Structural Folds

Figure S.7 The subunit structure of the neuraminidase headpiece (residues 84-469) from influenza virus is built up from six similar, consecutive motifs of four up-and-down antiparallel fi strands (Figure 5.6). Each such motif has been called a propeller blade and the whole subunit stmcture a six-blade propeller. The motifs are connected by loop regions from p strand 4 in one motif to p strand 1 in the next motif. The schematic diagram (a) is viewed down an approximate sixfold axis that relates the centers of the motifs. Four such six-blade propeller subunits are present in each complete neuraminidase molecule (see Figure 5.8). In the topological diagram (b) the yellow loop that connects the N-terminal P strand to the first P strand of motif 1 is not to scale. In the folded structure it is about the same length as the other loops that connect the motifs. (Adapted from J. Varghese et al.. Nature 303 35-40, 1983.)...

Forimer, G.H. GroEF structure a new chapter on assisted folding. Structure 2 1125-1128, 1994. 

Subunits VP2 and VP3 from different pentamers alternate around the threefold symmetry axes like subunits B and C in the plant viruses (Figure 16.12b). Since VP2 and VP3 are quite different polypeptide chains, they cannot be related to each other by strict symmetry, or even by quasi-symmetry in the original sense of the word. To a first approximation, however, they are related by a quasi-sixfold symmetry axis, since the folded structures of the cores of the subunits are very similar. 

Lysozyme from bacteriophage T4 is a 164 amino acid polypeptide chain that folds into two domains (Figure 17.3) There are no disulfide bridges the two cysteine residues in the amino acid sequence, Cys 54 and Cys 97, are far apart in the folded structure. The stability of both the wild-type and mutant proteins is expressed as the melting temperature, Tm, which is the temperature at which 50% of the enzyme is inactivated during reversible beat denat-uration. For the wild-type T4 lysozyme the Tm is 41.9 °C. 

Glycine residues have more conformational freedom than any other amino acid, as discussed in Chapter 1. A glycine residue at a specific position in a protein has usually only one conformation in a folded structure but can have many different conformations in different unfolded structures of the same protein and thereby contribute to the diversity of unfolded conformations. Proline residues, on the other hand, have less conformational freedom in unfolded structures than any other residue since the proline side chain is fixed by an extra covalent bond to the main chain. Another way to decrease the number of possible unfolded structures of a protein, and hence stabilize the native structure, is, therefore, to mutate glycine residues to any other residue and to increase the number of proline residues. Such mutations can only be made at positions that neither change the conformation of the main chain in the folded structure nor introduce unfavorable, or cause the loss of favorable, contacts with neighboring side chains. 

The way in which molecular chaperones interact with polypeptides during the folding process is not completely understood. What is clear is that chaperones bind effectively to the exposed hydrophobic regions of partially folded structures. These folding intermediates are less compact than the native folded proteins. They contain large amounts of secondary and even some tertiary... 

The stresses in some folded structures can be determined with acceptable accuracy by applying elementary beam theory to the overall cross-sections of the plate assemblies. When assemblies are plates whose lengths are large relative to their cross-sectional dimensions (thin-wall beam sections, ribbed panels, and so on) and are in large plates... 

This has a folded structure (Figure 2.27) similar to that of rhodium carbonyl chloride (Figure 2.18) with ethene acting as a two-electron donor, but ethene is more weakly held and readily displaced by CO and certain alkenes (e.g. cycloocta-1,5-diene). 

ChEs possess the a/ 3-fold structure, which is shared with other esterases and non-catalytic proteins such as thyroglobulin, glutactin, neurotactin, gliotactin and neuroligins, all of these include a single ChE domain. Both ChEs are ellipsoidal molecules of 45-60-65 A3. Their structure consists of a central, highly twisted, 8-12-stranded (3-sheet, in which most strands are parallel, flanked on both sides by a-helices. Studies have indicated three major domains within the protein ... 

Proteins derive their powerful and diverse capacity for molecular recognition and catalysis from their ability to fold into defined secondary and tertiary structures and display specific functional groups at precise locations in space. Functional protein domains are typically 50-200 residues in length and utilize a specific sequence of side chains to encode folded structures that have a compact hydrophobic core and a hydrophilic surface. Mimicry of protein structure and function by non-natural ohgomers such as peptoids wiU not only require the synthesis of >50mers with a variety of side chains, but wiU also require these non-natural sequences to adopt, in water, tertiary structures that are rich in secondary structure. 

Patch, ).A., Wu, C.W., Sanborn, T.J., Huang, K., Zuckermann, R.N., Barron, A. E., and Radhakrishnan, I. A peptoid oligomer with a unique, cyclic folded structure and a solvent-depend conformational switch. (Manuscript in preparation). 

Like the other paralytic toxins from Conus venom, a-conotoxins are small and very tightly folded, structural features which may be advantageous for rapid paralysis of prey (1). a-Conotoxins are typically 13 to 15 amino acids long with two disulfide bridges (see Table III). In addition to the five a-conotoxins shown, two new a-conotoxins (SIA and SIB) from C. striatus have recently been isolated, sequenced, and chemically synthesized. SIA is very unusual because it is 19 amino acid residues long and it contains 6 cysteine residues, three of which are contiguous near the amino terminus (C. Ramilo et al., unpublished results). 

The A20 antibody did not bind significantly to native SR vesicles, but solubilization of the membrane with C Eg or permeabilization of the vesicles by EGTA exposed its epitope and increased the binding more than 20-fold [139], By contrast, the A52 antibody reacted freely with the native sarcoplasmic reticulum, while the A25 antibody did not react either in the native or in the C Eg solubilized or permeabilized preparations, and required denaturation of Ca " -ATPase for reaction, Clarke et al, [139] concluded that the epitope for A52 is freely exposed on the cytoplasmic surface, while the epitope for A20 was assigned to the luminal surface, where it became accessible to cytoplasmic antibodies only after solubilization or permeabilization of the membrane. The epitope for A25 is assumed to be on the cytoplasmic surface in a folded structure and becomes accessible only after denaturation. 

It might be amusing to conclude this section by noting the structure that a l,2,3,4-tetrahydro-l,2,3,4-tetraborete assumes. Treatment of ferf-butylboron difluoride with sodium-potassium alloy (Eq. 28) gives a derivative (92) of such a system, whose XRD analysis reveals that the nuclei assume a maximally folded structure—namely a tetrahedron.91... 

Stabilizing the folded state also benefits from optimizing hydrogenbonding interactions, with water providing donor and acceptor groups to polar side chains and main chain C=0 and N—H groups left exposed on the surface of the folded structure. Direct evidence for such... 

Because of the intrinsic flexibility and poor resonance dispersion of unfolded and partly folded proteins, long-range NOEs are generally very difficult to observe and assign. While observation of a long-range NOE between two protons provides a definitive indication that they are in close proximity in at least some structures in the conformational ensemble, determination of the nature of the folded structures is difficult unless an extensive network of NOEs can be observed. This has so far been achieved in only one case (Mok et al., 1999). 

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