Mixed a-p proteins

Because only two types of secondary structures (a and p) exist, proteins can be divided into three main structural classes. These are mainly a pro-teins, mainly p proteins,and mixed a-p proteins. A fourth class includes proteins with little or no secondary structures at all that are stabilized by metal ions and/or disulphide bridges. A significant effort has been made by... 

We have chosen in this chapter to focus our efforts on a-helical and mixed a/p-proteins below 100 residues in size. In previous work [2] we showed that p-strand proteins present more of a challenge to our prediction methodology than a-helical or mixed o/p-proteins [9-12] the modified size-dependent potential function discussed above improves the results of earlier work on p-strand containing proteins, but does not change the basic conclusion. For larger systems, our results are quite promising but not yet at the stage of completeness that we have been able to achieve for the smaller proteins. Consequentiy, we defer discussion of these cases to a subsequent publication. 

Although the tertiary stmcture prediction protocol employed in our previous work [2] was more or less able to consistently generate native-like stmctures for a- and mixed a/p-proteins, the energetic rank of these stmctures was not always satisfactory. An analysis of high-RMSD, low-energy stmctures obtained from those simulations reveals a systematically incorrect behavior of the statistical potential function of Sippl and co-workers [7] at large separations, most prominently for pairs of hydrophilic residues. This feature of statistical potentials has been uncovered in several other computational experiments [8,14]. 

In this structure the loop regions adjacent to the switch point do not provide a binding crevice for the substrate but instead accommodate the active-site zinc atom. The essential point here is that this zinc atom and the active site are in the predicted position outside the switch point for the four central parallel p strands, even though these p strands are only a small part of the total structure. This sort of arrangement, in which an active site formed from parallel p strands is flanked by antiparallel p strands, has been found in a number of other a/p proteins with mixed p sheets. 

Once proteins are divided into domains the domains are then classified hierarchically. At the top of the classification we usually find the class of a protein domain, which is generally determined from its overall composition in secondary structure elements. Three main classes of protein domains exist mainly a domains, mainly (3 domains, and mixed a p domains (the domains in the a — p class are sometimes subdivided into domains with alternating a/p secondary structures and domains with mixed a + p secondary structures). In each class, domains are clustered into folds according to their topology. A fold is determined from the number, arrangement, and connectivity of the domain s secondary structure elements. The folds are subdivided into superfamilies. A superfamily contains protein domains with similar functions, which suggests a common ancestry, often in the absence of detectable sequence similarity. Sequence information defines families, i.e., subclasses of superfamilies that regroup domains whose sequences are similar. 

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

N. F. Tabachnik, P. Blackburn, C. M. Peterson, A. Cerami, Protein Binding of JV-2-Mer-captoethyl-2,3-diaminopropane via Mixed Disulfide Formation after Oral Administration of WR 2721 , J. Pharmacol. Exp. Ther. 1982, 220, 243 - 246. 

The arrangement in space of all the atoms in a single polypeptide chain or in covalently linked chains is termed the tertiary structure. Most proteins can be considered crudely as layered sandwich structures, with each layer consisting of either a helixes or a P sheet. Four classes of protein molecules have been identified, based upon different combinations of these structures ala (all a), p/p (all P), a/p a and p elements are in a mixed order in the sequence), and a + P (the a and p elements are segregated in the sequence, the a occurring in one region and the p in another—see Figure 1.15). 

Prepare the standard and unknown protein samples for analysis by mixing 10 p of each with 5 pi of 4X sample buffer in microcentrifuge tubes, mixing gently, and heating at 100°C for 5 min in a boiling water bath. This step is to ensure that all of the proteins in the sample are completely denatured. Remove the samples from the water bath and allow them to cool to room temperature. 

Various schemes have been developed for the classification of protein three-dimensional structures. One common scheme is the classification based on the four tertiary super classes, namely, all a (proteins having mainly a-helix secondary structure), all P (mainly P-sheet secondary structure), a+p (segment of a-helices followed by segment of P-sheets), and o/p (alternating or mixed a-helix and P-sheet segments) (Levitt, 1976). A fifth class is often added to account for globular proteins with irregular secondary... 

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