Single chain folding

GcL contains 544 amino acids in a single chain folded into one domain, making it one of the largest structural domains observed to date in a protein. Like RmL, GcL is an a structure with a central, predominantly parallel jS sheet. There are 11 strands in the central sheet, 3 more in a small additional sheet, and 17 a helices (Fig. 2). The catalytic Ser-217, a part of the G-X-S-X-G pentapeptide, is located at a tight turn between the C terminus of a /3 strand and an N terminus of an a helix, exactly as observed in RmL. The hydroxyl of Ser-217 is hydrogen bonded to the imidazole of His-463, which in turn donates a hydrogen bond to Glu-354. Thus, GcL constitutes the first known example of a serine hydrolase in which the acid residue of the triad is a glutamate and not an aspartate. 

Fig. 2.7. An extended chain crystal is obtained by cutting all loops of a single chain, folded crystal...

Fig. 1.6 Schematic illustration of three possible states of linear multiblock copolymer chains in a selective solvent single-chain folding, single-chain association and multi-chain association...

The fl-sheet consists of two more fragments of fuUy extended peptide chains which can be arranged in either parallel or anti-parallel direction. The hydrogen bonds are formed by adjacent segments of polypeptides. This structure can be formed by either multiple chains or by a single chain folding onto itself. A typical jS-sheet is shown in Fig. 18. 

Amines can also swell the polymer, lea ding to very rapid reactions. Pyridine, for example, would be a fairly good solvent for a VDC copolymer if it did not attack the polymer chemically. However, when pyridine is part of a solvent mixture that does not dissolve the polymer, pyridine does not penetrate into the polymer phase (108). Studies of single crystals indicate that pyridine removes hydrogen chloride only from the surface. Kinetic studies and product characterizations suggest that the reaction of two units in each chain-fold can easily take place further reaction is greatiy retarded either by the inabiUty of pyridine to diffuse into the crystal or by steric factors. 

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

The single crystal of a polymer is a lamellar structure with a thin plateletlike form, and the chain runs perpendicular to the lamella. The crystal is thinner than the polymer chain length. The chain folds back and forth on the top and bottom surfaces. Since the fold costs extra energy, this folded chain crystal (FCC) should be metastable with respect to the thermodynamically more stable extended chain crystal (ECC) without folds. 

PTC was coupled with (Pro-Ala-Gly)n, n = 12. The covalently bridged three-chain compound could be separated by gel chromatography from the respective two chains and the single chain in low yield, PTC-[(Pro-Ala-Gly-)12]3 shows a strong fold (Figs. 20,21) in comparison to the dimer or the monomer. 

The maximum at 223 nm is remarkably high, though the chain is relatively short. Also remarkable is the higher folding velocity in comparison to the use of single-chain collagen-peptide models as shown in Fig. 22. The folding is also completely reversible. 

The most potent thrombin inhibitor is hirudin, originally isolated from the salivary glands of the medicinal leech Hirudo medicinalis. Its inhibition constant is in the femtomolar (10-15 M) range (57). It is a 65-amino-acid tyrosine-sulfated single-chain polypeptide. Recombinant hirudin differs from native hirudin by the absence of the sulfate group on tyrosine 63 (Tyr-63) and is referred to as desulfato hirudin. The loss of this sulfate group reduces the thrombin inhibitory potency by 10-fold. 

Then we extended the 2D-model to a 3D one [21]. We considered crystallization of a single polymer chain C500 from a vapor phase onto a solid substrate, taking into account detailed interactions between the chain and the substrate. Though the polymer molecule in a vacuum was collapsed, like in a very poor solvent, under the influence of bare van der Waals interactions between atoms, the molecule was found to show quick adsorption and crystallization into a rather neat chain folded lamella. 

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