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KineticDB help

KineticDB is the thoroughly curated database of protein folding kinetics data which contains currently 87 unique proteins. The main goal of KineticDB is to provide users with the diverse set of protein folding rates known from experiment. For each record of KineticDB the following data can be obtained, which can be grouped in four categories:
Experimentally Studied Protein: Details about the experimentally studied protein.
Name
The full name of the protein
Acronym
The acronym used for the protein
Organism
The source organism, from which the protein was taken. In the case when the protein was obtained by de novo design, we use the word "Synthetic"
Length
The number of amino acid residues in the sequence of the experimentally studied protein
Sequence
The sequence of the experimentally studied protein
Mutation
Indicates difference between the sequence of the best available structure and the corresponding wild-type sequence
Ref ID
The reference identifier of the original paper containing all the data concerning the present experiment
Reference
The full description of the original paper containing all the data concerning the present experiment

Details about the best available structure corresponding to experimentally studied protein. For some proteins there is no exact match in the PDB to the protein studied experimentally. In this case the structure of the closest homolog is given. Though, in the case when there is no close homolog available in PDB, PDB code is not given at all. It should be noted that for proteins studied in the paper of Maxwell et al. (PMID: 15689503) we took PDB codes recommended in this paper while for other proteins we took available X-ray structure; otherwise, we took NMR averaged structure; otherwise, NMR structure.
PDB
Code of the entry in the Protein Data Bank containing the structure best corresponding to the experimentally studied protein
Chain
The corresponding chain identifier inside PDB entry
Method
The method of structure resolution with numerical value of resolution in case of X-ray structure and with the number of models in case of NMR structure. "Aver" indicates NMR averaged structure
SCOP
The SCOP identifier of the fragment best corresponding to the experimentally studied protein
Mutation
Indicates difference between the sequence of the best available structure and the corresponding wild-type sequence
PDB Length
The sequence length of the structure best corresponding to experimentally studied protein
PDB Numeration
Contains identifiers of the start and end residues of the structure fragment best corresponding to the experimentally studied protein
PDB Sequence
The sequence of the structure fragment best corresponding to the experimentally studied protein

Results Of Kinetic Measurements
ln kf
Natural logarithm of protein folding rate extrapolated (or measured directly) in water provided kf is measured in s-1
mf
The dependence of natural logarithm of folding rate on denaturant concentration multiplied by RT, where R = 8.314 J/mol is the gas constant, and T is the absolute temperature. It is measured in kJ/mol/M. It should be noted that mf < 0 since folding rate decreases with increase denaturant concentration
ln ku
Natural logarithm of protein unfolding rate extrapolated (or measured directly) in water provided ku is measured in s-1
mu
The dependence of natural logarithm of unfolding rate on denaturant concentration multiplied by RT, where R = 8.314 J/mol is the gas constant, and T is the absolute temperature. It is measured in kJ/mol/M
ln kmt
Natural logarithm of mid-transition folding rate provided kmt is measured in s-1. It should be noted that it equals to the natural logarithm of mid-transition unfolding rate. ln kmt is obtained as crossing point of folding and unfolding arms of chevron plot
m*f
Correction coefficient for dependence of logarithm of folding rate on denaturant concentration. It is measured in kJ/mol/M2
ln k*f
Natural logarithm of protein folding rate extrapolated to water from mid-transition region provided k*f is measured in s-1. It can be taken as ln k*f in water if the protein were two-state. For two-state proteins ln k*f equals to ln kf in water
m*u
Correction coefficient for dependence of logarithm of folding rate on denaturant concentration. It is measured in kJ/mol/M2
βTS
The position of transition state in the reaction coordinate. Its value is enclosed between 0 and 1
Tmt
The absolute temperature of mid-transition point. In the case of using chemical denaturant the temperature of mid-transition is the same as the temperature corresponding to in-water folding/unfolding rates
ΔGeqN-U
The free energy of unfolding in water measured in kJ/mol
[D]mt
The denaturant concentration of mid-transition point. In the case of temperature denaturation experiment the denaturant concentration is the same as in the case of in-water folding/unfolding rates
ΔGkinN-U
Equilibrium free energy in water, derived from kinetics parameters
Kinetic type
The type of kinetic behavior (two-state or multi-state of type 'kin' or 'eq')
meq
The dependence of the free energy of unfolding on the denaturant concentration measured in kJ/mol/M
Φ
Φ parameter for mutant protein derived from the same experiment as with the wild type protein
mkin
The dependence of the free energy of unfolding on the denaturant concentration, derived from kinetics parameters, measured in kJ/mol/M
Φ exp ID
Wild type protein experiment ID from which Φ parameter for mutant protein was derived

Conditions Of The Experiment. All conditions refer to the point where logarithms of folding and unfolding rate in water are obtained. Thus, in the case when denaturing agent is a chemical denaturant, such as GdHCl or urea, the denaturant concentration in this section contains zero anyway. Other conditions are suggested to be kept constant at all denaturant concentrations studied.
pH
pH value
T
Absolute temperature
[D]
Denaturant concentration
Buffer
Type of buffer and its concentration
Other
Any other additional conditions used in experiment
Denaturing Agent
The type of agent used for protein denaturation


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