localizing flexible regions in proteins using hydrogen deuterium exchange mass spectrometry

... receptor-binding domain The C and T domains remain covalently linked by a disulfide bond Following binding to its cell-surface receptor, diphtheria toxin is internalized through the clathrin-coated ... diphtheria toxin is cleaved by furin into two fragments: the A chain corresponding to the catalytic domain (C domain); and the B chain corresponding to the translocation domain (T domain) and the ... rhizopuspepsin as a new tool for protein digestion in H ⁄ D exchange mass spectrometry Rapid Commun Mass Spectrom 23, 3431–3438 Zhang Z & Smith DL (1993) Determination of amide hydrogen exchange by mass...

Ngày tải lên: 16/02/2014, 09:20

... 1.10 MAPPING LEPIRUDIN BINDING SITES ON THROMBIN Amide hydrogen/ deuterium exchange was used to map the binding regions of the thrombin inhibitor lepirudin Using the procedures outlined in Figures ... MAPPING LEPIRUDIN BINDING SITES ON THROMBIN 12 1.11 ALLOSTERIC CHANGES IN THROMBIN STRUCTURE INDUCED BY LEPIRUDIN BINDING 13 1.12 RESOLVING CONFORMATIONAL CHANGES AND LIGAND BINDING ... labeled protein and analysis by mass spectrometry Hydrogen/ deuterium exchange mass spectrometry has been used to track structural changes in proteins involved in processes such as viral infection...

Ngày tải lên: 13/11/2014, 16:12

... proximity to both the C-terminal and turn residues, possibly interfering with these regions This explains how an altered conformation in the N-terminal region upon metal binding can affect sections ... mutagenesis combined with H ⁄ D exchange NMR [11], and cysteine scanning mutagenesis [49], where the Abs (which form two b-strands with a turn region involving Val24–Ala30) stack in an inregister ... because they lack tinctorial properties and fibrillar morphology, and they can be completely dissociated using chelating agents or by a slight increases in pH [19,28] Interesting parallels can...

Ngày tải lên: 30/03/2014, 01:20

... over-represented in gene regions encoding intrinsically disordered regions of proteins (a) The ratio of positive to negative sites is higher in IDRs than in regions of regular protein structure The ... of intact genes and proteins Intrinsically disordered protein regions have a higher proportion of fixed non-synonymous polymorphisms Having observed that intrinsically disordered protein regions ... Orengo C, Jones D: Inferring function using patterns of native disorder in proteins PLoS Comput Biol 2007, 3:e162 21 Wright PE, Dyson HJ: Linking folding and binding Curr Opin Struct Biol 2009, 19:31-38...

Ngày tải lên: 09/08/2014, 23:20

... of Surveying Engineering, Environmental Remote Sensing, Digital Image Processing, Graduation Date: 1995 M.Sc In Surveying Engineering (Remote Sensing), Building and Construction Engineering Department, ... Geomatics Engineering, Environmental Remote Sensing, Digital Image Processing, Graduation Date: 2012 B.Sc In Building and Construction Engineering Management, Building and Construction Engineering Department, ... Application of Geomatics Engineering, Environmental Remote Sensing, Digital Image Processing, Graduation Date: 1978 B.Sc In Surveying Engineering, Building and Construction Engineering Department, University...

Ngày tải lên: 09/09/2015, 10:06

... biomass, lysine, ammonia, threonine, valine, methionine, leucine and pyruvate in the chemostat medium throughout the continuous culture quantities in the medium Threonine, methionine and leucine ... The aspartate kinase enzyme of C glutamicum ATCC 21799 is insensitive to feedback inhibition from threonine and lysine [5] An excess of threonine, methionine and leucine was added in the preculture ... rigidity and metabolic engineering in metabolite overproduction Science 252, 1675–1681 44 Klapa, M.I., Aon, J.C & Stephanopoulos, G (2003) Using iontrap mass spectrometry in combination with gas chromatography...

Ngày tải lên: 08/03/2014, 08:20

... peaks formed corresponding to masses of m/z 279 (11.19 min, 12.37 min), m/z 265 (9.30 min, 11.87 min), m/z 295 (7.97 min, 8.86 min, 9.37 min, 10.34 min, 11.59 min) (summarized in Table 2-1) From ... 2' O 3' Indigo O N1 H Isoindigo FIG 1-2 Chemical structures of indigo and isoindigo In vitro metabolism of indirubin and its derivative, indirubin 3’-oxime in rat liver microsomes was investigated ... substituents are indirubin, a 3,2’-bisindole (Fig 1-1); indigo, a 2,2’-bisindole (Fig 1-2); and isoindigo, a 3,3’-bisindole (Fig 1-2) The chemical structures of indigo and isoindigo are shown in Fig 1-2...

Ngày tải lên: 14/09/2015, 14:08

... Amide Hydrogen/ Deuterium Exchange Amide hydrogen/ deuterium exchange followed by mass spectrometry is a method used to analyze the structure and dynamics of proteins Some hydrogen atoms in proteins ... binding cassette (PBC), serves as the cAMP binding site and is highly conserved amongst the PKA-R family and cAMP-binding proteins in general (Fig.1-6) (25) cAMP binds both domains of PKA-R in ... CBD-B), at the carboxy terminal each have cAMP binding domains with distinct roles Dimerization/ Inhibitor Docking Domain sequence Domain A Domain B RIα Figure 1-2 Domain organization of the PKA...

Ngày tải lên: 16/10/2015, 15:36

... terminus of helices in proteins J Mol Biol 322, 871–880 Manikandan K & Ramakumar S (2004) The occurrence of C– H…O hydrogen bonds in alpha-helices and helix termini in globular proteins Proteins ... Saenger W (1991) Hydrogen Bonding in Biological Structure Springer, Berlin Steiner T & Koellner G (2001) Hydrogen bonds with p acceptors in proteins: Frequencies and role in stabilising local 3D ... Thornton JM (1994) Satisfying hydrogen bonding potential in proteins J Mol Biol 238, 777– 793 Stickle DF, Presta LG, Dill KA & Rose GD (1992) Hydrogen bonding in globular proteins J Mol Biol 226, 1143–1159...

Ngày tải lên: 07/03/2014, 17:20

... H2O2-induced apoptosis by using HeLa cells in which expression of Hsp105a or Hsp105b was regulated using doxycycline Our results suggest Hsp105a and Hsp105b suppress H2O2-induced apoptosis by inhibition ... Apoptosis signal-regulating kinases (ASKs) are serine ⁄ threonine kinases that activate both the p38 MAPK and JNK signaling pathways as MAPK kinase kinase ASKs are activated in response to various ... St Louis, MO, USA) in buffer A containing 10 lm Hoechst 33342 for 10 in the dark Cells displaying phosphatidylserine externalization were observed using a confocal laser scanning microscope (LSM410;...

Ngày tải lên: 16/03/2014, 06:20

... membrane proteins involved in secretion of haemolysins or adhesins in various Gramnegative pathogens, proteins of the endosymbiotic organelles belong to the increasing list of such proteins [53] ... C-terminus of the investigated sequences (A) The positioning of the starting amino acid of motif in relation to the C-terminus and (B) the positioning of the starting amino acid of motif in relation ... polypeptidetransporting proteins and that it is involved in pore formation The possible function is discussed Results Motifs in b-barrel-shaped polypeptide-transporting proteins b-barrel type proteins are...

Ngày tải lên: 16/03/2014, 18:20

... IN inhibitors on HIV-1 and ASV IN joining activities Tests of the metal cofactor effects of HIV-1 IN inhibitors on HIV-1 and ASV IN joining activities A Dose response curves showing the joining ... biochemistry of IN proteins has been the focus of intense investigation IN proteins catalyze two sequential and temporally distinct reactions during infection, see (Figure 1A) [2,3] In the first ... of HIV-1 IN inhibitors that are effective against ASV IN We were also interested in evaluating the utility of the fluorescent assay for determining IC50 values for integrase inhibitors In this...

Ngày tải lên: 10/08/2014, 05:21

... Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Albumin Prolactin-inducible ... Prolactin-inducible protein Prolactin-inducible protein Prolactin-inducible protein Prolactin-inducible protein Cystatin S Cystatin S Cystatin SN Hemoglobin beta chain Hemoglobin beta chain Intersectin ... Table 2: Proteins differently expressed in allergic and non-allergic individuals Protein Psoriasin Psoriasin Prolactin-inducible protein Transthyretin Ig gamma chain c region Wnt-2B protein (splice...

Ngày tải lên: 12/08/2014, 18:22

... anion-binding regions of proteins J Mol Biol 2002, 315:183-191 Watson JD, Milner-White EJ: A novel main-chain anion-binding site in proteins: the nest A particular combination of phi,psi values in ... peptide) bonds, in linear amidines; GO:0019239, deaminase activity; GO:0043167, ion binding; GO:0043169, cation binding; GO:0046872, metal ion binding) The level of each GO term is indicated in the round ... building blocks approach to analyzing and predicting structure of proteins Proteins 1989, 5:355-373 Haspel N, Tsai CJ, Wolfson H, Nussinov R: Reducing the computational complexity of protein folding...

Ngày tải lên: 14/08/2014, 08:20

... form flexible regions of proteins that might have a number of functions, including binding to other proteins and small molecules and providing flexibility in multidomain proteins In an analysis ... mammalian proteins and 13% of chicken proteins contained some kind of tandem AAR and 12% of mammalian proteins and 9% of chicken proteins contained some kind of C4 repeat; 4.6% of IURs contained a ... be involved in protein-ligand binding, including protein-protein interactions, forming compact structures only when bound to a cognate ligand [24] Tompa [25] pointed out that many IURs contain...

Ngày tải lên: 14/08/2014, 21:20

... neuroprotection in glaucoma [26-28] The HSPs, called by stress proteins, are a group of proteins that exist in all of the living creatures covering bacteria to human beings HSPs can be induced in living ... Identification of Induction of Heat Shock Proteins 72 - Cell Staining (Fluorescein Isothiocyanate and 4’, 6-Diamino-2Phenylindole) and Western Blot Analysis 60 3.6 61 Infusion of SPNPs to Retina in Animal ... induction of HSPs 72 in RGCs using MFH and improvement of HSP 72 induction efficiency a Measurement of the AC heating temperature in RGCs treated by SPNPs b Control of the AC heating stress in...

Ngày tải lên: 09/09/2015, 10:08

... coastline Winds acting on this sub-region are generated from strong typhoons directly approaching the coastline between Hai Phong and Ninh Binh, the coastline of Thanh Hoa and the southern coastline ... mountains extend to the ocean causing wind speed sharply reduces in the lowsea level areas In the valleys of Binh Lieu and Ba Che, effects of typhoons are almost insignificant In areas of high altitude, ... branches in motion; whistling heard in telephone wires; umbrellas used with difficulty 51-62 (32-38) Near typhoon / 13-18 Whole trees in motion; inconvenience felt when walking against the wind 63-75...

Ngày tải lên: 01/04/2013, 22:47

... departments interfere as little as possible in each other's Try mixing large and small chunks Try pausing after single words like but, so and first p,-esentinginenplish 3.5 using- yourvoice Chunking ... Ignore everything everything I'm telling you I'm telling you What is this thing What is this thing called What called love? love? is this thing called love? presenting if? engiish using JIUUT YO~CE ... will be outlining this afternoon all concern, in one way or another, this fundamental flaw in the free market system presenting i english n using your voice Chunking m TASK The following extract...

Ngày tải lên: 25/10/2013, 19:20

... profiling, and utilizes lectins, a group of glycan-discriminating proteins In general, however, the glycan–lectin interaction is relatively weak in comparison with, for example, antigen–antibody interactions ... current principal technologies in use are: (a) de novo sequencing; (b) glycan mass fingerprinting [29]; and (c) MSn spectral matching [2,30–32] Determination of glycan structures using the first ... lectin binding to increase their sensitivity The final challenge to be faced is the feasibility of using biomarkers in the drug development process Incorporation of biomarkers into phase II clinical...

Ngày tải lên: 16/02/2014, 08:20