Guidelines

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

 

Today more than 55 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 1.8, November 30, 2021; doi:10.3762/strenda.18

 

Data

Comments

Identiy of the enzyme  
Name of the reaction catalyst name, preferably the accepted name from the IUBMB Enzyme list
Fully balanced chemical reaction equation elements and charges balanced.
See convention in R.A. Alberty "Thermodynamics of Biochemical Reactions", doi:10.1002/0471332607
EC number  
Oligomeric state number of different subunits
Sequence or sequence accession number  
Organism/species & strain NCBI Taxonomy ID
Additional information on the enzyme  
Isoenzyme naturally occuring variant or indication of selection of alternative
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. e.g., apparently homogeneous by PAGE, crude mitochondrial fraction, determined by MS
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. If pH is adjusted by addition of acid or base not shown in the buffer name, make this clear - e.g., 50 mM sodium acetate adjusted with HCl.
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% v/v glycerol, 20% w/w DMSO, 1 mg/ml PEG2000,
2 mg/ml BSA, peptidase inhibitors
Enzyme/protein concentration molar concentration if known, otherwise mass concentration;
e.g., µM or mg ml-1
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  
Identity and purity of all assay components identified unambiguously, ideally by reference to ID from database (such as PubChem, ChEBI), or using a textual identifier (such as InChI), and/or showing chemical structure (or SMILES).
Origin of compounds used with statement on purity.
Measured reaction as a stoichiometrically balanced equation
e.g., 2 mol substrate oxidized per mol O2 consumed, with all products identified
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.
If pH is adjusted by addition of acid or base not shown in buffer name, make this clear;
e.g., 50 mM sodium acetate adjusted with HCl.
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, estimate ranges in substrate/product concentrations at the last data point.e.g., true initial tangent or average over specified time.
Proportionality between initial velocity and enzyme concentration if available
Enzyme activity Ideally kcat (i.e. Vmax/enzyme concentration), otherwise expressed as amount product formed per amount enzyme protein present per time unit.
Activity is sometimes reported 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).
Specify at which (range of) concentration(s) this was determined.
Equilibrium measurements
 
Evidence that reaction reached equilibrium e.g., approached from both (or all if multiple substrates/products) directions
State which of all reactants were measured directly e.g., glucose phosphate and glucose measured directly, excess phosphate estimated by mass balance
Range of starting material and product concentrations in the experiment ideally a table of all initial and measured equilibrium concentrations
Complexing metal ions if the reaction involved species that might bind these (e.g., phosphate esters), essential to report estimated pMg and/or pCa
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
   
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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 1.8, November 30, 2021, doi:10.3762/strenda.28

 

Information required

Comments

Required data for all enzyme functional data  
Reproducibility, number of independent experiments Indicate how many times the measurement was reproduced and what changed between replicates; just repeat reactions, different enzyme preparations, different ways, alternative staff, different laboratories.
Precision of measurement e.g., standard error of the mean, standard deviation, confidence limits, quartiles.
Comments on possible systematic errors are also useful.
Specification whether relative to subunit or oligomeric form  
Preferably deposit measured/raw data (e.g., time course of product concentrations to enable re-analysis Make data findable by citing DOI or URL, accessible by making it open, interoperable by structuring and describing the dfata by using formats such as EnzymeML.
Data necessary for reporting
kinetic parameters
(choose which ones are available from your experiments)
Kinetic equation (which will then define parameters)
Name or state the model or equation used and the variable in it, e.g., Michaelis-Menten, varying concentration of ATP, fixed glucose or
v = Vmax/(1+KA/[2-aminopropane]+KB/[2-butanol)
kcat Vmax in terms of mol reaction per mol enzyme per time, so units often reported as s-1 or min-1
Vmax Should be as a specific activity, with units like mol min-1 (g enzyme)-1, or
(mol product)min-1 (g protein in the preparation)-1,
see
List Level 1A
kcat/Km kcat/Km given as per concentration per time,
e.g., mM-1 s-1
Km units or concentration necessary, e.g., mM,
define, how Km was defined operationally (e.g. as S0.5)
S0.5 concentration, e.g., mM
Hill coefficient, saturation ratio (RS) or other coefficients of cooperativity with equation defining the parameter as noted above
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.
KM2 Michaelis constants for all co-substrates, inclusive the coenzymes
KP
Km for reverse operation or product inhibition constants (with equation above showing definition).
This is for all products inclusive of cofactors. If information is absent, indicate at what product concentrations there was not effect on enzyme rate.
Choice of model used to determine the parameters report any measures of quality of fit, and for any alternative models considered.
High-substrate inhibition, if observed, with Ki value with defining equation above
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. McDonald, A.G. & Tipton, K.F. In: Nature Encyclopedia of Life Sciences, London (2020). doi:10.1002/9780470015902.a0000601.pub3

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
   
Data required for reporting
equilibrium measurement
 See further details in IUBMB document:
Alberty, R.A. et al. (2011) Biophys. Chem. 155:89-103. doi:10.1016/j.bpc.2011.03.007
Measured equilibrium concentrations preferred that these are tabulated
Keq' or K' (i.e. the pH dependent equilibrium constant) with reference to full reaction equation presented and direction identified,
with units where not symmetrical, e.g., M, mM-1, mol kg-1 (molality).
Explain any reactants not treated by way of dissolved concentrations, e.g., water, gases as partial pressures, activities for reactants not behaving as infinitely dilute.

Estimates of equilibrium constants may sometimes also be obtained by fitting to kinetic (progressive) data. If so, follow the recommendations as for other kinetic parameters, including stating the equation fitted.
Convention used by default, assume biochemical convention using total concentrations of ionising or complexing compounds.
But state clearly if using defined chemical species.
   
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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