Determine the molecular weight of proteins using their size and amino acid composition.
Protein Molecular Weight Calculator
Enter the total count of amino acid residues in the protein sequence.
Average molecular weight per amino acid residue (typically around 110 Da).
The molecular weight of a water molecule (H2O), approximately 18.015 Da.
Molecular weight of the terminal hydrogen atom (or other substituent) at the N-terminus.
Molecular weight of the terminal hydroxyl group (or other substituent) at the C-terminus.
Calculation Results
— Da
Total MW from Amino Acids:— Da
Total MW of Water Molecules Released:— Da
Net Protein Molecular Weight:— Da
The molecular weight of a protein is calculated by summing the molecular weights of all its amino acid residues, accounting for the water molecules released during peptide bond formation, and adding the molecular weights of the N-terminus and C-terminus.
Formula: MW = (N * AvgAA_MW) – ((N-1) * H2O_MW) + N-Terminus_MW + C-Terminus_MW
*(Note: For simplicity, AvgAA_MW often implicitly includes the net change from peptide bond formation, making the calculation sometimes simplified as: MW ≈ N * AvgAA_MW + N-Terminus_MW + C-Terminus_MW, but the more precise method accounts for water release explicitly.)*
Molecular Weight Distribution Chart
Distribution of molecular weight contribution across different components.
Amino Acid Composition Table
Typical Amino Acid Molecular Weights
Amino Acid
1-Letter Code
Average MW (Da)
Avg. Contribution to Protein MW (Da)
Alanine
A
89.09
—
Cysteine
C
121.16
—
Aspartic Acid
D
133.10
—
Glutamic Acid
E
147.13
—
Phenylalanine
F
165.19
—
Glycine
G
75.07
—
Histidine
H
155.16
—
Isoleucine
I
131.17
—
Lysine
K
146.19
—
Leucine
L
131.17
—
Methionine
M
149.21
—
Asparagine
N
132.12
—
Proline
P
115.13
—
Glutamine
Q
146.15
—
Arginine
R
174.20
—
Serine
S
105.09
—
Threonine
T
119.12
—
Valine
V
117.15
—
Tryptophan
W
204.23
—
Tyrosine
Y
181.19
—
What is Protein Size and Molecular Weight?
The "protein size" and "molecular weight" are fundamental properties describing proteins. Molecular weight, typically measured in Daltons (Da) or kilodaltons (kDa), quantifies the mass of a protein molecule. This mass is derived from the sum of the atomic masses of all atoms within the protein's amino acid sequence. Protein size can also refer to dimensions or hydrodynamic radius, but molecular weight is a direct, quantifiable measure of its mass. Understanding a protein's molecular weight is crucial for numerous biological and biochemical applications, including separation techniques, enzyme kinetics, and structural biology.
Who should use this calculator? Researchers, students, biochemists, molecular biologists, pharmacologists, and anyone working with proteins will find this tool invaluable. Whether you're designing an experiment, analyzing gel electrophoresis results, or validating protein expression, knowing the precise molecular weight is essential.
Common misconceptions about protein molecular weight include assuming all proteins of similar "size" (e.g., on a gel) have identical molecular weights, or that the calculated molecular weight perfectly reflects its behavior in all experimental conditions. Factors like post-translational modifications, protein folding, and buffer conditions can subtly influence experimental measurements compared to theoretical calculations. This protein size molecular weight calculator provides the theoretical mass based on the primary sequence.
Protein Size Molecular Weight Formula and Mathematical Explanation
Calculating the molecular weight of a protein involves a straightforward, albeit detailed, summation. When amino acids link together to form a polypeptide chain via peptide bonds, a molecule of water (H₂O) is released for each bond formed. Therefore, the total mass is not simply the sum of individual amino acid masses. The formula accounts for the amino acids, the water molecules lost, and the terminal groups.
Step-by-step derivation:
Calculate the total mass of all amino acids: Multiply the number of amino acids by the average molecular weight of an amino acid residue.
Calculate the total mass of water released: For a polypeptide chain of N amino acids, N-1 peptide bonds are formed, meaning N-1 water molecules are released. Multiply the number of water molecules by the molecular weight of water.
Subtract the mass of released water: This accounts for the atoms lost during peptide bond formation.
Add terminal group masses: The N-terminus typically has a free amino group (often considered as -NH₃⁺, but for mass calculation, the elemental composition like H for a simple amine or the whole residue mass is used), and the C-terminus has a free carboxyl group (often -COO⁻, with components like O and OH). We add the molecular weights of these terminal groups.
The precise formula used by this protein size molecular weight calculator is:
MW_Protein = (Number of Amino Acids * Average Amino Acid MW) – ((Number of Amino Acids – 1) * Water Molecule MW) + N-terminus MW + C-terminus MW
Variable explanations:
Protein Molecular Weight Variables
Variable
Meaning
Unit
Typical Range
Number of Amino Acids (N)
The total count of amino acid residues in the protein sequence.
Unitless
10 to > 10,000
Average Amino Acid MW (AvgAA_MW)
The average molecular weight of a single amino acid residue. This is the molecular weight of the amino acid minus the molecular weight of water.
Daltons (Da)
~100 – 200 Da (average is ~110 Da)
Water Molecule MW (H₂O_MW)
The molecular weight of a single water molecule.
Daltons (Da)
~18.015 Da
N-terminus MW
The molecular weight contribution of the terminal group at the N-terminus (e.g., H for a simple amine).
Daltons (Da)
~1.008 Da (for H) to ~18.011 (for NH2)
C-terminus MW
The molecular weight contribution of the terminal group at the C-terminus (e.g., OH for a simple carboxyl).
Daltons (Da)
~17.007 Da (for OH) to ~45.017 (for COOH)
MW_Protein
The calculated net molecular weight of the complete protein molecule.
Daltons (Da)
Varies widely based on protein size
*Note: The "Average Amino Acid MW" input in the calculator is often used as a simplified proxy. For highly accurate calculations, one might sum the exact MW of each specific amino acid in the sequence and subtract the precise number of water molecules (N-1) plus the exact terminal group masses.*
Practical Examples (Real-World Use Cases)
Understanding the protein size molecular weight calculation is key to interpreting experimental data and planning research. Here are a couple of practical scenarios:
Example 1: Estimating MW of a Small Peptide
A researcher synthesizes a small peptide consisting of 25 amino acids. They use an average amino acid residue weight of 115 Da, assume standard N-terminus (H, 1.008 Da) and C-terminus (OH, 17.007 Da) groups, and use the average water molecule weight of 18.015 Da.
Inputs:
Number of Amino Acids: 25
Average Amino Acid MW: 115 Da
Water Molecule MW: 18.015 Da
N-terminus MW: 1.008 Da
C-terminus MW: 17.007 Da
Calculation:
Total AA MW = 25 * 115 Da = 2875 Da
Water Released MW = (25 – 1) * 18.015 Da = 24 * 18.015 Da = 432.36 Da
Net Protein MW = 2875 Da – 432.36 Da + 1.008 Da + 17.007 Da = 2460.655 Da
Result: The calculated molecular weight of this 25-amino acid peptide is approximately 2460.66 Da. This value is crucial for designing mass spectrometry experiments to confirm peptide identity or for predicting its behavior during size exclusion chromatography.
Example 2: Analyzing a Larger Recombinant Protein
A scientist expresses a recombinant protein sequence containing 500 amino acids. They know the exact average molecular weight of the residues in their protein is closer to 112 Da due to a specific amino acid composition. They use standard water molecule (18.015 Da) and terminal group values (N-terminus H: 1.008 Da, C-terminus OH: 17.007 Da).
Inputs:
Number of Amino Acids: 500
Average Amino Acid MW: 112 Da
Water Molecule MW: 18.015 Da
N-terminus MW: 1.008 Da
C-terminus MW: 17.007 Da
Calculation:
Total AA MW = 500 * 112 Da = 56000 Da
Water Released MW = (500 – 1) * 18.015 Da = 499 * 18.015 Da = 8989.485 Da
Net Protein MW = 56000 Da – 8989.485 Da + 1.008 Da + 17.007 Da = 47028.53 Da
Result: The theoretical molecular weight for this 500-amino acid protein is approximately 47028.53 Da (or 47.03 kDa). This estimate is vital for troubleshooting purification steps (e.g., SDS-PAGE gels, FPLC chromatography) and for comparing against experimentally determined molecular weights. A significant deviation might suggest post-translational modifications or assembly into larger complexes.
How to Use This Protein Size Molecular Weight Calculator
Our protein size molecular weight calculator is designed for simplicity and accuracy. Follow these steps to get your protein's molecular weight:
Input Number of Amino Acids: Enter the total count of amino acid residues in your protein's primary sequence.
Enter Average Amino Acid MW: Input the average molecular weight per amino acid residue. A common value is around 110 Da, but this can vary slightly based on the specific amino acid composition of your protein.
Input Water Molecule MW: The calculator uses a standard value of 18.015 Da for water. You can adjust this if using highly precise isotopic data, but it's rarely necessary.
Input Terminal Group MWs: Provide the molecular weights for the N-terminus and C-terminus. Standard values for a free amine (-H) and carboxyl (-OH) are pre-filled.
Click 'Calculate': Press the button, and the results will update instantly.
How to read results:
Primary Highlighted Result: This is your protein's calculated net molecular weight in Daltons (Da).
Intermediate Values: These show the breakdown: the total mass contribution from amino acids, the mass of water released during polymerization, and the net protein weight.
Formula Explanation: Provides context on how the calculation is performed.
Chart: Visually represents the contribution of each component to the total weight.
Table: Lists typical molecular weights for individual amino acids.
Decision-making guidance: Compare the calculated molecular weight to your experimental results (e.g., from SDS-PAGE, mass spectrometry). Significant differences might indicate:
This calculation provides a theoretical baseline for understanding your protein's mass.
Key Factors That Affect Protein Molecular Weight Results
While the calculation for protein size molecular weight based on sequence is precise, several factors can influence the *experimentally measured* molecular weight or its interpretation:
Amino Acid Composition: Different amino acids have vastly different molecular weights (e.g., Tryptophan vs. Glycine). A protein rich in heavier amino acids will have a higher molecular weight than a protein of the same length composed of lighter ones.
Post-Translational Modifications (PTMs): These are chemical modifications that occur after protein synthesis. Glycosylation (adding sugars), phosphorylation (adding phosphate groups), lipidation, and disulfide bond formation can significantly increase a protein's measured molecular weight. Our calculator provides the *unmodified* theoretical weight.
Number of Amino Acids (Protein Length): This is the most direct determinant. Longer proteins inherently have higher molecular weights. The calculation scales linearly with the number of residues.
N- and C-termini Modifications: While standard calculations assume simple terminal groups, biological proteins can have modified termini (e.g., acetylation, cyclization). These will alter the final mass.
Protein Folding and Secondary Structure: While molecular weight is a measure of mass and not volume, complex folding can affect how a protein interacts with certain detection methods (like some forms of gel electrophoresis if SDS is not fully denaturing). However, the fundamental mass remains unchanged.
Presence of Cofactors or Bound Ligands: If a protein binds tightly to small molecules, metal ions, or other non-proteinaceous components, its apparent molecular weight in solution might seem higher than calculated. The calculator focuses solely on the polypeptide chain itself.
Isotopic Abundance: While the standard atomic weights used are averages, the precise mass can vary slightly based on the specific isotopes of elements present. For most biological applications, average weights are sufficient.
Frequently Asked Questions (FAQ)
What is the unit of molecular weight?
Molecular weight is typically measured in Daltons (Da) or kilodaltons (kDa), where 1 kDa = 1000 Da. Daltons are a unit of mass, approximately equal to the mass of a single hydrogen atom.
Why do I need to subtract water molecules?
Peptide bonds are formed through a dehydration synthesis reaction. For every peptide bond formed between two amino acids, one molecule of water (H₂O) is released. The calculated molecular weight must account for this mass loss.
Can this calculator handle proteins with post-translational modifications?
No, this calculator provides the theoretical molecular weight based on the primary amino acid sequence only. Post-translational modifications like glycosylation or phosphorylation add mass and must be calculated separately or determined experimentally.
What is the typical average molecular weight of an amino acid residue?
The average molecular weight of an amino acid residue (after water removal) is approximately 110 Da. However, this can vary depending on the specific amino acid composition of the protein, ranging roughly from 75 Da (Glycine) to over 200 Da (Tryptophan).
How does this protein size molecular weight calculation compare to SDS-PAGE results?
SDS-PAGE separates proteins primarily by size, estimating molecular weight. However, factors like glycosylation or unusual amino acid composition can cause deviations between the calculated/theoretical MW and the MW estimated by SDS-PAGE.
What if my protein sequence has unusual N- or C-termini?
If your protein has known modifications at the N- or C-termini (e.g., acetylation, methylation), you should adjust the 'N-terminus MW' and 'C-terminus MW' inputs accordingly for a more accurate calculation. If unknown, the default values represent standard free amine and carboxyl groups.
Is the calculated molecular weight the same as the protein's mass in biological function?
The calculated molecular weight is the mass of the polypeptide chain. A protein's biological function often depends on its 3D structure, interactions with other molecules, and localization, which are related to but not solely determined by its mass.
Can I use this calculator for predicting protein behavior in size exclusion chromatography?
Yes, the calculated molecular weight is a key parameter for predicting protein behavior in size exclusion chromatography. However, the protein's hydrodynamic radius (influenced by its shape and folding) also plays a significant role.