Protein Molecular Weight Calculator from Nucleotide Sequence
Instantly translate DNA/RNA sequences into protein mass (Daltons/kDa).
Accepts A, T, G, C, U. Whitespace and numbers are automatically removed.
Invalid characters detected. Please use only A, T, G, C, U.
DNA (Coding Strand)
RNA (mRNA)
Select DNA to treat T as U, or RNA for direct translation.
Total Molecular Weight0.00 Da
Weight in kDa0.00 kDa
Amino Acid Count0
Nucleotides Used0
*Calculation assumes average isotopic masses and subtraction of water (18.015 Da) per peptide bond.
Property
Value
Description
Sequence Length
0 bp
Total nucleotides processed
GC Content
0%
Percentage of G and C bases
Stop Codons
0
Number of termination signals found
What is a Protein Molecular Weight Calculator from Nucleotide Sequence?
A protein molecular weight calculator from nucleotide sequence is a specialized bioinformatics tool designed to predict the mass of a polypeptide chain based on its genetic coding sequence (DNA or RNA). By simulating the biological processes of transcription and translation, this calculator converts a string of nucleotides (A, T/U, G, C) into a corresponding sequence of amino acids and sums their atomic weights.
This tool is essential for molecular biologists, biochemists, and students who need to verify cloning experiments, estimate protein migration on SDS-PAGE gels, or determine if a specific gene sequence produces a protein of the expected size. Unlike generic mass calculators, this tool specifically accounts for the loss of water molecules during peptide bond formation, providing a more accurate biological mass estimation.
Common misconceptions include assuming that nucleotide length directly correlates to protein weight by a fixed ratio without considering the specific amino acid composition, as different amino acids have varying molecular weights (e.g., Tryptophan is much heavier than Glycine).
Protein Molecular Weight Formula and Explanation
The calculation involves two primary steps: Translation and Summation. The process mimics the central dogma of biology.
Total MW = Σ (MW of Amino Acid Residues) + MW of Water (N-terminus/C-terminus adjustments)
Where:
MW_Residue = MW_AminoAcid – 18.01524 (Water lost in bond)
The calculation follows this logic:
Translation: The nucleotide sequence is read in triplets called "codons". Each codon maps to a specific amino acid according to the standard genetic code.
Summation: The average isotopic weight of each mapped amino acid is added to the total.
Water Adjustment: For a protein of n amino acids, there are n-1 peptide bonds. Since a water molecule (H2O) is released during the formation of each bond, the weight of the water must be subtracted from the sum of the free amino acids, or one can simply sum the "residue weights" and add back the weight of one water molecule (for the free H on the N-terminus and OH on the C-terminus).
Process: The calculator identifies codons TTT (Phe), GTC (Val), etc. It translates these 10 codons into a decapeptide.
Output: The calculated molecular weight would be approximately 1,150 Da (1.15 kDa). A researcher would use this value to confirm the identity of the synthesized peptide via mass spectrometry.
Example 2: GFP (Green Fluorescent Protein) Verification
Input Scenario: A lab technician has sequenced a cloned plasmid and obtained a 720bp sequence. They want to check if it encodes the full-length GFP protein.
Calculation: Input: 720 nucleotides
Translation: 240 amino acids (approximate, minus stop codon)
Result: ~27,000 Da (27 kDa)
Interpretation: Since wild-type GFP is known to be approximately 27 kDa, the result confirms the sequence likely encodes the correct full-length protein without premature stop codons.
How to Use This Calculator
Enter Sequence: Paste your raw DNA or RNA sequence into the text box. The tool automatically ignores numbers (often found in FASTA formats) and whitespace.
Select Type: Choose "DNA" if your sequence contains Thymine (T) or "RNA" if it contains Uracil (U). The calculator handles the T-to-U conversion logic internally.
Review Metrics:
MW (Da): The precise atomic mass.
MW (kDa): Useful for comparing with protein ladders on gels.
Amino Acid Count: Confirms the length of the translation product.
Analyze Composition: Use the chart to see the distribution of nucleotides, which can indicate GC-rich regions (harder to amplify via PCR) or specific bias.
Key Factors That Affect Protein Molecular Weight Results
Several biochemical factors influence the final calculated mass compared to experimental results:
Post-Translational Modifications (PTMs): This calculator determines the predicted unmodified mass. In reality, proteins may undergo phosphorylation (+80 Da), glycosylation (adds sugars, significant mass increase), or lipid attachment.
Signal Peptides: Many proteins have N-terminal signal sequences that are cleaved off after translocation. The mature protein will be lighter than the value calculated from the full gene sequence.
Isotopic Averaging: The calculator uses average atomic weights (C=12.011). Mass spectrometry might measure monoisotopic mass (using C=12.000), causing slight discrepancies.
Stop Codons: If your sequence contains internal stop codons due to mutation, the translation will terminate early, resulting in a "truncated" protein with significantly lower mass.
Reading Frame: Shift the sequence by just one nucleotide (frameshift), and the entire amino acid sequence—and thus the weight—changes completely.
Splice Variants: In eukaryotes, mRNA splicing removes introns. Calculating weight from genomic DNA (with introns) will yield a wildly incorrect, massive value compared to the cDNA (mRNA) sequence.
Frequently Asked Questions (FAQ)
Does this calculator handle degenerate nucleotides (N, R, Y)?
No, this calculator requires specific standard nucleotides (A, T, G, C, U) to accurately determine amino acid identity. Degenerate bases introduce ambiguity in mass calculation.
Why is the calculated weight different from my Western Blot result?
Western Blots estimate size based on migration through a gel matrix. PTMs, protein charge, and folding structure can cause proteins to migrate faster or slower than their true molecular weight would suggest.
Does the calculator include the weight of the Stop codon?
No, stop codons signal the ribosome to release the polypeptide chain; they do not add an amino acid to the final structure.
Can I use this for short peptides?
Yes, the math remains valid for sequences as short as a single codon, though it is most useful for longer chains where manual calculation is tedious.
How does the calculator handle 'Start' codons?
It treats the first codon as the start of the sequence. It does not automatically scan for the first ATG; it translates from the very first character you input.
What is the difference between Da and kDa?
Da (Dalton) is the base unit. 1 kDa (Kilodalton) equals 1,000 Daltons. kDa is the standard unit used in protein biology literature.
Does this account for disulfide bridges?
Disulfide bridges involve the loss of two hydrogen atoms (~2 Da). This calculator calculates the reduced (linear) weight, so it does not subtract the mass for disulfide bonds.
Is the water weight subtraction accurate?
Yes, the formula sums the residue weights (amino acid MW minus water) and adds one water molecule back to account for the free termini, which is the standard biochemical method.