To facilitate documentation and submission of biocatalytic data, we provide an Excel template to unambiguously describe an experiment. An empty Excel template can be downloaded as BioCatNet_template.xlsx.
This file template can be filled in and sent to the BioCatNet administrator. Please give the name of the desired enzyme family database in your e-mail.
The following two datasets were used for kinetic parameter estimations published in Buchholz et al. 2018:
The following use cases correspond to an outdated version of the BioCatNet template, as previously published in Buchholz et al. 2016. Nevertheless, they provide additional examples of real measurements.
The excel template contains the following sheets:
A brief documentation is available in the comment sections of each sheet and by clicking on the headers (coloured fields). More details are available below.
Throughout the BioCatNet Excel template, mandatory input is indicated by capital letters. Insert a new row, if you need more than one set of attributes (e.g. for multiple time points of measurement or more than one substrate). For empty values just leave a blank field. Please do not delete any headers! Additional information can be added at the end of each sheet under COMMENTS. This comments, however, will not be uploaded to BioCatNet automatically.
Please avoid special characters when filling out the BioCatNet Excel template, e.g. write alpha-ketoglutaric acid instead of α-ketoglutaric acid. Indicate known, distinct values instead of ranges of values, e.g. write 4.5 for pH instead of pH 4-5. If a value is unknown, simply leave it out.
The BioCatNet Excel template requires a strict and consistent naming, e.g. the names of enzymes and chemical compounds have to be spelled the same way throughout the file.
The sheet user information is provided to include the name (first name followed by last name) and e-mail contact of the experimenter. This information is only used to contact the experimenter in case of further questions when processing the data.
The EXPERIMENT section contains the name for the individual experiment. EXPERIMENT SET NAME should be identical for all experiments within an experiment set. Note that one file will correspond to a single experiment. BioCatNet assigns experiments to experiment sets. An example for an experiment set would be a series of measurements under varying pH. An individual experiment would comprise the result for a distinct set of conditions, i.e. an individual pH adjustment. Results obtained for all the other pH values should be documented as separate experiments in separate files. You can specify multiple measurements in a single file, as long as these measurements were observed under the same conditions. More information is given below.
In this sheet, you have to list all protein sequences, i.e. amino acid sequences, of the enzymes used in the experiment in one-letter amino acid abbreviations. The protein sequences should be listed completely, including amino acid substitutions or tags.
The sequence's name has to be given as enzyme name in the following sheets, too: Under ENZYME TREATMENT in the conditions sheet and under ENZYMES in the reaction sheet. Use the same sequence/enzyme name's spelling throughout the file.
The indication of the source organism is optional but highly recommended. You will find a link to NCBI taxonomy in the first row, since organism names can only be used in BioCatNet if they are mentioned in the NCBI taxonomy. The name of the expression host will be added later (in the conditions sheet under ENZYME TREATMENT).
The REACTION CONDITIONS section can comprise multiple attributes. The entry below the description field can contain detailed information as plain text (up to 600 characters). Please note that temperature has to be given in Celsius and the shaking in rotations per minute (rpm). For the pressure unit, you will find a drop-down menu that allows you to select bar or Pa, if desired. For the unit of the initial reaction volume, you will find a drop-down menu that allows you to select units such as l, ml, µl (given as ul) and nl, if desired.
The ENZYME TREATMENT section should repeat the sequence name from the sequences sheet. The indication of the expression host organism is mandatory. You will find a link to NCBI taxonomy, since organism names can only be used in BioCatNet if they are mentioned in the NCBI taxonomy. The name of the source organism is to be listed elsewhere (in the sequences sheet under source organism). The fields below preparation/purification can be selected by a drop-down menu, too: purified enzyme, crude cell (extract), immobilized enzyme or whole cell. More descriptions, e.g. on the purification/immobilization method, can be given as keywords or plain-text under application.
The BUFFER section contains the name as well as a more detailed description of the used reaction buffer, i.e. the reaction solvent. The indication of the concentration is mandatory, including the selected unit from the drop-down menu: mol/l, mmol/l, µmol/l (given as umol/l) or nmol/l. The field under additives/ions can give more details such as salt concentrations, buffer additives (e.g. DMSO) or ion strength as plain-text.
The reaction sheet describes the reaction(s) under investigation. The COMPOUNDS section must list all applied compounds, i.e. substrates, products and (where applicable) additives (e.g. inhibitors or detergents which are added in the course of the experiment). Co-substrates/co-products and cofactors should be listed here, too. To unambiguously identify a compound, the usage of the SMILES code is recommended. This simplified molecular-input line-entry system code represents the structure of a compound as a string. You can retrieve SMILES code for your compounds from other repositories, e.g. NCBI PubChem, or generate SMILES Code using external tools such as PubChem Sketcher.
Please list all compound names under the COMPOUNDS section, i.e. all compounds that are mentioned in the reaction equation (see below) and all compounds mentioned in the sheets measured compounds (concentrations) or measured parameters (ratios such as yield, conversion or enantiomeric excess).
The name field within the REACTION section provides an annotation for the investigated reaction. (For cascade systems there is more than a single reaction, so just add new lines in this section when your experiment investigates more than one reaction.) The fields below REACTION specify the reaction stoichiometry by using coefficients and compound names from the COMPOUNDS section:
A reaction converting 1 mol of substrate A and 1 mol of substrate B to form 1 mol of product C would be given as 1 A + 1 B -> 1 C.
Note that the stoichiometric coefficients are given, even if they equal one. The reaction equation contains
-> to distinguish between substrate(s) and product(s).
The ENZYMES section must repeat the sequence name(s) from the sequences sheet. The measurement number refers to an individual measurement, which in turn can comprise several replicates. Replicates are numbered in the sheets measured compounds (concentrations) and measured parameters (ratios such as yield, conversion or enantiomeric excess). Currently, BioCatNet does not distinguish between technical or biological replicates, but the later might be distinguished by having one experiment (one file) per biological replicate.
The section additives is optional, e.g. for the addition of inhibitors, activators or other compounds (such as detergents) during the reaction. Note that the fields below COMPOUND in the SUBSTRATES and additives section should repeat the name from the COMPOUNDS section of the same sheet.
For ENZYMES, SUBSTRATES and additives, one has to specify the addition to the reaction, e.g. time-point zero for initial concentrations, or a later time point for s.th. like a fed-batch approach. The time point of addition is a mandatory input, including the time unit selected from the drop-down menu: hours (h), minutes (min), seconds (s) or milliseconds (ms). It is recommended to specify the concentration, too. If the volume changes during the reaction, one might also indicate the chemical amount and the volume of the added enzyme/substrate/additive. Note that for fed-batch approaches or similar experiments, the indication of the initial reaction volume in the REACTION CONDITIONS section of the conditions sheet can become useful.
The amount of enzyme can be specified by various units as chemical amount (mol, mmol/ µmol given as umol, nmol) or mass (g, mg, µg given as ug, ng). For the substrate or additive amounts, only chemical units for chemical amount (mol, mmol/ µmol given as umol, nmol) are available. If you do not change the volume or the solvent composition during the reaction, e.g. by fed-batch, you might want to simply indicate initial concentrations at time point zero.
The sheet for measured compounds is used to report time-course data, e.g. progress curves on substrate depletion or product formation. This sheet is optional, i.e. if you measured ratios such as yield, conversion or enantiomeric excess instead, the other sheet named measured parameters must be used and vice versa.
The measurement number refers to an individual measurement, which in turn can comprise several replicates. Currently, BioCatNet does not distinguish between technical or biological replicates.
The measurements must list the same compound names as listed previously in the reaction sheet. The measurement method can be given as plain text.
For the sheet measured parameters, one can also specify an abbreviation, the measurement method and information on the ratio under investigation, i.e. you can define terms such as conversion or yield for your experiment and describe in plain text how these ratios were calculated from your raw data. Currently, only percentages are available as parameter units. The reference sequence name must match the sequence name from the sequences sheet, e.g. when conversion of a substrate is observed for a mutant and refers to a wild-type sequence given in the sequences sheet.
Last updated on 13 October 2020.