Guidelines of the STRENDA Commission



Many journals have already adopted the guidelines for the "Instructions for authors".

STRENDA and the Guidelines are registered at MIBBI. MIBBI stands for Minimum Information for Biological and Biomedical Investigations and is a project which provides a portal for recommended “Minimum Information” checklists for supporting authors, referees and editors to improve the quality of scientific data publication. Additionally, the project aims at improving the communication, knowledge transfer and coordination of the diverse checklist efforts.

An introductory text about the STRENDA Guidelines for inclusion in the instruction for authors is provided at the downloads section. This file can be used by everybody who is interested to refer to the STRENDA Guidelines under the terms of the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Level 1 A: Data Required for a complete Description of an Experiment

Level 1 B: Description of Enzyme Activity Data

Level 2: Organism-related Definitions of Experimental Conditions (preliminary draft)

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Level 1 A



Data required for a complete Description of an Experiment

The information is required to allow a quality check on the data and
to ensure their value to others

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

 

Top

Level 1B



Description of Enzyme Activity Data

The information is 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       

Top

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