Glycine model structure

Figure 5 shows the modeled structure for the a helix F interface in human 11(3-HSD-1, in which phenylalanine-188 and alanine-189 form an anchor. Alanine-189 is 3.5 A and 4.7 A from alanine-189 and alanine-185, respectively, on the other subunit. The phenylalanine-188 side chain is 3.2 A from glycine-192. There is a hydrogen bond between serine-185 and serine-196, which are 3.2 A apart. Alanine-185 is 4.7 A from phenylalanine-193. There also is a hydrophobic interaction between phenylalanine-193 and alanine-181, which are 3.9 A apart. 

This paper reports the systematic study of the apparent anhydrous micellar weights of the three principal bile salts found in man and their glycine and taurine conjugates in respect to bile salt concentration, counterion concentration, temperature, pH, and urea concentration. On the basis of these studies, model structures of bile salt micelles are proposed. Sodium dehydrocholate, a triketo bile salt, was also studied but was not found to form micelles. 

Edwards, J.V., Sethumadhavan, K., Lfllah, A.R Conjugation and Modeled Structure/Function Analysis of Lysozyme on Glycine Estmfied Cotton Cellulose-Fibers. (2000) Biocmjugate Qiemistry 11,469-473. 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

Glycine and serine form two dipeptides, Gly-Ser and Ser-Gly. As the ball-and-stick models show, even dipeptides have distinctive shapes that depend on their primary structure. 

Ivanciuc, 0. Design of topological indices. Part 25. Burden molecular matrices and derived structural descriptors for glycine antagonists QSAR models. Rev. Roum. Chim. 2001, 46, 1047-1055. 

Figure 1.6 The left-hand panel shows a molecular model of the glycinate/Cu l 1 0 structure with both enantiomers present in the heterochiral (3 x 2) unit cell, superimposed on an STM image of this surface. (Adapted with permission from Ref. [12]. Copyright 2002,...

Fig. 2.6 Comparison of the calculated structures for glycine in the gas-phase and in water (COSMO solvation model). Note that the central bond angle in the zwitterionic form 1 is distorted by the hydrogen bond length of 1.96A computed for this structure in the gas phase. When solvation effects are included in the calculation using COSMO, the electrostatic interaction is reduced in magnitude due to charge screening by water, and the bond angle distortion is no longer present.

Fig. 14. Structural prediction and modeling of a fragment of FHA from B. pertussis containing Rl-repeats. (A) Successive stages in the modeling. From top to bottom identification of the consensus sequence repeat, generation of 2D template of the coil, and the modeled 3D structure. In the consensus sequence, letters indicate residues that are conserved at the level of >60% identity, x is any residue and filled circles represent bulky nonpolar residues. Apolar residues are in red glycine in green. In the 2D template, open circles denote any (but mainly polar) residues, while filled circles denote conserved, mainly nonpolar, residues. Circles inside the coil contour indicate side chains located inside the structure and circles outside the contour denote side chains facing the solvent. Arrows indicate /(-strands. (B) A fragment of the crystal structure of FHA (Clantin et al, 2004) (on the top, in green color) and the 3D model (bottom, in brown).

Fig. 3. Structure and sequence of repeats present in the fibrous proteins discussed in this chapter. (A) The adenovirus triple -spiral. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Amino acids contributing to the hydrophobic core are labeled, as is the glycine in the turn. (B) Triple -spiral sequence repeats. Conserved hydrophobic residues are indicated by a hash sign, the conserved glycine or proline by an asterisk. (C) The T4-hber fold. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Several of the conserved amino acids are labeled. (D) Repeating sequences present in bacteriophage T4 fiber proteins (Cerritelli et al., 1996). Conserved amino acids are indicated by a small letter conserved hydrophobic residues by a hash sign, and conserved small amino acids by a dot.

To validafe the CT-REDOR concept, the experiments described above were performed on different model compoimds with known structure. As an example for a two-spin system, doubly labelled glycine ( N,... 

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