Polar residues bulky

I-Solenoid repeats usually have several x or x x sequence patterns that correspond to the /1-strands (here, denotes an apolar residue, and x is mostly polar but can be any residue except pro line). The middle -position in x x usually has a bulky apolar residue, while -residues in positions close to turns are often alanine, glycine, serine, or threonine. These positions are also occupied by asparagine residues that stack to form H-bonded ladders inside the /1-solenoid. The strand-associated x and x x patterns are interrupted by regions enriched in polar residues and glycine (Hennetin et al., 2006). These are regions of turns and loops. The long loops frequently contain proline residues. In several /1-solenoids, the alternation of apolar and polar residues that is typical for /1-strands is not well observed and outside positions are occupied by apolar residues. 

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).

Finally, L-type /2-solenoids have an unusual inverted arch (Fig. 12). Stacking of these arches makes a groove which forms the center of the binding site for polysaccharides or pectins (Jenkins and Pickersgill, 2001). In contradistinction to the other arches, the arc residues of inverted arches are interior-facing and are apolar, while residues in the -conformation which bound the arc, face the solvent and are mostly polar (Fig. 12). These arcs have ab conformations. Frequently the first arc residue is small, glycine or alanine, and the second position is occupied by a bulky apolar residue. 

Fig. 16.14. Configuration of the M2 helices of the acetylcholine receptor in the closed and open states. The schematic representation is based on a comparison of the electron density map of the acetylcholine receptor in closed and open states. Only three of the five M2 helices are shown, a) Closed state the M2 helices are bent at the middle. The leucine residues point into the interior of the pore and prevent passage of ions, b) Open state the M2 helices are turned outwards at a tangent and the bulky leucine residues are removed from the center of the pore. Reorientation of the M2 helices causes a reorientation of polar amino adds that coat the interior of the pore. The polar amino acids (Ser and Thr residues) are oriented closer to the center of the pore and create a hydrophilic coating of the pore inner wall, which facilitates ion passage. According to Unwin,...

In these studies, the input sequence was represented by seven non-orthogonal physicochemical properties, namely, hydrophobicity, volume, surface area, hydrophilicity, bulkiness, refractivity, and polarity, with normalized values of (-1, 1). Thirteen-amino acid sequence windows were used, resulting in an input vector of 91 (i.e., 13 x 7) units. With the small number of training examples, the input units were only partially connected to the hidden layer in order to reduce the number of free parameters and avoid overtraining the network. The constraint was to connect each first hidden layer unit to one amino acid property exclusively, and that the size of the second hidden layer size was no larger than the first hidden layer. The output layer had exactly one unit to indicate whether the middle residue was in a membrane/non-membrane boarder. The process of development started with randomly generated architectures and resulted in 18 and 8 units in the first and second hidden layers, with a total number of free parameters of... 

The products made by the above synthetic processes still have large numbers of residual silanols, which lead to poor peak shapes or irreversible adsorption, because chemically bonded groups on the silica gel surface have large, bulky molecular sizes and, after the bonding, the functionalized silane cannot react with the silanols around the bonded ligands. Because such alkyl-bonded phases are used for reversed-phase separations, especially for chromatography of polar molecules, any silanol groups that remain accessible to sol-... 

More recently, the substrate specificity of /9-secretase has been explored and compared with that of other aspartic proteases using a range of dodecameric substrates based mainly on the j3 -cleavage site of APP (67). The substrate recognition site of /3-secretase extended over several amino acids, and /9-secretase accepted a wide range of peptidic substrates. In common with other aspartic proteases, /9-secretase prefers a leucine residue at position PI. However, unlike these enzymes, /3-sccrctasc accepts polar or even acidic residues at positions PI and P2. and prefers bulky hydrophobic residues, preferably valine, at position P3. 

The number and nature of unreacted surface silanols affects the character of a stationary phase. Initially free, geminol or associated silanols are minimized through a process known as endcapping, which bonds various species to the residual silanols. Hydrophilic endcaps or bulky steric endcaps that separate the hydrocarbon chains and prevent analyte interaction with the silica surface can be used. If residual silanols are left unreacted (and some always are), the analyte will be separated based on a combination of interactions with both the reverse-phase support and the highly polar silanol groups. Increased retention, changes in elution order, and tailing will result for basic compounds. 

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