Learn Amino Acid Composition Analysis | Protein and Amino Acid Analysis

Amino acid composition analysis is a core technique in protein bioinformatics. By determining the proportion of each amino acid within a protein sequence, you gain valuable insights into the protein's characteristics, such as its structure, function, and interactions. For instance, a protein rich in hydrophobic amino acids may be more likely to be embedded in cell membranes, while a high content of charged residues often correlates with water solubility.

Calculating amino acid composition involves:

Counting the occurrence of each amino acid in the sequence;
Expressing these counts as percentages of the total sequence length.

This information is directly relevant to predicting protein folding, localization, and interaction with other molecules.


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def amino_acid_composition(sequence):
    """
    Calculate the percentage composition of each amino acid in a protein sequence.

    Args:
        sequence (str): Protein sequence using single-letter amino acid codes.

    Returns:
        dict: Amino acid as key, percentage as value.
    """
    sequence = sequence.upper()
    total = len(sequence)
    composition = {}
    for aa in sequence:
        if aa not in composition:
            composition[aa] = 1
        else:
            composition[aa] += 1
    for aa in composition:
        composition[aa] = (composition[aa] / total) * 100
    return composition

To understand how the amino acid composition function operates, start by recognizing that protein sequences are represented as strings of single-letter amino acid codes. The function processes the sequence by first converting it to uppercase to ensure consistency. It then uses a dictionary to keep track of how many times each amino acid appears in the sequence. For every character in the string, the function increments the count for that amino acid in the dictionary. After counting, it calculates the percentage for each amino acid by dividing its count by the total number of amino acids in the sequence, then multiplying by 100. The result is a dictionary mapping each amino acid found in the sequence to its percentage composition, giving you a clear picture of the protein's makeup.


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# Example protein sequence (hemoglobin fragment)
protein_seq = "VLSPADKTNVKAAW"
composition = amino_acid_composition(protein_seq)
for aa, percent in sorted(composition.items()):
    print(f"{aa}: {percent:.2f}%")

1. What does a high percentage of hydrophobic amino acids suggest about a protein?

2. Fill in the blank: To calculate amino acid composition, count each amino acid and divide by the _____ of the sequence.

3. How can amino acid composition inform protein solubility?

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