Side-chain interactions hydrophobic bond

The Ufson-Roig matrix theory of the helix-coil transition In polyglycine is extended to situations where side-chain interactions (hydrophobic bonds) are present both In the helix and in the random coil. It is shown that the conditional probabilities of the occurrence of any number and size of hydrophobic pockets In the random coil can be adequately described by a 2x2 matrix. This is combined with the Ufson-Roig 3x3 matrix to produce a 4 x 4 matrix which represents all possible combinations of any amount and size sequence of a-helix with random coil containing all possible types of hydrophobic pockets In molecules of any given chain length. The total set of rules is 11) a state h preceded and followed by states h contributes a factor wo to the partition function 12) a state h preceded and followed by states c contributes a factor v to the partition function (3) a state h preceded or followed by one state c contributes a factor v to the partition function 14) a state c contributes a factor u to the partition function IS) a state d preceded by a state other than d contributes a factor s to the partition function 16) a state d preceded by a state d contributes a factor r to the partition function. 

These achiral poly(A -propargylamides) form helices with an equivalent amount of right- and left-handed screw senses. Addition of chiral alcohols induces predominantly one-handed screw sense in polyl7a and polyl7d. NMR spectroscopic analysis has revealed that the amide side chains interact with optically active alcohols by hydrogen bonding. Terpenes also induce a one-handed helix. In this case, hydrophobic interaction plays an important role for helix induction. 

The simplest j3 structure is the hairpin (Chapter 1, section C3 and Figure 1.12). The /3 hairpin requires the pairing of hydrophobic side chains to stabilize it. The hairpin has to nucleate at its central turn, unlike the helix, which can nucleate at any residue whose >C=0 can form a hydrogen bond with residue i + 4. The formation of j3 structure is inherently slower than the formation of a helixes because of the fewer nucleation sites and the requirements to make side-chain interactions.5 Depending on precise structure, helixes form with half-lives of a few hundred nanoseconds, and /3 structures form with half-lives 10 times longer. 

EXAMPLE 2.4 Proteins are polymers of polar and nonpolar amino acids the amino acid nnits in the polymer are called residues becanse when the peptide bond between an amino acid and a peptide is formed, water is removed in a condensation reaction, leaving a residne of the amino acid. Amino acid residnes that have polar side chains form hydrogen bonds with water so they are hydrophilic (Fig. 2-5). Nonpolar side chains of amino acid residnes do not form hydrogen bonds with water, so they do not dissolve readily in it they are said to be hydrophobic. Thns proteins tend to fold np so that their hydrophobic residnes are clnstered in an interior core, away from contact with the aqneons environment and the hydrophilic residnes tend to be arranged on the exterior interacting with water. Interactions also occnr with other proteins and other biomolecnles in general. 

---