Protein discussion

The fundamental unit of tertiary structure is the domain. A domain is defined as a polypeptide chain or a part of a polypeptide chain that can fold independently into a stable tertiary structure. Domains are also units of function. Often, the different domains of a protein are associated with different functions. For example, in the lambda repressor protein, discussed in Chapter 8, one domain at the N-terminus of the polypeptide chain binds DNA, while a second domain at the C-terminus contains a site necessary for the dimerization of two polypeptide chains to form the dimeric repressor molecule. 

A second example of up-and-down p sheets is the protein neuraminidase from influenza virus. Here the packing of the sheets is different from that in RBP. They do not form a simple barrel but instead six small sheets, each with four P strands, which are arranged like the blades of a six-bladed propeller. Loop regions between the p strands form the active site in the middle of one side of the propeller. Other similar structures are known with different numbers of the same motif arranged like propellers with different numbers of blades such as the G-proteins discussed in Chapter 13. 

In addition to the proteins discussed above, a large number of reactive chemicals used in industry can cause asthma and rhinitis. Hypersensitivity pneumonias have also been described. Isocyanates and acid anhydrides are industrial chemicals that cause occupational asthma. Acid anhydrides, such as phthalic anhydride, seem to cause mainly type I reactions, whereas the IgE-mediated mechanism explains only a part of the sensitizations to isocyanates. Several mechanisms have been suggested, but despite intensive research no models have been generally accepted. The situation is even more obscure for other sensitizing chemicals therefore, the term specific chemical hypersensitivity is often used for chemical allergies. This term should not be confused with multiple chemical sensitivity (MCS) syndrome, which is a controversial term referring to hypersusceptibility to very low levels of environmental chemicals. ... 

Most of the stress proteins discussed in this account have a role either in helping the plants survive, or in minimising the effectiveness of the stress agent. In helping plants survive under stress conditions, the stress proteins perform the following functions (1) maintenance of the basic metabolism in the stressed cell, e.g. the induction of ADH and some... 

Flash photolysis techniques were unsuitable for measuring the slow off reactions for the iron(II) model complexes such as Fen(TPPS)(NO), since the experimental uncertainties in the extrapolated intercepts of kohs vs. [NO] plots were larger than the values of the intercepts themselves. When trapping methods were used to evaluate NO labilization from FeII(TPPS)(NO), k(,n values were found to be quite small but were sensitive to the nature of the trapping agents used. Lewis bases that could coordinate the metal center appeared to accelerate NO loss. More reliable estimates for the uncatalyzed off reaction were obtained by using Ru(edta)- as an NO scavenger, and the koS values listed in Table I were obtained in this manner (21c). The small kQ values found for Fe(II) models are consistent with the trend observed for the ferro-heme proteins discussed above. 

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.

Fig. 1. Typical values for the scalar couplings in perdeuterated proteins, which can be used for the coherence transfer through the spin system (a). Strategies for obtaining resonance assignment in 15N/13C/2H labelled proteins discussed in this chapter (b). The boxes, circles, and triangles indicate correlations established in the corresponding pulse scheme.

The roles played by the different groups of adhesion proteins in metastasis are now only beginning to be understood. For some of these proteins, decreased expression appears to promote cancer spread, while for others, increased expression enhances metastasis. Of the different adhesion proteins discussed earlier,... 

Among the many proteins that bind to RNA molecules437 39 are the aminoacyl-tRNA synthetases, a variety of other well known enzymes,440 the ribosomal proteins discussed in Chapter 29, and various proteins with dual functions of catalysis and regulation of... 

Section D,5, Fig. 11-8, and Chapter 19). Demethylation occurs by hydrolysis, which is catalyzed by esterases. Carboxylmethylation also occurs in eukaryotic cells but is often substoichiometric and part of a mechanism for repair of isomerized or racemized aspartyl residues in aged proteins (Box 12-A). However, the major eukaryotic protein phosphatase 2A is carboxylmethylated at its C terminus,131 as are the Ras proteins discussed in Section D,3. 

The amino acid sequence of a mature protein sometimes differs from that deduced from the DNA nucleotide sequence of the structural gene for that protein. Discuss three ways by which this may occur. 

B 1. Study the details of the Edman and dansyl chloride methods for amino-terminal analysis of proteins. Discuss the advantages and disadvantages of each method. 

The transferrins belong to the iron-tyrosinate group of proteins discussed in Section 62.1.5.5.2. Charge transfer from phenolate ligands to Fem accounts for the salmon-pink colour of transferrin. The detailed coordination environment of the iron in transferrin is not known with certainty, as... 

Compared with the heme proteins discussed in Section 2.2, the non-heme iron proteins presented here have a much more flexible coordination geometry. Taken together with the differences in electronic properties - heme enzymes contain mostly low-spin iron whereas non-heme enzymes contain mostly a high-spin iron - this is responsible for the more diverse chemistry found for the non-heme iron proteins. The great versatility of these enzymes makes them a treasure trove for the development of iron-based catalysts. Inspired by their biological archetypes, numerous catalytic reactions await to be reproduced by iron catalysts in organic synthesis. 

In addition to the proteins discussed above, neuronal SNAREs were reported to interact with numerous other proteins in a specific manner, but in most cases both the structural basis and the biological function of these interactions need to be defined. For instance, synaptophysin, a membrane protein of synaptic vesicles, forms a complex with synaptobrevin in which synaptobrevin is not available for interactions with its partner SNAREs syntaxin 1A and SNAP-25, suggesting that this complex represents a reserve pool of recruitable synaptobrevin (Becher et al. 1999) or regulates interactions between the vesicle-associated synaptobrevin and the plasmalem-mal SNAREs. Alternatively, it has been suggested that this complex is involved in synaptobrevin sorting to synaptic vesicles. 

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