Polypeptides chains

Three types of polypeptide chains are possible, open, cyclic and branched. 

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Photographic material containing gelatin can be hardened during manufacture the process involves cross-linking between the gelatine polypeptide chains induced by hardener. 

Insulin is built up of two polypeptide chains. A of 21 amino-acids and B of 30 amino-acids, linked by two disulphide bridges. 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

Because this problem is complex several avenues of attack have been devised in the last fifteen years. A combination of experimental developments (protein engineering, advances in x-ray and nuclear magnetic resonance (NMR), various time-resolved spectroscopies, single molecule manipulation methods) and theoretical approaches (use of statistical mechanics, different computational strategies, use of simple models) [5, 6 and 7] has led to a greater understanding of how polypeptide chains reach the native confonnation. 

In tire simple version of tire lattice representation of proteins tire polypeptide chain is modelled as a sequence of connected beads. The beads are confined to tire sites of a suitable lattice. Most of tire studies have used tire cubic lattice. To satisfy tire excluded volume condition only one bead is allowed to occupy a lattice site. If all tire beads are identical we have a homopolymer model the characteristics of which on lattices have been extensively studied. 

The basic features of folding can be understood in tenns of two fundamental equilibrium temperatures that detennine tire phases of tire system [7]. At sufficiently high temperatures (JcT greater tlian all tire attractive interactions) tire shape of tire polypeptide chain can be described as a random coil and hence its behaviour is tire same as a self-avoiding walk. As tire temperature is lowered one expects a transition at7 = Tq to a compact phase. This transition is very much in tire spirit of tire collapse transition familiar in tire theory of homopolymers [10]. The number of compact... 

Shakhnovich E and Gutin A 1989 Formation of unique structure in polypeptide chains. Theoretical... 

The data led to tire cycle shown in figure C2.7.8. Here, only tire active site on tire interior enzyme surface (section C2.6) is depicted, consisting of R groups including aspartic acid, glutamic acid and otliers, represented witli tire shortliand Asp, Glu etc tire subscripts represent tlie positions on tlie polypeptide chain. 

These events marked the beginning of the Ig domain unfolding, after which the strands unraveled one at a time, accompanied by a large reduction in the recorded force. After an extension of 260 A, the domain was completely unfolded further stretching of the already extended polypeptide chain caused the force to increase dramatically. 

A polymer is a macromolecule that is constructed by chemically linking together a sequent of molecular fragments. In simple synthetic polymers such as polyethylene or polystyrer all of the molecular fragments comprise the same basic unit (or monomer). Other poly me contain mixtures of monomers. Proteins, for example, are polypeptide chains in which eac unit is one of the twenty amino acids. Cross-linking between different chains gives rise to j-further variations in the constitution and structure of a polymer. All of these features me affect the overall properties of the molecule, sometimes in a dramatic way. Moreover, or... 

As more protein structures became available it was observed that some contained more that one distinct region, with each region often having a separate function. Each of these region is usually known as a domain, a domain being defined as a polypeptide chain that can folc independently into a stable three-dimensional structure. 

Domain Sequence of a polypeptide chain that can independently fold into a stable three-dimensional structure... 

Pauling L, R B Corey and H R Bronson 1951. The Structure of Proteins Two Hydrogen-bonded He Configurations of the Polypeptide Chain. Proceedings of the National Academy of Sciences USA y . 211... 

Rather than existing as a single polypeptide chain some proteins are assemblies of two or more chains The manner m which these subunits are organized is called the quater nary structure of the protein... 

Section 27 19 Two secondary structures of proteins are particularly prominent The pleated sheet is stabilized by hydrogen bonds between N—H and C=0 groups of adjacent chains The a helix is stabilized by hydrogen bonds within a single polypeptide chain... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

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