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Analysis of periodic patterns in amino acid sequences: collagen

McLachlan, A.D.
Biopolymers 1977 v.16 no.6 pp. 1271-1297
protein secondary structure, mathematics and statistics, collagen, amino acid sequences, hydrophobicity, molecular conformation
Methods are given for analyzing regularly spaced patterns of amino acids in proteins and applied to the alpha 1 chain of collagen. Fourier methods use the transform of the sequence either embedded in a very long array or folded onto a fundamental base period. Filtering through a moveable "window" of definite width is used to display almost regular features at any chosen frequency. A pattern detection method is described for patterns of general shape. Collagen has statistically significant periodicities at fractions of the stagger distance D = 670 angstroms. Hydrophobic groups show strong orders of 5, 6, 11; proline 5; charged groups 6, 18, 21. Charged residues mostly occur as neutral pairs. Their distribution has strong 6th and 21st orders which also appear in the charges which are paired at multiples of D. Charge pairs separated by (D + 3) residues show a strong 5D/89 pattern and may form a system of salt bridges across the fibril. There is no sign of any regular pattern of amino acids over the triple helix with a period close to its natural pitch of 30 residues. Supercoiled models with six relative turns of the contact edge between paired triple-helical strands are examined.