Amino acid sequences directionality

With respect to a solvent, the overall solvation capability for solutes. 2. A property of bodies or systems that have a distinct direction i.e., that have different or opposing physical properties or characteristics at different points. For example, an amino acid sequence in a polypeptide has polarity in that there is an amino end and a carboxyl end of the sequence. Similarly, microtubules and actin filaments have plus (+)-ends and minus (-)-ends that establish directionality for cellular and intracellular locomotion. 3. The state in which there is either a positive or negative aspect relative to the two poles of a magnet or to electrification. 4. Attraction toward an object or attraction in a specific direction. 5. In mathematics, the positive or negative sign of numbers. 

Cladistic analysis of molecular sequence characters differs from that described by Hennig17 for organismal characters in several important ways. Molecules do not leave fossils, thus there is no hard record of which character state (i.e., amino acid residue) is ancestral and which is derived at any position in a sequence. The 20 common amino acids are found in all living forms and therefore have nothing inherently ancestral or derived about them. Furthermore, amino acid replacements have no intrinsic directionality, even though some replacements are more likely to occur than others. In other words, amino add replacements are not inherently polarized. In addition, amino acid replacements and nucleotide substitutions are reversible. For these reasons, the character state(s) of the outgroup molecule(s) cannot be assumed to be ancestral. 

The lysozyme molecule was determined to have three antigenic sites with residues coming from widely separated portions of the polypeptide chain the residues proposed as contacting and those synthesized to produce a linear sequence considered as best simulating the active site are seen in Fig. 15. In some instances the peptide synthesized in the reverse direction —for example, using the C-terminal amino acid of the hypothesized determinant as the amino terminus—was used as a control. In some instances, the sequence was considered to have directionality whereas in others it did not. 

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