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...

Báo cáo khoa học: Mapping the binding domains of the aIIb subunit A study performed on the activated form of the platelet integrin aIIbb3 pot

... ﬁbrinogen -binding domains on the aIIb subunit was accomplished and their potential role in platelet aggregation was determined More speciﬁcally, a detailed mapping of the aIIb subunit was performed ... 57–64 are potential ﬁbrinogen -binding domains on the aIIb subunit of aIIbb3 and the corresponding peptides inhibit platelet aggregation and antagonize ﬁbrinogen association, possibly by interacting ... ﬁbrinogen Discussion The aim of the present study was to map the ﬁbrinogenbinding domains on the aIIb subunit of the platelet aIIbb3 receptor, in its activated form To achieve this, a highthroughput...

Báo cáo y học: "Mutation in the loop C-terminal to the cyclophilin A binding site of HIV-1 capsid protein disrupts proper virus assembly and infectivity" ppt

... analysis of capsid mutants Structural view and Western blot analysis of capsid mutants A close view of the structure of the cyclophilin A binding loop in the N-terminal (A) and the position of ... antibody Since the E9 8A mutation is located C-terminal to the CypA -binding site and CypA has been suggested to disrupt CA-CA interactions following cell entry of the virus, we tested whether the reason ... a 593 bp fragment of the p17 viral RNA The outer primer pair 5'-GCA GTG GCG CCC GAA CAG and 5'-TTCTGA TAA TGC TGA AAA CAT GGG TAT and inner primer pair 5'-CTC TCG ACG CAG GAC TC and 5'-ACC CAT...

Tài liệu Báo cáo khoa học: The role in the substrate speciﬁcity and catalysis of residues forming the substrate aglycone-binding site of a b-glycosidase docx

... Furthermore, these data may be of particular importance in understanding the physiological role of b-glycosidases and in designing inhibitors In addition, another important issue in understanding the aglycone ... details about the role of different residues of the aglycone-binding site in the stabilization of ESà and the interdependence between the binding of aglycone and the positioning of glycone in ... planned taking into account the residues found in the b-glycosidase from A B C D E Fig Comparison of the aglycone-binding site of some b-glycosidases (A) Aglycone-binding site of ZmGlu1 The aglycone...

Báo cáo khoa học: Binding of ATP at the active site of human pancreatic glucokinase – nucleotide-induced conformational changes with possible implications for its kinetic cooperativity doc

... interaction of ATP with hGK, with possible implications for the positive kinetic cooperativity with respect to Glc Results ATP binding at active site of human glucokinase (WT) hGK and WT GST–hGK enzymes ... steady-state kinetic analyses are also compatible with conformational control of GK catalytic activity by the binding of (Mg )ATP, with possible implications for kinetic cooperativity with respect ... The modelled structure of the hGK ATP binary complex shows the residue contacts involved in ATP binding at the active site Our ﬁndings further support conformational regulation of GK by ATP binding, ...

Báo cáo khoa học: Interactions of imidazoline ligands with the active site of puriﬁed monoamine oxidase A potx

... inhibitors of puriﬁed MAO -A, in agreement with the data of Ozaita et al (1997) for membrane-bound MAO -A and MAO-B [5] Spectral changes and the alteration of the redox properties of the ﬂavin (Figs and ... for the active site than reported values for I2BS It seems clear that the active site of MAO is not the site to which I2BS ligands bind with nanomolar afﬁnity However, imidazolines bind at the active ... idazoxan) in the human and rat brains J Pharmacol Exp Ther 264, 1187–1197 Ozaita A, Olmos G, Boronat MA, Lizcano JM, Unzeta M & Garcı´ a- Sevilla JA (1997) Inhibition of monoamine oxidase A and B activities...

Báo cáo Y học: Subsite mapping of the binding region of a-amylases with a computer program ppt

... has been made to use this program for subsite mapping of other a- amylases found in the literature Evaluations of subsite maps of rice and barley a- amylases are thus also presented MATERIALS AND ... way to explore the nature of the binding site and the process of catalysis for a- amylases Although the overall structure and the tertiary folding of the polypeptide chains of different a- amylases ... position of the cleavage site can vary according to the calculations The primary calculated subsite energy values can be reﬁned to the best agreement of the measured and recalculated BCF data by the...

$Báo cáo Y học: Differences in the binding capacity of human apolipoprotein E3 and E4 to size-fractionated lipid emulsions pot$

Báo cáo Y học: Differences in the binding capacity of human apolipoprotein E3 and E4 to size-fractionated lipid emulsions pot

... apoE3 and apoE4 bind preferentially to small and large lipid particles, respectively Interaction of ApoE3 and ApoE4 with EggPtdCho /TO lipid emulsions Direct binding analysis of ApoE3 and ApoE4 to ... apoE3 and apoE4 to fractionated lipid emulsions, we also employed a direct binding using Myr2Gro-PCho /TO fraction and physiological concentrations of apoE The binding isotherms for the apoE3 and ... possibility that any one or a combination of these properties may in uence the binding of apolipoproteins to lipoprotein particles The capacity to fractionate lipid emulsions into relatively homogeneous...

Báo cáo khoa học: Different roles of functional residues in the hydrophobic binding site of two sweet orange tau glutathione S-transferases pdf

... C-terminal domain, including the highly conserved GSH -binding site (G -site) and the more divergent cosubstrate -binding domain or hydrophobic binding site (H -site) [7,18] The G -site includes both a-helices ... structure elements The topological arrangement of these elements is usually bababba, similar to the thioredoxin fold of other GSH -binding or cysteine -binding proteins The H -site is entirely helical, ... quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal Biochem 72, 248–254 40 Laemmli UK (1970) Cleavage of structural proteins during the assembly of head of...

Báo cáo khoa học: Functional analysis of the aglycone-binding site of the maize b-glucosidase Zm-p60.1 pot

... and catalytic properties of the mutants, and simulations of the substrate–enzyme interactions of the wild-type and one of the mutants The results provide indications of the native enzymes’ catalytic ... construction of the mutant b-glucosidases Findings that cytokinin-O-glucosides are natural substrates for both of the two b-glucosidases, Zm-p60.1 and Bgl4:1, but the architecture of their sites that ... sites involved in the two modes of aglycone binding The amino acid sequence of Zm-p60.1 was compared with the sequences of 22 other members of the GH1 family from 13 plant genera The resulting alignment...

Báo cáo khoa học: Mapping of the interaction site of CP12 with glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii Functional consequences for glyceraldehyde-3-phosphate dehydrogenase pot

... observed with the A8B8 isoform of GAPDH leading to the A2B2 isoform with a higher NADPHdependent activity [39] By analogy with the CTE of the isoform of GAPDH [15,37], we hypothesize that the disulﬁde ... Involvement of the negative charge of the residue D36 of CP12 in the interaction between CP12 and GAPDH In order to conﬁrm that residues from the central part of CP12 are involved in the interaction with ... of CP12 to thioredoxin in the GAPDH ⁄ CP12 complex is speciﬁcally due to the interaction of CP12 with GAPDH Impact of cysteine residues of CP12 on the reconstitution of the subcomplex GAPDH/CP12...

Báo cáo khoa học: Mapping of the active site of glutamate carboxypeptidase II by site-directed mutagenesis potx

... domains of GCPII cooperate to form the active site and substrate binding cavity of GCPII [26,27] A more detailed insight into the active site was obtained by an analysis of crystal structures of the ... Fig 4A) A B Active site of glutamate carboxypeptidase II A model of the rhGCPII ⁄ NAAG complex: identiﬁcation of residues delineating the S1 pocket QM ⁄ MM calculations of the rhGCPII ⁄ NAAG complex ... B & Neale JH (2004) Synthesis of ureabased inhibitors as active site probes of glutamate Active site of glutamate carboxypeptidase II 35 36 37 38 39 40 carboxypeptidase II: efﬁcacy as analgesic...

Báo cáo khoa học: High-resolution NMR studies of the zinc-binding site of the Alzheimer’s amyloid b-peptide pdf

... envisaged as coordination of the metal ion by the nitrogens of the imidazole rings of the histidines and the amino group in the N-terminus Use of the signal intensity reduction of the 1H–13C HSQC crosspeaks ... J Danielsson et al Zinc-binding site of the amyloid b-peptide The aromatic region of the 1H–13C HSQC spectrum is particularly informative about the effects of Zn2+ (Fig 2) The Tyr10 aromatic ... complexation with the buffer, we can only obtain an estimate of the order of magnitude of the dissociation constants On the other hand, from NMR we obtain an unambiguous description of the binding...

Báo cáo khoa học: Characterization of mutations in crucial residues around the Qo binding site of the cytochrome bc1 complex from Paracoccus denitriﬁcans pdf

... change in the redox state of the stigmatellin In conclusion, the redox-induced FTIR difference spectra of the site- directed mutations in the Qo binding site of the bc1 complex from P denitriﬁcans, ... within the Infrared spectroscopic characterization of mutations in the Qo site binding site This observation is not surprising in the light of previous data showing that mutations on the Y302 site ... complexes from other organisms The mutated residues are highlighted in Fig Results Site- directed mutations in the Qo binding site Mutations in conserved positions of cytochrome b at the Qo site were...

Báo cáo khoa học: Kinetics of the quinone binding reaction at the QB site of reaction centers from the purple bacteria Rhodobacter sphaeroides reconstituted in liposomes docx

... data [14] shows that the detergent itself is located in the channel into which the quinone isoprenoid chain sits in the enzyme This explains the slow exchange process of the quinone at its binding ... regardless of the the electron reaches the QA site in a reaction center without redox state of QA (Fig 1), as we assume that the presence of the quinone in the QB pocket, only the charge recombinathe ... primary quinone acceptor located in The geometry of the liposomes is in agreement with that the QA binding site For proteins in which the QB pocket is obtained by Palazzo et al [24] for liposomes...

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