|
Terms
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Explanations
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| 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. Accessibility (%) is defined as the ASA of the residue at the mutation site (X) in its parent protein, computed with DSSP divided by the ASA of the residue in an extended tripeptide Ala-X-Ala conformation.The extended state ASA was calculated using ECEPP/2 algorithm with dihedral angles given by Oobatake and Ooi (Prog. Biophys. Mol. Biol. (1993) 59, 237-284) and the van der Waals radius of atoms from Ooi et al. (Proc. Natl. Acad. Sci. USA. (1987) 84, 3086-3090). The values are Ala-110.2; Asp-144.1; Cys-140.4; Glu-174.7; Phe-200.7; Gly-78.7; His-181.9; Ile-185.0; Lys-205.7; Leu-183.1; Met-200.1; Asn-146.4; Pro-141.9; Gln-178.6; Arg-229.0; Ser-117.2; Thr-138.7; Val-153.7; Trp-240.5; Tyr-213.7 (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. |
