180, 21 0, 23 0 and 25 0 ms 15 N T1 and T2 relaxation times and {1H}-15N ... 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 on the 800...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 3

... characteristic of all SH3 domains Figure 3. 3C shows a superimposition of hNck2 SH3- 2 and Nck1 SH3- 2 domains recently 60 Figure 3. 2 HSQC and sequential assignments of SH3- 2 and SH3- 3 A shows the HSQC and ... 0 .37 Secondary structure regions 64 3. 2.2 HSQC identification of the residues involved in binding of the hNck2 SH3 Domains The interactions between hNck2 SH3 domains (SH3- 2 and SH3- 3) and their ... Comparison of the structures of the hNck2 SH3- 2 domain (blue) and Nck1 SH3- 2 domain (2CUB, green) (D and E) Superimposition of the ten lowest-energy NMR structures of the hNck2 SH3- 3 domain in...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 4

... β-sheets The first, the last and the first half of the second β-strand constitute the first β-sheet, whereas the second half of the second β-strand, together with the third and fourth β-strands constitutes ... with the lowest target function and its ensemble of ten structures superimposed over residues 32 44 Right: Ribbon representation of the NMR structure of the 4AlaMut SH3 domain at pH 6.5, with the ... Tyr9-Leu28 and Lys32-Thr 44 On the other hand, faster motions contribute to the wild type at pH2.0 and 4AlaMut, since higher values are observed, as shown in Figure 4. 8 4. 4 Discussion The folding...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 5

... HG Val53 HN Tyr52 HN Glu54 HN Arg 55 HN Glu54 HN Val53 HN Glu54 HN Tyr52 HB Arg 55 HN Val53 HG Arg 55 HN Val53 HB Table 5. 2 Native like long range NOEs Between the first and second beta strands Val3 ... between the SH3- 1-V22 and WT at and 1H frequencies, especially at the N- and C-terminals of SH3- 1 1 25 Figure 5. 3 Assignments of SH3- 1-V22 at pH 4.0 and V22△ in 8M urea The upper panel is the SH3- 1-V22 ... the right-hand corner 123 5. 3.3 Assignment, secondary CS analysis and dynamics study of SH3- 1-V22 As mentioned in the previous section, the insertion at the tip of the diverging turn of the SH3- 1...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 6

... both the CD and NMR spectra; the NMR titration experiment shows that the binding event mainly happens in the Cterminal of the ApLLP; 2) Consistent with the NMR study, the CD spectra show that there ... 159 Figure 6. 5 Bindings of the CRE DNA to two ApLLP proteins A–B) Superimposition of the 1H–15N NMR HSQC spectra of ApLLP-87, A) and ApLLP-55, B) in the absence and in the presence of the DNA fragments ... characterized their structural properties and binding interactions with the CRE DNA element by the use of CD and NMR spectroscopy 6. 2 Materials and Methods 6. 2.1 Cloning, expression, and purification of...

NMR study of the human NCK2 SH3 domains structure determination, binding diversity, folding and amyloidogenesis 7

... 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 hydrogen bond ... between SH3 and proline-rich peptides The dynamic information of loops and 310-helix in the complex system will give us more functional implication 3) If the solubility and stability problems of whole ... 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 the hydrogen bond connections...

Magnetic resonance spectroscopy correlation with histological analysis in gliomas and structure determination of a hypothetical protein

... N-Acetyl aspartate (NAA), N-Acetylaspartylglutamate (NAAG), Alanine, Choline, Creatine, Glutamate, Glycine, Myo-inositol, Lactate, Pyruvate, Serine, Threonine, Tyrosine and Valine Acetate is an ... Magnetic resonance spectroscopy correlation with histological analysis in gliomas and structure determination of a hypothetical protein Xu Ying A THESIS SUBMITTED FOR THE DEGREE OF MASTER OF ... and fatty acid energy reserves, and compounds associated with neuronal function including glutamate, glutamine, γ-aminobutyric acid (GABA), and N-acetylaspartate, a putative neuronal maker, are...

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