calculating steric effects from 3d molecular structures

... been compiled based on small-molecule structures [9–11] but there is growing evidence from high-quality protein models that the nuances of macromolecular structures should also be taken into account ... not obvious from the diffraction-space residuals Root-mean-square deviations from stereochemical standards Rmsd from standard stereochemistry indicate how much the model departs from geometrical ... by the deposition 2hyd [23] that corrected a series of faulty structures withdrawn from the PDB (together with papers retracted from several high-impact journals, vide infra) The header of the...

Ngày tải lên: 16/03/2014, 06:20

... homology [13] and the structures were expected to be similar Indeed, individual domains are similar although E differs from A and B in the domain organization The crystal structures of individual ... blue, SNAP-25 in green and the zinc ion in magenta as a sphere Coordinates were taken from PDB 1XTG Molecular structures of Clostridial neurotoxins In the hexapeptide (QRATKM)–BoNT ⁄ A complex, ... Garcia-Rodriguez C, Geren I, Lou J, Marks JD, Nakagawa T & Montal M (2008) Molecular structures of Clostridial neurotoxins Molecular architecture of botulinum neurotoxin E revealed by single particle...

Ngày tải lên: 22/03/2014, 15:21

... Results O2–-scavenging effects of organic selenium compounds in PMNs We demonstrated O2–-scavenging effects by testing whether selenoureas and selenoamides scavenged O2– from 4b-phorbol 12-myristate ... oxidase complex, p47phox, translocates from the cytosol to the cell membrane upon activation To examine the effects of selenoureas and selenoamides on O2– production from PMNs, we investigated the translocation ... stain Assay of effects on scavenging of O2– from PMNs Organic selenium compound solutions such as selenoureas and tertiary selenoamides were diluted with HBSS To analyze the real-time effects on...

Ngày tải lên: 23/03/2014, 07:20

... d-XI based on the X-ray structures According to the enediol mechanism, two bases transfer a proton from O2 to O1, and a proton from C1 to C2, respectively, producing ketose from aldose, as shown ... ion In the structures of d-XIs, a water molecule coordinating to the metal ion was thought to act as a base to transfer a proton from O2 to O1, but a suitable base to transfer a proton from C1 to ... located in the hydrophobic pocket formed by Trp57, Phe131, Trp179 and Phe66* from Mol-B without any steric hindrance from amino acid residues of the enzyme Trp179 nicely stacks with a pyranose...

Ngày tải lên: 29/03/2014, 08:20

... and removes SUMO to and from substrate proteins resembles that involved in ubiquitination [1,4] Like ubiquitin, SUMO Table Protein structures referred to in the review All structures except for ... are conserved from yeast to human [2] The crystal structures of human Aos1-uba2, human APPBP1-uba3, and of the partly resolved mouse uba1, are closely related [15,21,23] (Fig 3C) From the side ... involved in sumoylation, neddylation and ubiquitination reactions (A) and (B) are modified from [1], and (C) and (D) from [29] and [7], respectively The consensus lysine sites of SMT3 and SUMO-2 ⁄ 3,...

Ngày tải lên: 30/03/2014, 04:20

... in their frequency normalized by what we would expect More is to be learned from the fact that you can drink wine than from the fact that you can drink it even though there are more clauses in ... sink_, drift_, step off_, step from_ , dock_, righ L, submerge , near, hoist , intercept, charter, stay on_, buzz_, stabilize_, _sit on, intercept, hijack_, park_, _be from, r o c k , get off_, board, ... intercept-, stay with_, _be from, _hit, seize, damage_, _carry, t e a c h , use_, return_, destroy_, attack , " be, be in , take, -have_, -say_, _make, include_, see_ step from_ , park_, board , hit,...

Ngày tải lên: 31/03/2014, 18:20

Ngày tải lên: 24/05/2014, 10:27

... taken from areas along the nanowire growth direction till about 200 nm away from the end all show polycrystalline feature, as shown in Fig 4c (the transition area) The HRTEM image taken from the ... and 3D- 2D growth mechanism is believed to occur through a complex interplay between the lattice strain, surface energy, and surface migration It is worth note that the transition length from 3D ... investigated A transition from 3D nucleation to 2D growth in the initial growth stage was found in the nanoscaled channels, which resulting a structure transition of the nanowires from polycrystalline...

Ngày tải lên: 21/06/2014, 18:20

... Chapter 2: ELECTRONIC & STERIC EFFECTS Effects Electronic Steric Inductive Hyperconjugation Conjugation / Mesomeric INDUCTIVE EFFECTS (I) C-C σ bond in butane: almost completely ... stronger than I effects • C effects can be effective over much longer distances than I effects – provided that conjugation is present • I effects are determined by distance, C effects are determined ... of -CH2CH3 17 STERIC EFFECTS • A steric effect is an effect on relative rates caused by space-filling properties of those parts of a molecule attached at / near the reacting site • Steric hindrance:...

Ngày tải lên: 03/07/2014, 11:20

... Install ImageMagick from Binaries How to Install from UNIX-like Binary Releases 17 17 How to Install from a Windows Binary Release How to Install ImageMagick from Source Installing from a UNIX-like ... Options How to Extract Information from an Image How to get Brief Information from Images How to get Detailed Information from Images How to get Customized Information from Images How to Get Information ... Image Effects from the Command Line and PHP Unleash the power of ImageMagick with this fast, friendly tutorial and tips guide Sohail Salehi BIRMINGHAM - MUMBAI ImageMagick Tricks Web Image Effects...

Ngày tải lên: 03/07/2014, 16:10

... the underlying molecular mechanisms of AtHb1 function and signaling The hypothetical model deduced from transcriptome, metabolite and physiological analyses summarizes the main effects of AtHb1 ... statistically significant differences (t-test, p < 0.05) calculated from total N content * 6.25 analysed in three generations (T3-T5) calculated from seeds per pod * pods per plant >2 and a p-value of

Ngày tải lên: 11/08/2014, 11:21

... spectral studies for these complexes (vide supra) 4.7 3D Molecular modeling and analysis Based on the proposed structures (Fig 4), the 3D molecular modeling of one of the representative compounds, ... [UO2(bumphpbz)(H2O)2]2 (5), were carried out with the CS Chem 3D Ultra Molecular Modeling and Analysis Program The details of bond lengths, bond angles as per the 3D structures (Figs and 4) are given in Tables ... Advanced Inorganic Chemistry, fifth ed Wiley, New York, p 992 CS Chem 3D Ultra, Molecular Modeling and Analysis, Cambridge Available from: Durbin, P., Kullgren, B., Ebbe, S.N.,...

Ngày tải lên: 02/09/2015, 13:48

... matrix alignment We represent 3D protein structures as 2-dimensional (2D) distance matrices (see Section 2.4), and align these matrices instead of the original 3D structures The basic MatAlign ... Summary Analysis of 3-dimensional (3D) protein structures plays an important role in bioinformatics Since the functions of a protein is more closely related to its 3D structure than to its amino ... study of molecular evolution, drug design, genetic engineering, and enzyme synthesis, etc [LI03, Yon02] Protein functions can be studied by analysis based on either AA sequences or 3D structures...

Ngày tải lên: 15/09/2015, 17:10

Ngày tải lên: 15/09/2015, 17:10

... the result from our algorithm with that from Autodesk 1 23D, using similar number of patches As can be seen, the sliceform from our algorithm 37 Figure 7.1: Real paper sliceforms made from our algorithm ... algorithm that generates paper sliceform designs from 3D solid models The designs are guaranteed physically possible to be assembled Given an input 3D solid model (represented as polygon meshes), ... our algorithm 38 7.2 Comparison of sliceform generated from our algorithm (right) and that from Autodesk 1 23D (left) 7.3 Illustration of one side of...

Ngày tải lên: 01/10/2015, 11:39

... vasculature from MRA images Unlike existing MRA segmentation techniques, which have difficulty on extracting tiny vessels, the GCAC is able to segment the whole structures successfully from 3D MRA ... is a noninvasive medical imaging modality that produces 3D images of vessels and cavities Accurate extraction of 3D vascular structures from MRA images has become increasingly important for diagnosis ... [55] However, they may have difficulty in extracting tiny vessels from 3D images as they suffer from boundary leaking for complex structures [51] Moreover, the flow can be unacceptably slow to converge...

Ngày tải lên: 02/10/2015, 12:55

... two shortest peptides, extending from P3 to P4¢ and from P3 to P3¢, respectively The analogs NC-p1 and p1-p6 extended from P5 to P5¢, while p6pol-PR extended from P5 to P6¢ because lysine was ... difficult to obtain crystal structures of active PR with peptide substrates Two strategies have been used to analyze the structures of the transition state(s) We have analyzed structures of active PR ... using amore [40] The starting model for molecular replacement was chosen from the highest resolution structure available in the space group P21212 The structures were refined using the program...

Ngày tải lên: 30/03/2014, 20:20

... proteins from different Clostridium difficile clinical isolates Microb Pathog 28, 363-372 Chaves-Olarte, E., Weidmann, M., Eichel-Streiber, C., and Thelestam, M (1997) Toxins A and B from Clostridium ... S., Craig, J A., Putnam, C D., Carozzi, N B., and Tainer, J A (1999) Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex Nat Struct Biol 6, 932-936 155 Hancock, ... Spigaglia, P., Maggioni, A., Mauri, P., and Mastrantonio, P (2001) Molecular and genomic analysis of genes encoding surfaceanchored proteins from Clostridium difficile Infect Immun 69, 3442-3446 Karlsson,...

Ngày tải lên: 16/09/2015, 15:54

... transferase from hen heterophil, preventive efficacy of the vitamin derivative nicotinamide has differed depending on ADPRT source (Banasik et al., 1990; Rankin et al., 1989) Here we report in vitro effects ... (37%) preincubation MgCl2 and MnCl2 effects were diminished except by calmodulin which enhanced photoinsertion by 14-27% EDTA lowered Zn2+, Mn2+ and Mg2+ effects by 43%, 38% and 34% respectively ... (data not shown) 117 118 Figure 5.2 Representative phosphorimages showing effects of various compounds on CDT actions Effects of cations and chelators on [32P]NAD photoinsertion into CDT AC, CDTa...

Ngày tải lên: 16/09/2015, 15:54

... green (from 186.87+16.6 to 239.66+11.5) and decrease in red fluorescence (from 106.68+11.2 to 82.79+6.8) with combined effects resulting in a 1.2-fold rise in G-actin and registering 8.6-fold (from ... eluates, respectively M, high molecular weight protein ladder D, Lane contained cellular extract from pQE-30 of induced SK1203 Lane had CDTa and CDTb expressed from pDA576 of SK1216 in 10% SDS-PAGE ... in green (from 121.91+ 16.2 to 157.94+ 8.3) and 24.9% decrease in red signal (from 116.38+ 3.6 to 93.14+ 5.9), a trend reflected in single stained cells with 45.4% increase in green (from 102.98+...

Ngày tải lên: 16/09/2015, 15:54