Polypeptide folds of the

The overall polypeptide fold of the a subunit is that of an 8-fold a//8 barrel (Fig. 7.2 and color plate ).7) Similar structures have been observed in more than 18 other... 

G. Wagner, W. Braun, T. F. Havel, T. Schaumann, N. Go, and K. Wiithrich, /. Mol. Biol., 196, 611 (1987). Protein Structures in Solution by Nuclear Magnetic Resonance and Distance Geometry The Polypeptide Fold of the Basic Pancreatic Trypsin Inhibitor Determined Using Two Different Algorithms. DISGEO and DISMAN. 

Fig. 3 Structure of the carbon monoxide dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) hetero-tetramer. A Polypeptide fold of the CODH dimer (center) and of ACS in the closed (left) and open subunit conformation (right). Metal sites and inorganic sul-furs are shown as spheres an extensive hydrophobic tunnel network is highlighted in dark grey. B Zoomed depiction of the CODH active site. Dashed lines indicate putative H-bonds...

Figure 4.5 The polypeptide chain of the enzyme pyruvate kinase folds into several domains, one of which is an a/p barrel (red). One of the loop regions in this barrel domain is extended and comprises about 100 amino acid residues that fold into a separate domain (blue) built up from antiparallel P strands. The C-terminal region of about 140 residues forms a third domain (green), which is an open twisted a/p structure.

The polypeptide chain of the 92 N-terminal residues is folded into five a helices connected by loop regions (Figure 8.6). Again the helices are not packed against each other in the usual way for a-helical structures. Instead, a helices 2 and 3, residues 33-52, form a helix-turn-helix motif with a very similar structure to that found in Cro. 

The polypeptide chain of the bacterial channel comprises 158 residues folded into two transmembrane helices, a pore helix and a cytoplasmic tail of 33 residues that was removed before crystallization. Four subunits... 

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

X-ray structures are determined at different levels of resolution. At low resolution only the shape of the molecule is obtained, whereas at high resolution most atomic positions can be determined to a high degree of accuracy. At medium resolution the fold of the polypeptide chain is usually correctly revealed as well as the approximate positions of the side chains, including those at the active site. The quality of the final three-dimensional model of the protein depends on the resolution of the x-ray data and on the degree of refinement. In a highly refined structure, with an R value less than 0.20 at a resolution around 2.0 A, the estimated errors in atomic positions are around 0.1 A to 0.2 A, provided the amino acid sequence is known. 

Cluster 1 is a conventional [4Fe-4S] cubane cluster bound near the N-terminus of the molecule as shown in Fig. 13. Within the cluster the Fe-S bonds range from 2.26 to 2.39 A. The cluster is linked to the protein by four cysteine residues with Fe-S distances ranging from 2.21 to 2.35 A, but the distribution of the cysteine residues along the polypeptide chain contrasts markedly with that found, for example, in the ferredoxins as indicated in Section II,B,4 [also see, for example, 41) and references therein]. In the Fepr protein all four cysteine residues (Cys 3, 6, 15, and 21) originate from the N-terminus of the molecule, and the fold of the polypeptide chain in this region is such that it wraps itself tightly around the cluster, yet keeps it near the surface of the molecule. In such a position the cluster is ideally placed to participate in one-electron transfer reactions with other molecules. 

An enzyme consists of a polypeptide chain with a particular spatial configuration specific to that sequence of amino acids. The molecule twists and turns, forming structural features that are catalytically active, these being known as active sites. There may be more than one active site per enzyme molecule. Sometimes an auxiliary catalyst, known as a coenzyme, is also needed. Apparently, only the relevant active site of the enzyme comes into contact with the substrate and is directly involved in the catalysed reaction. The active site consists of only a few amino acid residues. These are not necessarily adjacent to one another in the peptide chain but may be brought into proximity by the characteristic folding of the enzyme structure. The active site may also include the coenzyme. The remainder of the enzyme molecule fulfils the essential function of holding the components of the active site in their appropriate relative positions and orientation. 

A particular goal of chemical theory is to predict protein structure from the amino acid sequence—to calculate how polypeptides fold into the compact geometries of proteins. One strategy is to develop methods (often based on bioinformatics) for predicting structures approximately and then refining the structures... 

Protein folding Glycosylation can effect local protein secondary structure and help direct folding of the polypeptide chain... 

Fig. 26a,b. High resolution height SFM-micrographs of a 14-ABG-PS on mica [86] b Twisted ribbon structure of polypeptide /i-sheets [ 167]. The plectoneme conformation is caused by the backward folding of the torsionally stressed molecules [86]. Insert in (a) depicts a plectoneme supercoil... 

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