structural dynamics of the vault ribonucleoprotein particle

... cloning of the gene encoding the secreted CM from Yersinia pestis (*YpCM, y2828), purification of the protein, investigation of the properties of the enzyme, and the crystal structure analysis of the ... the tail of one protomer to almost reach the active site of the neighbor Active site of 90-MtCM The structure of EcCM includes the TSA, which clearly identifies the active site From structural ... 2 N H 2 N H 2 N Fig 6 The active site of 90-MtCM: a diagrammatic view of the active site of 90-MtCM is shown, with the superimposition of the TSA from the EcCM structure The corresponding residue

Ngày tải lên: 17/03/2014, 17:20

... inwards, the arms close and the tips of the arms wrap around the DNA The amplitudes and time scales of the intramolecular motions experienced by the protein backbone are com-monly determined from the15N-NMR ... role in the stabilization of the proteinÆDNA complex The arm of MC1 can also be compared with the DNA-binding b-hairpin arms of HUs, which showed high mobility relative to the core (Fig 2) The b-ribbon ... variations of 25% on the nanosecond time scaleduring the 20 ns trajectory (Fig 5) These variations, resulting from the position of the arm, are correlated with internal motions of the overall

Ngày tải lên: 22/03/2014, 17:20

... Because of the large size of the core of the oligomer, the NMR spectra do not show any signals from the interior of the core and thus do not give any informa-tion on its structural details Nevertheless, ... assembles in the form of ringsaround the necks of budding vesicles, and then a con-formational change in the dynamin collar aids the scis-sion of the vesicle from the parent membrane The coiled-coil ... characteristics of the individual domains has the potential to throw valuable light on the interac-tions of the individual domains, and the mechanism and variety of the overall functions of the full length

Ngày tải lên: 23/03/2014, 11:20

... comparison of its MS with that of the reference compound The absolute configuration of glycoses was established by capillary GLC of their acetylated (-)-2-butyl glycosides, according to the method of ... studies have determined the structure of the O-chain polysaccharide of A salmonicida strain SJ-15 [11] Partial structure of the core oligosaccharide from the same strain of A salmonicida was also ... stainless steel needle (27 g) was butted against the low dead volume tee and enabled the delivery of the sheath solution to the end of the capillary column The separations were obtained on
90-cm long

Ngày tải lên: 23/03/2014, 13:20

... involved in the specificity of the enzymes compared According to the descriptions of the active sites of DPP-IV [3,18–22] and PepX [9], the residues involv-ed in the positioning of the substrate ... be the reference); 2, docked into the active site of the human DPP-IV; 3, docked into the active site of the crystalline structure of PepX from L lactis; and 4, docked into the active site of the ... The interactions of the bound ligand with the resi-dues of the specificity site (Fig 4A) reveal good stack-ing between the pyrrolidine rstack-ing of the drug and the side chain of Tyr380 (Pos1

Ngày tải lên: 23/03/2014, 13:20

... However, there is not much informa-tion about the existence of the soluble subcomplex (which is the electron input device in bacterial complex I) in the composition of the Ndh com-plex Furthermore, there ... the membrane subcomplex, while the remaining four subunits (NdhH–K) form the connect-ing subcomplex, both of them homologous to the bac-terial subcomplexes The theoretical molecular mass of the ... about the viability of ndh mutants [2,23,25] have clearly restarted the debate about the real function(s) of the Ndh complex To contribute to the structural and functional char-acterization of this

Ngày tải lên: 23/03/2014, 13:20

... origin of the moving object Meteors originate from the asteroid belt while comets are believed to originate from the Oort cloud The comet theory is substantiated by the observance of the body in the ... cP is the specific heat of the gas at constant pressure, y is the ratio of specific heats, c is the speed of sound, (T is the Stefan-Boltzmann constant, pa is the air density and T,, is the temperature ... considerable amounts of hydrogen and hence the deu- terium isotope As the comet entered the atmosphere, perature of the gas cap in front of the comet’s leading comet’s surface Consequently, the deuterium

Ngày tải lên: 23/03/2014, 13:20

... majority of the sulfated sugar In conclusion, the results obtained provide evidence of the nature of the glycans present in the unique N-glycosylation site present in the C-terminal domain of cruzipain ... Altogether, these data confirm the presence of sulfated high-mannose type oligosaccharides in cruzipain and in its C-terminal domain This is the first report of the use of nor-harmane as matrix for structural ... to characterize the N-linked glycans present in the protein In this paper we report, for the first time, the presence of sulfate in the N-linked oligosaccharides of cruzipain This structural feature

Ngày tải lên: 23/03/2014, 15:20

... located in the vicinity of the carbohydrate-binding pocket on the globular domain and of the protein disulfide isomerase ERp57, which is bound to the distal part of the arm domain [36] Although the precise ... surface of GABARAP, suggesting that this part of the structure should be relatively unaf-fected.) The overview at the top gives an impression of the overall variation among the three structures The ... throughout the GABARAP spectrum and the disappearance of certain peaks (Fig 2A) Again, the mutation of Trp183 to alanine in CRT(178–188) had a tremendous effect on the binding properties of the molecule

Ngày tải lên: 30/03/2014, 02:20

... the involvement of one of these clusters in the stability of the quaternary structure The present study focuses on the role of the same cluster in the stability of the cofactor binding site The ... follows that the last folding event may correspond to the formation of the third cluster of CHCs The for-mation of the cluster presumably fastens together all the structural components of the protein ... cofactor binding, substrate binding and catalysis (Fig 1) On the other hand, the mutations did not affect either the capability to bind the cofactor or the catalytic activity of the enzyme The

Ngày tải lên: 30/03/2014, 02:20

... of the chemical shifts of the protein-bound nucleotide analogue we first studied GTPcS in the presence and absence of Mg2+ ions within a pH range of 2–13 The rate of exchange between Mg2+and the ... broadening of the two lines of the c-phosphate group, and not to significant changes in chemical shift or the relative populations of the resonances In particular, the relative intensity of the downfield-shifted ... importance of the conform-ational equilibria Results Chemical shifts of the nucleotide analogue GTPcS in the absence and in the presence of magnesium ions Chemical shift values for the phosphates and the

Ngày tải lên: 30/03/2014, 09:20

... conformations in the vicinity of Ala88 and Ala112 induced by the hydrophobic interaction between the a2-helix and the membrane interface were lost in the structure of the PH domain at the surface of the PC⁄ ... NaCl eliminate the possibility that NaCl affects the affinity for binding to the PC ⁄ PIP 2 membrane in the absence of PS. These suggest that the lowering effect of PS on the membrane binding affinity of the ... suppress the effects of PS on the PH domain As shown in Fig. 2B, the addition of 25 mm NaCl cau- ses a decrease in the intensity of the Ala88 peak at 17.48 p.p.m. in the spectrum of the PH domain

Ngày tải lên: 30/03/2014, 10:20

... are located near the crossing region of the helices, and the Nx atom of K8 is found at a distance of 6.2 A˚ from the nearest side-chain oxy-gen of D72 Taking the functionally and structurally interesting ... native conformation under the influence of destabiliza-tion of the latter Microcalorimetry studies In order to obtain the thermodynamic parameters of the thermal unfolding of cyt c6 and its mutants, ... inspection of the data revealed interesting deviations from the general trend A reversal of the charge effect of the mutation K8D in the mutant D72K⁄ K8D did not lead to recovery of wild-type

Ngày tải lên: 30/03/2014, 20:20

... cutoff distance (rc ẳ 6.0 A) The dynamics of the resulting network are then dened by the Ni ã Nj Kirchhoff connectivity matrix of interresidue contacts (G) where the off diagonal elements of ... measurements of protein structural dynamics were performed to explain the observed kinetic catalytic behavior Thus, the question of whether the kinetics of a-CT catalysis are inuenced by the enzymes ... electrostatic potentials (EP) for the Ne of the lysine residues of a-CT at pH EP, EwaldEi EP is the Ewald energy of placing a charge of +1 at the location of the ith ionizable atom [89] Reactivity...

Ngày tải lên: 19/02/2014, 05:20

... is the cross-sectional average of the bank-specific variable αi of those banks for which there is an observation in month t As the composition of this sample changes in the course of time, the ... responsible We choose the following method of mitigating the problem of changing sample composition: Instead of the exposure levels Xi (t), we investigate the change in the exposure of the same bank, ... contribution of the systematic factor and the regulation to the total timely variation of the exposure is 17.24% and, therefore, 82.76% of the variation is due to idiosyncratic effects These effects...

Ngày tải lên: 16/02/2014, 06:20

... amount of time At the end of the heat treatment the mixtures were placed in an ice/water bath, and the enzymatic activity was stopped by lowering the pH of the reaction mixture to by addition of ... during the thermal treatment, hydrolysis of BLG was extensive, in spite of significant inactivation of the enzymes This indicates that the transient conformers originating in the course of thermal ... in these preparations could stem from the inability of the hydrolytic reaction to address all the sequential epitopes even in the denatured protein In fact, despite the apparent simplicity of the...

Ngày tải lên: 21/02/2014, 15:20

... activity of the enzyme was determined using the Betamyl b-amylase test reagent (Megazyme, Wicklow, Ireland) To determine the pH stability of the b-amylase, aliquots of a solution of the purified ... for h at 25 8C Then 0.1 vol of a solution of 0.5 M sodium acetate (pH 5.0) was added and the activity of the enzyme was measured by the dinitrosalicylic acid method Inhibition of the enzyme activity ... at their 50 and 30 boundaries, respectively, and were inserted between the third letter of one codon and the first letter of the following codon Molecular modeling of the C sepium b-amylase The...

Ngày tải lên: 22/02/2014, 07:20

... 1H,15N-HSQC spectra of the M domain of human eRF1 The numbering of the residues corresponds to that of the full eRF1 protein (A) The Gly region of the 15 H, N-HSQC spectrum of the M domain of human eRF1 ... hydrolysis at the PTC of the large ribosomal subunit [20] The three-domain structure of eRF1, with the shape of the protein resembling the letter ‘Y’, partly mimics the ‘L’-shape of the tRNA molecule, ... )42 The mean value in the family of 25 structures and the SD is no preferred conformation of the side-chain in the family 4228 v1 b There Fig The relaxation parameters of the amide 15N spin of...

Ngày tải lên: 07/03/2014, 05:20

... value of the mutant TNSALP was less than one-tenth of the Kcat ⁄ Km value of the soluble form of the wild-type enzyme, indicating that the replacement of valine with alanine at position 406 in the ... of TNSALP In support of our hypothesis, the cysteine residue at position 433 in one subunit of TNSALP (R433C) becomes crosslinked to the counterpart of the other subunit [29], implying that the ... containing the SV40 early promoter [11] Shortage of a precursor of GPI in the endoplasmic reticulum may be one of the reasons why a small but significant fraction of the wild-type TNSALP forms the aggregate...

Ngày tải lên: 07/03/2014, 05:20

... parameters, there is no relationship between S2 and the location of structural elements (Fig 4) Furthermore, the Rex terms are distributed throughout the 3D structure of the protein, and most of them ... Furthermore, the internal motions of each bond vector are independent of each other, but the rotational diffusion of the molecule affects each of those bond vectors identically [42,43] On the other ... responsible, from a thermodynamic point of view, for the binding of the monomeric species of CAC? We have previously discussed the variation in the free energy of binding as a function of the changes...

Ngày tải lên: 07/03/2014, 06:20