KT-Pro

Kinetics and Thermodynamics of Proteins and Mutants



Data Search


Thermodynamic data can be retrieved using two 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 Advanced search form can be used to define more complex queries to based on three groups of information (Molecule, Themodynamics, and Publication). Since collected data includes different types of experiments, this form allows to select the subset of data for which a specific thermodynamic measure is available.



Protein Visulization


When the structure of the protein under study is availanle, KT-Pro interface allows to display the structure of the wild-type protein through JSmol plugin. If thermodynamic data on protein mutants are returned, the web interface allow to visualize all the residues surrounding the wild-type amino acid within a given radio shell. The visulaization of the structure is activated through the link in the Mutation column.



Displayed Data


The data collected in KT-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.
Mol. Weight: 
Molecular weight calculated considering the amino acid sequence with NC terminals and mutations.
UniProt: 
Protein identifier in UniProt database. It is also reported as SWISSPROT_ID.
EC Number: 
Enzyme Commission number.
PDB: 
Protein Data Bank code of the wild-type protein. It is also reported as PDB_wild.
PDB mutant: 
Protein Data Bank code of the mutant protein.
Chain: 
Protein chain in the PDB file. It is also reported ad MUTATED_CHAIN.
Mutation: 
Mutation with format XPOSY (X/Y: wild-type/mutant residue, POS: PDB or Sequence position).
No. Molecule: 
Number of Molecules (e.g. 1 = Monomer, 2 = Dimer, etc.).
Sec. Structure: 
Protein secondary structure of the wild-type residue (Helix,Sheet,Turn,Coil).
RSA: 
Relative solvent accessibility of the wild-type residue.
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 Conc.: 
Concentration of the buffer in the experiment. It is also indicated with BUFFER_CONC and [BUFFER].
Ion: 
Name of the Ions added during the experiment. It is also indicated with ION_NAME.
Additives: 
Details about the additives (e.g. glycerol).
Protein Conc.: 
Concentration of the protein when the experiment has been performed.
Measure: 
Experiment for determining the thermodynamic measures.
Method: 
Denaturation method.
ΔGH2O: 
Unfolding free energy at zero denaturant concentration (kcal/mol).
ΔΔGH2O: 
ΔGH2O(mutant) - ΔGH2O(wild-type).
ΔGu: 
Unfolding free energy in presence of denaturant(kcal/mol).
ΔΔGu: 
ΔGu(mutant) - ΔGu(wild-type). or obtained by Schellman equation.
Tm: 
Midpoint temperature for thermal denaturation methods [°C].
ΔTm: 
Tm(mutant) - Tm(wild) [°C].
ΔHvH: 
van't Hoff enthalpy change of denaturation (enthalpy obtained from the temperature dependence of the denaturation equilibrium constant).
ΔHcal: 
Calorimetric enthalpy change of denaturation (enthalpy measured by calorimetry).
m: 
Slope of ΔG on denaturant concentration (ΔG vs urea/GdnHCl; ΔG=ΔG(H2O)-m[Denaturant]) [kcal/mol/M].
Cm: 
Concentration of denaturant at which 50% of the protein is unfolded [M].
ΔCp: 
Heat capacity change of denaturation [kcal/mol/K].
State: 
Number of transition states.
Reversibility: 
Reversibility of denaturation process.
Remarks: 
Comments on the reported data.
Author: 
Name of the authors.
Reference: 
Journal and voluome of the publication.
PMID: 
PubMed ID of the publication.
Keywords: 
List of keywords used for the specific protein/article.
Review date: 
Date of the last modification of the data.



Parsable Output


All the data returned by the query search can be locally downloaded from the server. The file is a tab separated file that reports all the information described above.