Protein folding class

Different protein folding classes can be identified by differences in their amino acid compositions (Nakashima et al., 1986) thus, we reasoned that, if disorder were encoded by the sequence, then regions of disorder would be analogous to a new folding class and hence should... 

Dubchak, I., Holbrook, S. R. Kim, S.-H. (1993a). Prediction of protein folding class from amino acid composition. Proteins 16,79-91. 

The inherent variability of predictive success rate depending on the protein fold class brings important observations (1) When reporting accuracies the selection of the test set proteins should be balanced In order to include a representative number of each of the protein fold classes. (2) the prior knowledge of the protein fold class (Chou and Zhang, 1995) can be a valuable aid for the predictions and with that one can use the different algorithms in combination to predict a specific structural element of the chain. 

The relationship between structure and function is a true many-to-many relation. Recent studies have shown that particular functions can be mounted onto several different protein folds [85] and, conversely, several protein fold classes can perform a wide range of functions [259]. This limits our potential of deducing function from structure. But it is still possible to use aforementioned knowledge on the range of folds supporting a particular function and the range of functions implemented by particular folds in order to make functional prediction from structure. 

Proteins can be classed into groups based on their overall 3-D shapes, known as protein folds (O Figure 22-la). In general, proteins that have similar functions have similar folds. This means that if you are the proud parent of an unknown protein whose structure is solved, it may be possible to make educated guesses as to the function of the protein based on its overall fold. There are a number of well-known exceptions to this [notably, the serine protease family, subtilisin and trypsin/chymotrypsin (Hartley, 1979)], but the... 

A representative sampling of non-heme iron proteins is presented in Fig. 3. Evident from this atlas is the diversity of structural folds exhibited by non-heme iron proteins it may be safely concluded that there is no unique structural motif associated with non-heme iron proteins in general, or even for specific types of non-heme iron centers. Protein folds may be generally classified into several categories (i.e., all a, parallel a/)3, or antiparallel /8) on the basis of the types and interactions of secondary structures (a helix and sheet) present (Richardson, 1981). Non-heme iron proteins are found in all three classes (all a myohemerythrin, ribonucleotide reductase, and photosynthetic reaction center parallel a/)8 iron superoxide dismutase, lactoferrin, and aconitase antiparallel )3 protocatechuate dioxygenase, rubredoxins, and ferredoxins). This structural diversity is another reflection of the wide variety of functional roles exhibited by non-heme iron centers. 

Protein folding is likely to be a more complex process in the densely packed cellular environment than in the test tube. More classes of proteins that facilitate protein folding may be discovered as the biochemical dissection of the folding process continues. 

The linear polypeptide chains of a protein fold in a highly specific way that is determined by the sequence of amino acids in the chains. Many proteins are composed of two or more polypeptides. Certain proteins function in structural roles. Some structural proteins interact with lipids in membrane structures. Others aggregate to form part of the cytoskeleton that helps to give the cell its shape. Still others are the chief components of muscle or connective tissue. Enzymes constitute yet another major class of proteins, which function as catalysts that accelerate and direct biochemical reactions. 

Although proteins can fold in vitro (in the laboratory) without the presence of accessory proteins, this process can take minutes to days. In vivo (in the cell) this process requires only a few minutes because the cells contain accessory proteins which assist the polypeptides to fold to their native conformation. There are three main classes of protein folding accessory proteins ... 

The overall three-dimensional structure of a protein is called the tertiary structure. The tertiary structure represents the spatial packing of secondary structures (Ofran and Rost, 2005). As for secondary structures, there are several different classes of tertiary structures. More advanced classification schemes take into account common topologies, motifs, or folds (Wishart, 2005). Common tertiary folds include the a/p-barrel, the four-helix bundle, and the Greek key (we will discuss protein folding further in Chapter 14). Any change to any part of the structure of a protein will have an impact on its biological activity (Thomas, 2003). 

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