|
Terms
|
Explanations
|
| No |
Entry number. This option can be used for
getting data from a particular entry (Eg. 31243) |
| Protein Name |
Name of the protein |
| E_C_number |
Enzyme Commission number |
| PDB |
Protein Data Bank code for the
native protein |
| STATE |
Number of transition states
|
| Mutation |
Details about the mutation:
residue in wild type, residue number and residue in mutant protein (e.g. G145R)
|
| Sec str |
Secondary Structural Information for the mutation site
(Helix, Strand, Turn and Coil; we obtain the data from PDB)
In search result : H = Helix, S = Strand, T = Turn, C = Coil.
|
| Accessible Surface Area |
Accessible surface area (ASA)
of the residue in wild type ((the units are in A**2). We classifed the
residues with less than 20% accessibility as buried, between 20% and 50%
as partially buried and more than 50% as exposed. |
| Measure |
The experiments performed to
measure the thermodynamic parameters (Fluorescence spectroscopy, Circular
Dichroism, Differential Scanning Calorimetry, Absorbance, NMR, etc.) Keywords:
Fl, CD, DSC, Abs, NMR, others |
| Method |
Experimental method of denaturation
(keywords: Thermal, Urea, GdnHCl etc.). (activity: 50% relative remaining
activity of the enzyme after the heat treatment) |
| pH |
the pH value. |
| m
|
Slope of ΔG on denaturant concentration
(ΔG vs urea/GdnHCl; ΔG = ΔG(H2O) - m[Denaturant]).Unit is kcal/mol/M. |
| Cm |
Concentration of denaturant
at which 50% of the protein is unfolded [M] |
| ΔTm |
Tm(mutant) - Tm(wild) [degree
Celsius]. Positive and negative values of ΔTm indicate stabilizing and destabilizing mutations, respectively. |
|
T |
In the case of denaturant denaturation methods,
T is the temperature used in the experiment.[degree Celsius] |
| Tm |
Midpoint temperature of the
thermal unfolding for thermal denaturation methods [degree Celsius] |
| ΔG |
(1) Free energy of unfolding
at a certain concentration of denaturant in the case of denaturant denaturation
methods
(2) Free energy of unfolding obtained for extrapolation temperature T using
ΔCp in the case of thermal denaturation method [kcal/mol] |
| ΔΔG |
ΔG(mutant) - ΔG(wild) [kcal/mol]
Free energy of unfolding obtained with Schellman equation (ΔΔG = dTm.ΔS)
in the case of thermal denaturation method [kcal/mol]. Positive and negative values of ΔΔG indicate stabilizing and destabilizing mutations, respectively.
|
| ΔΔG_H2O |
ΔG_H2O(mutant) - ΔG_H2O(wild)
[kcal/mol]. Positive and negative values of ΔΔGH2O indicate stabilizing and destabilizing mutations, respectively. |
| ΔH
|
Enthalpy change of
denaturation [kcal/mol] |
| ΔHvH |
van't Hoff enthalpy change of
denaturation (enthalpy obtained from the temperature dependence of the denaturation
equilibrium constant) |
| ΔCp |
Heat capacity change of denaturation
[kcal/mol/K] |
| ΔG_H2O |
Free Energy of unfolding in
water, determined by denaturant (urea; GdnHCl; GSSG/GSH; GdnSCN) denaturation
of proteins and extrapolation of the data to zero concentration of denaturant
[kcal/mol] |
| Reversibility |
Reversibility of denaturation.
If the reversibility is mentioned in the paper, "Yes" (and % of reversibility
if described) or "No" is listed, or otherwise this field is set to Unknown.
|
| Key_words |
List of keywords used for the
specific protein/article Multiple words can be entered with spaces. |
| Author |
Name of the authors. |
| Year |
Year of publication. |
| Reference |
Complete reference of the article
with a link to NCBI database with PMID |
| Remarks |
Some specific comments |
| Source |
Source of the protein |
| Length |
Total number of Amino Acid residues in
the protein |
| No of molecule |
Number of chains in protein |
| Buffer_name |
Name of the buffer used in the
experiment |
| Buffer_conc |
Concentration of the buffer
|
| Ion_name |
Name of the added ion |
| Ion_conc |
Concentration of the ion |
| ADDITIVES |
Details about the additives (e.g. glycerol) |
| Protein_conc
|
Concentration of the protein
when the experiment has been performed |
| RELATED_ENTRIES |
List of all the entries that
contain other data reported in the same reference. |
