Protein strands

Ionic bonding between charged amino acid side chains or as salt bridges, and 3) hydrophobic and related attractions along protein strands. 

The protein strand can be cleaved if it lies close to the cleavage center or it could be transported forward by one amino acid. We assume that the probability of transport depends only on the length of the strand inside the proteasome. The probability of transport is, therefore, given by a translocation rate function, v(x + D) where x + D is the length of the strand inside the proteasome, in terms of amino acids. The probability of cleavage is assumed to be a constant, denoted by y. We also assume that the degradation of proteins by the proteasome is a highly processive mechanism [2], i.e., in other words, the protein is not released by the proteasome until it is completely processed. This leads to the possibility of the proteasome... 

Fig. 14.5 Schematic diagram of the protein degradation by the proteasome. The protein strand (denoted by 0-0-0-0 ) enters the proteasome from the left to be cleaved by the cleavage centers (denoted by the scissors). The length of the strand after crossing the cleavage center is denoted byx.

We take the offset of the coordinate x (measured in amino acids) along the proteasome at the first cleavage center (see Fig. 14.5). During the time interval dt, the protein strand can move by one amino acid with the probability v(x + D)dt and can be cut with the probability ydt. 

How may such minute field strengths have macro effects This may be made understandable in terms of cooperative action. Consider, for example, the strands of intramembranous proteins that protrude from the phospholipid membrane. They contain charges, and each would react to an applied field. In a membrane at least 10% of the sites will be occupied by proteins. If each protein strand reacts to the field, the very small but coherent signals may be magnified by, for example, 1013 strands cm2. In growing bone cells subjected to a 100-Hz field, say, a significant effect becomes understandable. 

Icosahedral capsid viruses and clathrins are examples of coat proteins of which there are many. Another example that has been extensively studied is coat protein II, or COPII, which is composed of an inner cage and outer coat [5], The inner cage is a cuboctahedron approximately 60 nm across. It has square and triangular faces which can only be constructed if four protein strands emanate from the structure s hub, rather than the three seen in clathrins. It also transpires that the proteins interact with each other at the vertices without any of the extensive interdigitation seen in clathrin cages. 

Zheng X, Stuchebrukhov AA. Electron tunneling in the His126 Ru-modified azurin tunneling jumps between protein strands via hydrogen bonds. J Phys Chem B 2003 107 9579-84. 

The enmeshed fat globules occupy the spaces between the protein strands and may be considered to impede physically the aggregation of the para-casein matrix, to a degree dependent on their volume fraction and size distribution. Consequently, a higher fat level leads to slower syneresis during manufacture (Dejmek and Walstra, 2004), and an increase in the level of MNFS in the cheese (Tunick et al., 1995 Poudaval and Mistry, 1999 Fenelon and Guinee, 1999) the increase in MNFS has a major impact on cheese yield and quality, as discussed in Sections 11.4, 11.6-11.9. 

Amyloid fibrils show a characteristic diffraction pattern, the so called P-cross pattern (35), which is indicative of P-sheets parallel to the fibril axis with the protein strands perpendicular to the fibril s long axis (36, 37). The pattern of amyloid is characterized by reflections at 4.75 A (along the fibril axis) and 10 A (perpendicular to the fibril axis) which occur from regular repeats and stacking of monomers. 

Figure 12. Schematic concept of a polyribosome showing stepwise growth of a polypeptide chain and assembly of protein strands. Soluble ribonucleic acid is also called transfer RNA (tRNA). Adapted from Refs. 73, 79, and 80.

Shifting from one interdisciplinary nomenclature to another we can view the bidentate molecule as an amino acid, the amide becomes a peptide and the polyamide a polypeptide or a protein. Hence, we have abjured organic chemistry in favour of biochemistry. Proteins are built up from approximately 20-25 different a-amino acids, the individual order of which decide the chemical and physical properties of a particular protein. Due to a combination of certain attributes of e peptide linkage, and the presence of functionalities enabling the formation of hydrogen bonds, protein strands fall into one of three geometrically different categories random coil, a-helix and pleated sheet. 

The larger fracture strain at pH 7.6 indicates that at this pH the protein strands are likely to be somewhat more curved (tortuous) than at pH 3.8.32,33 It... 

The keratin of hair is essentially a bundle of long protein strands joined together by disulfide bonds. If these bonds are broken (reduced) by the addition of a thiol and the hair curled, the keratin chains slip past each other into a new configuration. When an oxidizing agent is added, new disulfide bonds are formed, thus stabilizing the new curled state. 

Many bacterial cells have appendages used for movement called flagella. Some cells also have pill, which are a protein strand used for attachment of the bacteria. Pili may also be used for sexual conjugation (where the DNA from one bacterial cell is transferred to another bacterial cell). 

FIGURE 3.7.7 Surface charge on a protein strand attracts a water dipolar molecule (top). The adsorbed dipole attracts additional dipoles to form a structured organization within the liquid (middle). Additional surface charges on the protein reinforce the external dipole network (bottom). (Redrawn from Pollack, G.H., Cells, Gels, and the Engines of Life A New, Unifying Approach to Cell Function, Ebner and Sons, Seattle, WA, 2001.)... 

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