computer modeling in molecular biology.pdf

2 Modelling Protein Structures 19Families of related proteins tend to retain similar folding patterns. If one examinessets of related proteins (see Figures 2-3 and 2-4) it is clear that although the generalfolding pattern is preserved, there are distortions which increase progressively as theamino acid sequences diverge. These distortions are not uniformly distributedthroughout the structure. Instead, in any family of proteins there is a core of thestructure that retains the same qualitative fold, and other parts of the structure thatchange conformation radically. To explain the idea of the common core of two structures,consider the letters B and R. Considered as structures they have a commoncore which corresponds to the letter P. Outside the common core they differ: at thebottom right B has a loop and R has a diagonal stroke.Figure 2-3. -0 closely-related proteins: (a) actinidin (crystal structure by E. N. Baker andE. J. Dodson [go]) and (b) papain (crystal structure by I. G. Kamphuis et al. [91]). The aminoacid sequences of these molecules have about 50 070 identical residues.Figure 2-4. Wo distantly-related proteins: (a) poplar leaf plastocyanin (crystal structure by J.M. Guss and H. C. Freeman [92]) and (b) A. denitrificuns azurin (crystal structure byG. E. Norris, B. F. Anderson and E. N. Baker [93]). The circle near the top of the structuremarks the position of the copper. In this case the double P-sheet portion of these moleculesretains the same fold, but the long loop at the left changes its conformation completely.