STRENDA Guidelines

This page contains previous versions of the STRENDA Guidelines in order to fulfill the requirement of versioning and consistency. However, please note that these Guidelines are not longer applied.

STRENDA Guidelines - List Level 1A

Data required for a complete Description of an Experiment

This list defines data that are recommended for the methods section for publishing enzyme data. This information should allow the reproducibility of the results.

Version 1.7, September 22, 2016; doi:10.3762/strenda.17

 

Data

Comments
Identiy of the enzyme  
Name of the reaction catalyst name, preferably the accepted name from the IUBMB Enzyme list
EC number  
Sequence accession number  
Organism/species & strain NCBI Taxonomy ID
Additional information on the enzyme  
Isoenzyme naturally occuring variant
Tissue  
Organelle  
Localization within cell. Specify what localization is based on
Post-translational modification add only when determined
Preparation  
Description e.g., commercial source, procedure used or reference along with modifications
Artificial modification e.g., truncated, His-tagged, fusion protein, lacking native glycosylation
Enzyme or protein purity purity defined by which criteria. Specify whether protein or enzyme was purified
Metalloenzyme mutant, content, cofactors
Storage Conditions  
Storage temperature If frozen, freezing method, e.g., -20 °C flash
Atmosphere if not air  
pH e.g., 7.0
At which temperature was the pH measured? e.g., 25 °C
Buffer & concentrations (including counter-ion) e.g., 200 mM potassium phosphate, 100 mM HEPES-KOH
Metal salt(s) & concentrations e.g., 10 mM KCl, 1.0 mM MgSO4
Other components e.g., 1.0 mM EDTA, 1.0 mM dithiothreitol, 10% glycerol, 20% DMSO, 1 mg/ml PEG2000, 2 mg/ml BSA, peptidase inhibitors
Enzyme/protein concentration molar concentration if known, otherwise mass concentration;
e.g., mg ml-1 or better: µM
Optional:
Statement about observed loss of activity under the above conditions		 e.g., less than 10% loss after 1 month
Statement about the thawing procedure e.g., on ice
Assay Conditions  
Substrate purity Origin of substrate
 Measured reaction as a stoichiometrically balanced equation
e.g., 2 mol substrate oxidized per mol O2 consumed
 Assay temperature  
 Assay pressure if it is not atmospheric; indicate if not aerobic
 Atmosphere if not air  
 Assay pH How was it measured?
 Buffer & concentrations e.g., 100 mM Tris-HCl, 200 mM potassium phosphate, including counter-ion
Metal salt(s) & concentrations e.g., 10 mM KCl, 1.0 mM MgSO4
Other assay components e.g., 1.0 mM EDTA, 1.0 mM dithiothreitol
Coupled assay components if relevant
Substrate & concentration ranges e.g., 1 - 100 mM glucose, 5 mM ATP
Enzyme/protein concentration molar concentration if known, otherwise mass concentration,
e.g., mg ml-1 or better: µM
Varied components e.g., inhibitor concentration
Total assay mixture ionic strength  
Activity  
Initial rates of the reaction measured determine how established
Proportionality between initial velocity and enzyme concentration if available
Enzyme activity Ideally kcat otherwise expressed as amount product formed per amount enzyme protein present - sometimes referred to as enzyme unit or international unit (1 IU) = 1 µmol min-1. The katal (mol/s) may alternatively be used as a unit of activity (conversion factor 1 unit = 16.67 nkat)
Methodology  
Assay method a literature reference may suffice for an established procedure but any modification should be detailed
Type of assasy e.g., continuous or discontinuous, direct or coupled
Reaction stopping procedure in the case of discontinuous assays
Direction of the assay with respect to the reaction equation provided,
e.g., NAD reduction by alcohol dehydrogenase;
alcohol + NAD+ → aldehyde or ketone + NADH + H+
Reactant determined e.g., NADH formation, O2 utilization
Additional material desirable  
Free metal cation concentration e.g., of Mg2+ and Ca2+, specify how calculated
Reaction equilibrium constant define conditions and reaction direction
   
schnitt linie

STRENDA Guidelines List Level 1B

Description of Enzyme Activity Data

This list defines those data that are required to allow a quality check on the data and to ensure their value to others. In principle, this is the minimum information to describe enzyme activity data.

Version 1.7, September 22, 2016, doi:10.3762/strenda.27

 

Information required

Comments
Required data for all enzyme functional data  
Number of independent experiments any problems of reproducibility should be stated
Precision of measurement e.g., standard error of the mean, standard deviation, confidence limits, quartiles
Specification whether relative to subunit or oligomeric form  
Data necessary for reporting kinetic parameters  
kcat Vmax may be divided by the specific activity units, measured in s-1 or min-1
Vmax Vmax given as units, as defined in List Level 1A
kcat/Km kcat/Km given as concentration per time,
e.g., mM-1 s-1
Km units or concentration necessary, e.g., mM
S0.5 concentration, e.g., mM
Hill coefficient, saturation ratio (RS) or other coefficients of cooperativity  
How was the given parameter obtained? e.g., non-linear curve fitting using least squares, non-parametric method such as direct linear plot, linear regression to tranformed form of rate equation.

Note: if commercial computer programs are used, determine which were used.
Model used to determine the parameters with explanation of why is the chosen model considered to be the "right" model
High-substrate inhibition, if observed, with Ki value  
Data required for reporting inhibition data  
Time-dependence and reversibility with method described
Inhibition Ki units necessary
types:  
     reversible e.g., competitive, uncompetitive, etc. with units and how values were determined
     tight-binding association/disscociation rates
     irreversible e.g., non-specific, mechanism-based, "suicide substrate" There are too many alternative parameters to list here. The reference to a quite comprehensive source is recommended:
Enzymes: Irreversible Inhibition. Tipton, K.F. In: Nature Encyclopedia of Life Sciences, London (2001). doi: 10.1038/npg.els.0000601.

Note: IC50 values These have been used for both reversible or irreversible inhibition. However, the use is not recommended because these values are without a consistent meaning. The relationship of these values to inhibition constants is analysed in details by e.g. Cortes, A. et al. (2001) Biochem. J. 357:263-268. doi: 10.1042/bj3570263
Data required for reporting activation data  similar to the requirements for inhibition data
   
 

STRENDA Guidelines, Version 1.6, Aug. 2010

STRENDA Guidelines List Level 1A

STRENDA Guidelines List Level 1B