Proteins loop-shaped

The main advantage of NMR spectroscopy is its use with proteins in solution. In consequence, rather than obtaining a single three-dimensional structure of the protein, the final result for an NMR structure is a set of more or less overlying structures which fulfill the criteria and constraints given particularly by the NOEs. Typically, flexibly oriented protein loops appear as largely diverging structures in this part of the protein. Likewise, two distinct local conformations of the protein are represented by two differentiated populations of NMR structures. Conformational dynamics are observable on different time scales. The rates of equilibration of two (or more) substructures can be calculated from analysis of the line shape of the resonances and from spin relaxation times Tj and T2, respectively. 

The re-entrant or Tammann loop-shape phase diagram as observed in proteins is also found in other systems and has been connected to exothermic disordering [88]. In this particular case, nematic - smectic A transitions in liquid crystals and the phase behaviour of a crystalline polymer, poly(4-methyl-pentene-l), the phase behaviour can be understood by... 

There are nevertheless complexes where the rmsd is well over 2 A and large movements take place. The conformation change modifies the shape and chemical character of regions of the protein surfaces, which are not preformed and complementary before they start interacting. The conformational change may be localized at the interface or affect the whole protein. Loops of polypeptide chain can move like the H3 loop... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Because the tertiary structure of a globular protein is delicately held together by weak intramolecular attractions, a modest change in temperature or pH is often enough to disrupt that structure and cause the protein to become denatured. Denaturation occurs under such mild conditions that the primary structure remains intact but the tertiary structure unfolds from a specific globular shape to a randomly looped chain (Figure 26.7). 

Figure 26.7 A representation of protein denaturation. A globular protein loses its specific three-dimensional shape and becomes randomly looped.

Many calcium-binding proteins can be described in terms of loops containing potential metal-binding sites linked by helices of various shapes and lengths. There are several families of closely related proteins, in particular the groups of EF-hand species and... 

The FhuA receptor of E. coli transports the hydroxamate-type siderophore ferrichrome (see Figure 9), the structural similar antibiotic albomycin and the antibiotic rifamycin CGP 4832. Likewise, FepA is the receptor for the catechol-type siderophore enterobactin. As monomeric proteins, both receptors consist of a hollow, elliptical-shaped, channel-like 22-stranded, antiparallel (3-barrel, which is formed by the large C-terminal domain. A number of strands extend far beyond the lipid bilayer into the extracellular space. The strands are connected sequentially using short turns on the periplasmic side, and long loops on the extracellular side of the barrel. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

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