Protein Charge At PH

Estimate sequence net charge at pH from caller-supplied terminal and side-chain pKas.

Description

A sequence-charge model sums fractional protonation of termini and selected ionizable side chains.

A sequence-charge model sums fractional protonation of termini and selected ionizable side chains. Nine supplied pKas control those fractions.^[1]

Estimate sequence net charge at pH from caller-supplied terminal and side-chain pKas.

When to use Protein Charge At PH

Use this tool to estimate sequence net charge at pH from caller-supplied terminal and side-chain pKas.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Protein Charge At PH and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence, ph, pkas using the field table and calculation rules, then run the tool.
Read netCharge. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required
ph	Ph	number	Required
pkas	Pkas	list of number	Required

Enter canonical sequence, pH in 0–14 and exactly nine finite pKas ordered N terminus, C terminus, K, R, H, D, E, C, Y. Include one of each terminus and multiply side-chain fractions by residue counts.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

positiveFraction=1/(1+10^(pH−pKa)); negativeFraction=1/(1+10^(pKa−pH)); net=positive contributions−negative contributions

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
netCharge	Net charge	number

json

{
  "input": {
    "sequence": "A",
    "ph": 7,
    "pkas": [
      7,
      7,
      10,
      12,
      6,
      4,
      4,
      8,
      10
    ]
  },
  "output": {
    "netCharge": 0
  }
}

Limitations and assumptions

This is a charge-in-elementary-units model, not a titration measurement. pKas, modifications and local environments are not derived from structure.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Protein Sequence Isoelectric Point: Estimate sequence isoelectric pH by bisection of caller-parameterized charge. For a complementary task, use Protein Extinction 280: Estimate 280-nm molar extinction coefficient from Trp, Tyr, and cystine.

References

Protein Charge At PH — tool.io

Similar or alternative tools

Protein Sequence Isoelectric Point
Estimate sequence isoelectric pH by bisection of caller-parameterized charge.
Protein Extinction 280
Estimate 280-nm molar extinction coefficient from Trp, Tyr, and cystine.