Guidelines

Both the STRENDA project and the STRENDA Guidelines are registered in biosharing.org, a web portal that collects inter-related data standards, databases, and policies in the life, environmental and biomedical sciences.

 

Today more than 50 international biochemistry journals recommend their authors to consult the STRENDA Guidelines when publishing enzyme kinetics data.

The STRENDA Guidelines aim to support authors to comprehensively report kinetic and equilibrium data from their investigations of enzyme activities. The following is the prose description of those parameters that need to be provided in scientific publications.

All reports of kinetic and binding data must include a description of the identity of the catalytic or binding entity (enzyme, protein, nucleic acid or other molecule). This information should include the origin or source of the molecule, its purity, composition, and other characteristics such as post-translational modifications, mutations, and any modifications made to facilitate expression or purification. The assay methods and exact experimental conditions of the assay must be fully described if it is a new assay or provided as a reference to previously published work, with or without modifications.

The temperature, pH and pressure (if other than atmospheric) of the assay must always be included, even if previously published. In instances where catalytic activity or binding cannot be detected, an estimate of the limit of detection based on the sensitivity and error analysis of the assay should be provided. Ambiguous terms such as “not detectable” should be avoided. A description of the software used for data analysis should be included along with calculated errors for all parameters.

First-order and second-order rate constants should be reported in units of s-1 and
M-1•s-1, respectively. Equilibrium binding constants should normally be reported as dissociation constants with units of concentration (M, mM, µM, nM). The values kcat, kcat/Km and Km from steady-state enzyme kinetics should be reported in units of s-1, M-1•s-1 and concentration (mM, µM, nM), respectively. The steady-state specific activity of an enzyme should normally be reported as a kcat. If there is considerable uncertainty in the molar concentration of the catalyst, the specific activity should be reported as a Vmax (nmol, µmol) of product formed per amount of protein per unit time (e.g. µmol•mg-1•s-1).

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

 

DataComments
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:
Data required for reporting activation data  similar to the requirements for inhibition data
   
 
schnitt linie

STRENDA GUidelines List Level 2

Organism-related Definitions of Experimental Conditions

(Preliminary draft)

Suggestions which have to be decided by the experts:

Conditions

  • assay temperature
  • assay pH
  • buffer & concentrations
  • metal salt(s) & concentration(s)
  • other assay components & concentrations
  • total assay mixture ionic strength


Preparation

  • description
  • artificial modification
  • purity


Extra suggestions

  • crowding agents (PEG, proteins, etc.)
  • posttranslational modifications
  • artificial modifications

Archive

STRENDA Guidelines List Level 1A

STRENDA Guidelines List Level 1B