Data Search
Kinetic data can be retrieved using different forms. The Basic search form allows to browse
the database searching for specific Protein Data Bank (PDB)
and UniProt codes.
The form allows to select data corresponding to wild-types and different classes of variants
(single, double, multiple).
The PDB ID associated with each protein is unique.
It is either mentioned in the original publication or selected by the curators based on the highest quality structural parameters
and the best match between the PDB ID sequence and the protein sequence used in the kinetic measurements.
Alternative protein structures can be found through the UniProt search.
To simplify this task, the "Match UniProt" checkbox allows for the automatic
retrieval of the UniProt ID associated with the input PDB ID, thereby expanding the search to encompass all related structures.
Advanced search can be performed activating three alternative forms that allow to post
more complex queries based on three groups of information
(Molecule, Experimental, and Publication). Since collected data includes different types of experiments,
these forms allow to select the subset of data for which a specific kinetic measure is available.
When the result of the search is returned a plus button allow to load the query and modify the initial search.
Data Visualization
The output if the search is displayed using DataTables a
table plugin for jQuery. For each record by default the table reports 12 columns (UniProt, Structure, Chain, Mutation, Sec. Str.,
RSA, T, pH, ln(kfH2O), Δln(kfH2O), ln(kuH2O), Δln(kuH2O).
A plus button allow to expand each row showing all data of each record.
When the structure of the protein under study is available, K-Pro interface allows to display the structure
of the wild-type protein through JSmol plugin.
If kinetic data on protein mutants are returned, the web interface allow to visualize all the residues
surrounding the wild-type amino acid with
Displayed Data
The data collected in K-Pro database are organized reporting the following fields for each record:
Protein: | Common name of the protein. |
Source: | Source of the protein. |
Length: | Total number of amino acid residues in the protein. |
UniProt: | Protein identifier in UniProt database. |
Class: | Structural class based on CATH classification. |
PFAM: | PFAM identifier. |
CATH: | CATH identifier. |
EC_NUMBER: | Enzyme Commission number. |
Structure: | Protein Data Bank or AlphaFold code of the wild-type protein. In general, for each protein, the PDB code indicated by the authors of the kinetic measurements was maintained, except in a few cases, in which a crystal structure with the best resolution, and highest coverage, had been published in the meantime. |
Chain: | Protein chain in the PDB file. It is also reported as MUTATED_CHAIN. |
Mutation_UNIPROT: | Mutation with format XPOSY (X/Y: wild-type/mutant residue, POS UniProt Sequence position). |
Mutation_PDB: | Mutation with format XPOSY (X/Y: wild-type/mutant residue, POS: PDB or Sequence position). |
Sec. Str.: | Protein secondary structure of the wild-type residue in the mutated position (Helix,Sheet,Coil). |
RSA: | Relative solvent accessibility of the wild-type residue in the mutated position. |
T: | Temperature (°C). |
pH: | The pH value of the experiment. |
Buffer: | Name of the buffer used in the experiment. It is also indicated with BUFFER_NAME. |
[Buffer]: | Concentration of the buffer in the experiment (BUFFER_CONC) |
Ion: | Name of the Ions added during the experiment. It is also indicated with ION_NAME. |
Additives: | Details about the additives (e.g. glycerol). |
Measure: | Experiment for determining the kinetic measures. |
Method: | Denaturation method. |
ln(kfH2O): | Logarithm of the folding rate (referred to 1 s-1)
|
Δln(kfH2O): |
Variation of the logarithm of the folding rate:
ln(kfH2O)mut - ln(kfH2O)wt.
|
ln(kuH2O): |
Logarithm of the unfolding rate (referred to 1 s-1).
|
Δln(kuH2O): |
Variation of the logarithm of the unfolding rate:
ln(kuH2O)mut - ln(kuH2O)wt.
| ln(kfDEN): | Logarithm of the folding rate (s-1)
Δln(kfDEN):
| Variation of the logarithm of the folding rate measured in denaturant:
ln(kfDEN)mut - ln(kfDEN)wt.
ln(kuDEN): Logarithm of the unfolding rate
Δln(kuDEN):
| Variation of the logarithm of the unfolding rate measured in denaturant:
ln(kuDEN)mut - ln(kuDEN)wt.
ΔGH2O: Unfolding free energy at zero denaturant concentration (kJ/mol) from equilibrium measurements. ΔΔGH2O: ΔGH2O(mutant) - ΔGH2O(wild-type). mf: Slope of ln(k) on the left side of the asymptodes of the Chevron plot [kJ/mol/M]. mu: Slope of ln(k) on the right side of the asymptodes of the Chevron plot [kJ/mol/M]. Cm: Concentration of denaturant at which 50% of the protein is unfolded [M]. β-T: Tanford β represents the compactness of the transition state and measures
of the average degree of exposure in the transition state relatively to the denatured state.
φH2O: Phi-Value represents the change in stability of the transition state upon mutation of a residue, relatively to the effect of the same mutation on the native state. Background Mutation UniProt/PDB: UniProt or PDB modifications of the wild-type protein used as reference. State: Two-state or multi-state. Reversibility: Reversibility of denaturation process. Author: Name of the authors. Reference: Journal and volume of the publication. Year: Year of the publication. PMID: PubMed ID of the publication. Review date: Date of the last modification of the record. |