Guidelines

Both the STRENDA project and the STRENDA guidelines are registered in the MIBBI portal which is part of the BioSharing project. MIBBI stands for “Minimum Information for Biological and Biomedical Investigations” and is a project that provides the scientific community a compilation of recommended 'minimum information' guidelines. The aim of the guidelines is to support authors, reviewers and editors to improve the quality of published scientific data.

Up to now, there are three guideline lists. Two of them – List Level 1A and List Level 1B – deal with publication standards; a third guideline list Level 2 focuses on the standardization of assay conditions. The STRENDA guidelines can be accessed here and are also available in PDF format.


The STRENDA Commission has prepared an introductory text for journals to recommend the guidelines to their authors. This text can be included in the “Instructions for Authors” and is provided here. The file is licensed under the “Creative Commons Attribution License”, which permits unrestricted use, distribution and reproduction in any medium provided that the original document is properly cited.

Today more than 30 international biochemistry journals recommend their authors to consult the STRENDA guidelines when publishing enzyme kinetics data.



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 1.6, August 24th, 2010

 

1. Identity of the enzymes

Name of Reaction Catalyst
Name, preferably the accepted name from the IUBMB Enzyme List

EC-Number

Sequence accession number

Organism/species & strain

NCBI Taxonomy ID

 

2. 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

 

3. 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

Enyzme or protein purity
Purity defined by which criteria. Specify whether protein or enzyme was purified

E.g., apparently homogenous by PAGE, crude mitochondrial fraction, determined by MS

Metalloenzyme
Mutant, content, cofactors

 

4. 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
°C

Assay pressure
If is 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

Substrates & concentration ranges
E.g., 1 - 100 mM glucose, 5 mM ATP

Enzyme/protein concentration
Molar concentration if number of active sites known, otherwise mass concentration

E.g., mg ml-1 or better µM

Variable components
E.g., inhibitor concentration

Total assay mixture ionic strength

 

5. Activity

Initial rates of the reaction measured
Determine how established

E.g., true initial tangent or average over specified time

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 IU = 16.67 nkat).

6. Methodology

Assay method
A literature reference may suffice for an established procedure but any modification should be detailed

Type of assay
E.g., continuous or discontinuous, direct or coupled

Reaction of 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

 

7. Additional information desirable

Free metal cation concentrations
E.g., of Mg2+ and Ca2+, specify how calculated

Reaction equilibrium constant K
Define conditions and reaction direction

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 1.6, August 24th, 2010

 

1. Required data for all functional enzyme 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

 

2. Data necessary for reporting kinetic parameters

kcat
Vmax may be diveded by the specific activity units, measured in s-2 or min-1

Vmax
Vmax given as units or katal, as defined in List 1A

kcat/Km
kcat/Km given as concentration per time, e.g., mM-1s-1

Km
Units or concentration necessary, e.g., mM

S0.5
Concentrations, e.g., mM

Hill coefficient, saturation ratio (Rs) or other coefficients of co-operativity

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 ot transformed form of rate equation.

Note: If commercial computer programs were 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

 

3. Data required for reporting inhibition data

Time-dependenc and reversibility
With method described

Inhibitions types
Ki units necessary

Reversible:
E.g., competitive, uncompetitive, etc., with units and how values were determined.

Tight-binding:
Association/dissociaten rates.

Reversible:
E.g., non-specific, mechanism-based, „suicide substrate“.
There are too many alterantive parameters to list here. The reference to a quite comprehensive source is recommended: Tipton, Keith F. (2001) Enzymes: Irreversible Inhibition. In: eLS. John Wiley & Sons Ltd, Chichester.

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

 

4. Data required for reporting activation data

Similar to the requirements for inhibition data

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

Downloads

  • DownloadDownload

    STRENDA generic text

    The STRENDA Commission has prepared an introductory text for journals to recommend the guidelines to their authors. This text can be included in the “Instructions for Authors”. The file is licensed under the “Creative Commons Attribution License”, which permits unrestricted use, distribution and reproduction in any medium provided that the original document is properly cited.

  • DownloadDownload

    STRENDA List Level 1A

    Data required for a complete Description of an Experiment.

  • DownloadDownload

    STRENDA List Level 1B

    This is the minimum information to describe enzyme activity data.