Amino acid residue model

Fig. 23. Possible helical models for the gramicidin A ion channel. The polypeptides are represented as helical strips, one molecule being stippled for clarity. Numbers refer to the substituted terminal amino acid residues. Model (i), proposed originally by Urry, is the one now generally accepted...

Amino acid residue models such as a tyrosine residue model (p-cresol) lengthen remarkably the charge hopping distance, a phenomenon which can solve i he problem in the electrocatalysis mentioned in the above item 5) and enhance remarkably the catalytic activity. 

The aromatic amino acid residue model, 3-methylindole as a model of tryptophan residue, was codispersed in the above Ru(bpy)3 /MV system. In the presence of the mediator model the electron transfer was greatly enhanced [86]. An equation taking into account mediated electron transfer was derived (see [86]), and applied to the results giving mediated electron transfer of 2.7 nm, which is about twice that without the mediator. Tiyptophan itself or a model of tyrosine (p-cresol) was not effective for the mediation. 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

A model for the allosteric behavior of hemoglobin is based on recent observations that oxygen is accessible only to the heme groups of the a-chains when hemoglobin is in the T conformational state. Perutz has pointed out that the heme environment of /3-chains in the T state is virtually inaccessible because of steric hindrance by amino acid residues in the E helix. This hindrance dis-... 

It is known that native collagen contains tripeptide sequences which, because of being homopolypeptides, are not able to give rise to triple-helical tertiary structures (e.g. Gly-Pro-Leu, Gly-Pro-Ser). The reason for this and for the above-mentioned low thermostability of the synthetic homopolypeptides is presumably to be found in the fact that in the case of the model peptides with their monotonously repeated tripeptide sequences, special interactions between the side chains of the different amino acid residues as postulated by Ward and Mason are no more possible157). 

While conformation II (Fig. 2.34) of Uke-y -amino acids is found in the 2.614-helical structure, conformation I, which similarly does not suffer from sy -pen-tane interaction, should be an appropriate alternative for the construction of sheet-like structures. However, sheet-like arrangement have not been reported so far for y-peptides composed of acyclic y " -amino acid residues. Nevertheless, other conformational biases (such as a,/9-unsaturation, cyclization between C(a) and C(y)) have been introduced into the y-amino acid backbone to restrict rotation around ethylene bonds and to promote extended conformation with formation of sheets in model peptides. Examples of such short chain y-peptides forming antiparallel (e.g. 152 [208]) and parallel (e.g. 153-155 [205, 208]) sheet-hke structures are shown in Fig. 2.38. 

Several results are quite apparent from the data shown in Table II. It is evident from the pentapeptide model compounds that substitution of amino acid residues at positions 4 and 5 does not significantly affect the structure about the N-terminus. This observation corroborated earlier work from agglutination-inhibition assays, which demonstrated that the nature of the amino acid at position 4 of the peptide (or glycopeptide) is not a requirement for specificity. 

Fig. 3. Model for the two-dimensional arrangement of the human erythrocyte glucose transporter in the membrane. Amino acid residues are identified by their single letter code. Solid bars indicate the location of introns in the transporter gene. The regions coloured black are released from the membrane upon tryptic digestion. Shaded segments indicate the probable regions photolabelled by ATB-BMPA (helix 8) and by cytochalasin B (helix 11 and the loop connecting it to helix 10). The circles with heavy outlines indicate the region labelled by lAPS-forskolin (helix 10).

Guo, D, Mant, C. T., Taneja, A. K, Parker, J. M. R., and Hodges, R. S., Prediction of peptide retention times in reversed-phase high-performance liquid chromatography. I. Determination of retention coefficients of amino acid residues of model synthetic peptides, /. Chromatogr., 359, 499, 1986. 

A naturally occurring animal model of PFK-M deficiency has been reported in English springer spaniels. Molecular analysis of this canine PFK-M deficiency disclosed that the enzyme deficiency was caused by a nonsense mutation in the penultimate exon of the PFK-M gene, leading to rapid degradation of a truncated (40 amino acid residues) and therefore unstable enzyme protein (SI8). 

Comparison of solution pH with the pKa of a side chain informs about the protonation state. A unique pKa, termed the standard or model pKa, can be experimentally determined for each ionizable side chain in solution when it is incorporated in a model compound, often a blocked amino acid residue [73] (Table 10-1). In a protein environment, however, the pKa value of an ionizable side chain can substantially deviate from the standard value, due to desolvation effects, hydrogen bonding, charge-charge, charge-dipole, and other electrostatic interactions with the... 

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