Surface loop

Figure 6 Thermodynamic cycle for multi-substate free energy calculation. System A has n substates system B has m. The free energy difference between A and B is related to the substate free energy differences through Eq. (41). A numerical example is shown in the graph (from Ref. 39), where A and B are two isomers of a surface loop of staphylococcal nuclease, related by cis-trans isomerization of proline 117. The cis trans free energy calculation took into account 20 substates for each isomer only the six or seven most stable are included in the plot.

EGS and sulfo-EGS also have been used to study the surface loop motion in FepA (Scott et al., 2002), to characterize the high affinity copper transporter in Saccharomyces cerevi-siae (Pena et al., 2000), and in the study of protein interactions and large protein complexes (Petrotchenko et al., 2005(2005 a or b ). 

For proteins the X-ray structures usually are not determined at high enough resolution to use anisotropic temperature factors. Average values for B in protein structures range from as low as a few A2 for well-ordered structures to 30 A2 for structures involving flexible surface loops. Using equation 3.6, one can calculate the root mean square displacement fu2 for a well-ordered protein structure at approximately 0.25 A (for B = 5 A2) and for a not-so-well-ordered structure at... 

Farley. G.L. and Dickinson. L.C. (1992). Removal of surface loop from stitched composites can improve compression and compression-after-impact strengths. J. Reinforced Plast. Composites 11. 633-642. 

Figure 3.7. In situ growth of CS planes in dynamic reduction of M0O3 in the same area of sample, marked m (a) 400°C and (b) 460 C. Growth of CS defects, e.g. 1-7, along their length and nucleation of new surface loops (e.g. at N) are shown. (After Gai 1981).

L. Hedstrom, L. Sziiagyi, and W. J. Rutter, Converting trypsin to chymotrypsin the role of surface loops, Science 1992, 255, 1249-53. 

The sequences of these five yeast proteins are also congruent with the experimental three-dimensional structure of the horse liver enzyme, implying that these will have the same overall fold. The length of the Sfal protein (Sfalp) is virtually the same as that of the horse liver enzyme except for a three-amino acid insertion after Asp245 (HLADH numbering), which is located in a surface loop between a P-strand and an a-helix near the entrance to the active site (Fig. 

B)[50], The proteins encoded by the ADH1, ADH2, ADH3, and ADH5 genes also share a 22-amino acid deletion compared to the HLADH sequence. This region is part of a surface loop in HLADH relatively far from the active site. 

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