Calculate Molecular Weight from Amino Acid Sequence

Accurately determine the molecular weight of peptides and proteins.

Protein Molecular Weight Calculator

Enter your amino acid sequence to calculate its molecular weight. The calculator uses the average molecular weight of each amino acid residue, subtracting one water molecule per peptide bond formed.

Molecular Weight Contribution per Amino Acid

Average molecular weight contribution of each amino acid residue.

Amino Acid Residue Average Molecular Weights

Amino Acid	One-Letter Code	Average Molecular Weight (Da)

Average molecular weights (in Daltons, Da) for each amino acid residue.

What is Amino Acid Sequence Molecular Weight?

The molecular weight of a protein or peptide, determined from its amino acid sequence, is a fundamental characteristic in biochemistry and molecular biology. It represents the total mass of the molecule in Daltons (Da) or kilodaltons (kDa). This value is crucial for a wide range of experimental and analytical procedures, including mass spectrometry, gel electrophoresis, and understanding protein function. When you sum the molecular weights of individual amino acids, you must account for the release of water molecules during peptide bond formation. Additionally, a complete peptide or protein will have a free amino group at the N-terminus and a free carboxyl group at the C-terminus, each contributing their respective atoms to the total mass.

Who Should Use This Calculator?

This calculator is designed for:

• Biochemists and Molecular Biologists: For experimental design, data interpretation, and theoretical calculations.
• Students and Educators: To understand the relationship between amino acid sequence and molecular mass.
• Researchers: Working with proteins, peptides, and proteomics.
• Drug Developers: Estimating the mass of peptide-based therapeutics.

Common Misconceptions

A common pitfall is simply summing the molecular weights of individual amino acids without subtracting the mass of water released during peptide bond formation. Another misconception is forgetting to account for the terminal amino and carboxyl groups in a complete polypeptide chain. This calculator addresses both these points for accurate results.

Amino Acid Sequence Molecular Weight Calculation: Formula and Explanation

The Calculation Process

The molecular weight of a peptide or protein from its sequence is calculated by:

1. Summing the average molecular weights of all amino acid residues in the sequence.
2. Subtracting the molecular weight of water (approximately 18.015 Da) for each peptide bond formed.
3. Optionally, adding the molecular weight of terminal hydrogen atoms if calculating for a complete peptide/protein.

Formula Breakdown

The core formula is:

Molecular Weight = Σ(MW_residue) – (N-1) * MW_H2O + Terminal Hydrogens

Where:

• Σ(MW_residue) is the sum of the average molecular weights of each amino acid residue in the sequence.
• N is the total number of amino acids in the sequence.
• (N-1) is the number of peptide bonds formed, as each bond links two amino acids, and there's one less bond than amino acids in a linear chain.
• MW_H2O is the average molecular weight of water (approximately 18.015 Da).
• Terminal Hydrogens: This accounts for the -NH₂ group at the N-terminus and the -COOH group at the C-terminus. In a complete peptide/protein, this adds approximately 1.008 Da (for H on N) + 17.007 Da (for OH on C) = 18.015 Da to the total weight, which is essentially the molecular weight of a water molecule. If you are summing residue weights without considering termini, you would exclude this.

Variables Table

Variable	Meaning	Unit	Typical Range/Value
Amino Acid Sequence	The ordered list of amino acids that constitute the peptide or protein.	N/A	e.g., MKTIIALSYI
N (Number of Amino Acids)	The total count of amino acids in the sequence.	Count	≥ 1
MWresidue	The average molecular weight of a specific amino acid residue after water removal during peptide bond formation.	Daltons (Da)	~57.05 (Glycine) to ~204.23 (Tryptophan)
MWH2O	The average molecular weight of a water molecule.	Daltons (Da)	~18.015
Terminal Hydrogens	Contribution of the free amino group (-NH2) and carboxyl group (-COOH) at the peptide termini.	Daltons (Da)	~18.015 (if included) or 0 (if not)
Molecular Weight	The calculated total mass of the peptide or protein.	Daltons (Da)	Varies greatly with sequence length and composition.

Practical Examples (Real-World Use Cases)

Example 1: A Small Peptide – Angiotensin II

Angiotensin II is a peptide hormone with the sequence Asp-Arg-Val-Tyr-Ile-His-Pro-Phe.

• Input Sequence: DRVYIHPF
• Number of Amino Acids (N): 8
• Number of Peptide Bonds (N-1): 7
• Calculation Steps:
• Sum of average residue weights for D, R, V, Y, I, H, P, F. (Using the table values and calculator)
• Subtract 7 * 18.015 Da (for water released).
• Add ~18.015 Da for terminal hydrogens (N-terminus NH2 and C-terminus COOH).
• Using the Calculator: Input "DRVYIHPF" and select "Yes" for terminal hydrogens.
• Calculator Output (Approximate):
  • Main Result: ~1046.15 Da
  • Number of Amino Acids: 8
  • Total Residue Weight: ~1064.17 Da
  • Water Molecules Released: 7
• Interpretation: This calculated molecular weight is essential for mass spectrometry analysis to confirm the identity of synthesized or purified Angiotensin II. A difference of even a few Daltons could indicate a modification or an incorrect sequence.

Example 2: A Short Protein Fragment – Insulin Peptide C (Human)

Human Insulin C-peptide is a 31-amino acid peptide. For simplicity, let's consider a hypothetical short fragment like "GAVLIP" (Gly-Ala-Val-Leu-Ile-Pro).

• Input Sequence: GAVLIP
• Number of Amino Acids (N): 6
• Number of Peptide Bonds (N-1): 5
• Calculation Steps:
• Sum of average residue weights for G, A, V, L, I, P.
• Subtract 5 * 18.015 Da.
• Add ~18.015 Da for terminal hydrogens.
• Using the Calculator: Input "GAVLIP" and select "Yes" for terminal hydrogens.
• Calculator Output (Approximate):
  • Main Result: ~661.82 Da
  • Number of Amino Acids: 6
  • Total Residue Weight: ~679.84 Da
  • Water Molecules Released: 5
• Interpretation: Knowing the precise molecular weight helps researchers design experiments, such as sizing columns or mass spectrometry workflows, for analyzing this specific peptide fragment during studies of insulin processing or diabetes research.

How to Use This Amino Acid Sequence Molecular Weight Calculator

Using the Amino Acid Sequence Molecular Weight Calculator is straightforward. Follow these steps to get your results:

1. Enter the Amino Acid Sequence: In the provided text field, type or paste the amino acid sequence using the standard one-letter codes (e.g., 'ARNDCQEGHILKMFPSTWYV'). Ensure there are no spaces or special characters within the sequence itself.
2. Specify Terminal Hydrogens: Choose whether to include the terminal amino (-NH2) and carboxyl (-COOH) groups.
   • Select "Yes (Full Peptide/Protein)" if your sequence represents a complete, intact peptide or protein molecule. This is the most common choice for determining the absolute molecular weight.
   • Select "No (Residue Molecular Weight Sum)" if you are interested in the sum of the average weights of the amino acid residues themselves, excluding the terminal groups. This can be useful for calculating average residue mass or for specific comparative analyses.
3. Calculate: Click the "Calculate Molecular Weight" button.

Reading the Results

• Primary Result (Highlighted): This is the final calculated molecular weight of your peptide or protein in Daltons (Da).
• Number of Amino Acids: The total count of amino acids in your input sequence.
• Total Residue Weight: The sum of the average molecular weights of all the amino acid residues *before* accounting for water loss.
• Water Molecules Released: The number of water molecules that were removed during the formation of peptide bonds (equal to the number of amino acids minus one).

Decision-Making Guidance

The calculated molecular weight is a critical piece of information. Use it to:

• Validate Protein Identity: Compare your calculated mass to experimental results (e.g., from mass spectrometry) to confirm the identity of a protein or peptide.
• Estimate Migration in Gels: While not solely determined by mass, molecular weight is a primary factor in SDS-PAGE migration.
• Design Experiments: Plan purification strategies, buffer compositions, and concentration calculations.
• Interpret Biological Function: Understand how the size of a protein might relate to its cellular role or interactions.

Key Factors That Affect Molecular Weight Calculations

While the core calculation is based on amino acid composition, several factors and nuances can influence the perceived or experimentally determined molecular weight, or require careful consideration:

1. Amino Acid Residue Weights: The calculator uses average molecular weights. Actual isotopic composition can lead to slight variations (monoisotopic vs. average mass). For precise mass spectrometry, monoisotopic masses are often used. Our calculator uses standard average masses.
2. Post-Translational Modifications (PTMs): Many proteins undergo modifications after translation (e.g., phosphorylation, glycosylation, acetylation, disulfide bond formation). PTMs add or subtract specific molecular weights, significantly altering the final mass compared to the unmodified sequence. For example, glycosylation can add hundreds or thousands of Daltons.
3. Disulfide Bonds: The formation of a disulfide bond between two cysteine residues involves the loss of two hydrogen atoms (2 * 1.008 Da). While the calculator doesn't explicitly model this, it's a crucial factor for protein structure and stability that affects the final mass.
4. Sequence Accuracy: The accuracy of the input sequence is paramount. Any errors in the one-letter code will lead to an incorrect molecular weight calculation. Ensure your sequence data is reliable.
5. Terminal Modifications: Beyond simple protonation/deprotonation of N- and C-termini, some proteins might have their N-terminal methionine cleaved or other terminal modifications. This affects the final mass.
6. Hydration Shell: In aqueous solutions, proteins are surrounded by a layer of water molecules. While not part of the protein's intrinsic molecular weight, this hydration shell can influence behavior in certain biophysical measurements.
7. Ionization State in Mass Spectrometry: In techniques like Electrospray Ionization Mass Spectrometry (ESI-MS), proteins gain multiple charges (e.g., [M+nH]ⁿ⁺). The observed mass-to-charge ratio (m/z) is different from the molecular weight, but the molecular weight can be deconvoluted from the m/z values.

Frequently Asked Questions (FAQ)

Q1: What is the difference between molecular weight and molar mass?

Molecular weight is typically expressed in Daltons (Da) and refers to the mass of a single molecule. Molar mass is expressed in grams per mole (g/mol) and represents the mass of one mole of that substance. Numerically, they are virtually identical due to the definition of the mole and the relationship between the Dalton and the Avogadro constant.

Q2: Why are there two options for terminal hydrogens?

The option to include or exclude terminal hydrogens distinguishes between the sum of the average residue weights (excluding water loss from termini) and the total molecular weight of a complete peptide or protein molecule, which includes the N-terminal amino group and C-terminal carboxyl group. For most practical purposes of determining a protein's mass, including them ('Yes') is correct.

Q3: Does the calculator account for isotopic variation?

No, this calculator uses the average molecular weights of amino acids, which are weighted averages of the naturally occurring isotopes. For precise mass determination using techniques like high-resolution mass spectrometry, monoisotopic masses might be required.

Q4: How accurate are the results?

The results are highly accurate for the theoretical molecular weight based on the provided sequence and standard average residue weights. However, experimental results may differ due to post-translational modifications, isotopic variations, or errors in sequence determination.

Q5: Can this calculator determine the mass of cyclic peptides?

No, this calculator is designed for linear peptides and proteins. Cyclic peptides have different structures where the C-terminus is linked to the N-terminus or a side chain, altering the number of water molecules released and terminal groups.

Q6: What if my sequence contains non-standard amino acids?

This calculator uses a standard set of 20 common amino acids. If your sequence includes non-standard amino acids (e.g., selenocysteine, phosphoserine, or modified residues), you would need to manually find their average molecular weights and adjust the calculation or use a specialized tool.

Q7: How does molecular weight relate to protein function?

Molecular weight is a basic physical property that influences how a protein interacts with other molecules, moves through cellular compartments, and behaves in various experimental setups. Larger proteins might have more complex functions or require more energy for transport, while smaller proteins might act as signaling molecules or enzyme subunits.

Q8: What is the significance of the 'Water Molecules Released' value?

Each peptide bond formation between two amino acids releases one molecule of water. The value 'N-1' indicates how many such bonds are present in a linear peptide of length N. This number is directly used to subtract the mass of these released water molecules from the sum of the individual amino acid masses.