The Protein View |
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| The Protein View in Sesame allows the user to record information related to the production of a purified protein. The
protein record contains information on the physical characteristics and location of the protein. Protein
records can be created and manipulated in the same ways as other types of records. Similar to a plasmid record, a protein contains
fields for recording the amino acid sequence of the protein, however instead of being able to record just a single sequence, up to
three different sequences can be stored, detailing the sequence for versions of the protein both with and without affinity tags
(the Uncleaved and Cleaved types respectively). As well, the protein record
can also store information on a Quality Controlled sequence for once the identity of the purified protein
has been confirmed. As in the plasmid record, clicking on the purple icon to the left automatically calculates key physical
characteristics for the peptide sequence. When calculating the molecular weight of the protein, Sesame refers to the
Isotope Labeling field. In this field, the user can enter the estimated incorporation of various stable isotopes (Seleno-Methionine,
13Carbon and 13Nitrogen) depending on the growth conditions. Any number of isotopes can be selected. By default,
0% incorporation of all isotope types is considered to be Unlabelled. This information is then used to accurately account
for the labeling pattern when calculating the expected molecular weight of the target. Note that if labelling pattern or percent
incorporation is changed in a record, the user must re-calculate the molecular weight (using the purple icon found on the right hand side
of each sequence field) to make use of the new information. In other words, Sesame does not automatically recalculate the molecular
weight of a protein every time the isotopically labelling information is changed.
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| At the bottom of the record is the Protocol, a user modifiable tree useful for recording specifics of the purification
protocol. The default protocol tree is defined by the protocol that has been selected for the record, but by using the icons found
on the right hand side of the field, users can add and delete sibling and daughter nodes, creating a PC-style
directory tree to capture specific data. Results are captured by entering data into the boxes found adjacent to the field name.
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| Like all other record types, a protein record can be created by asking for a new protein record using the Options menu and then linking
to a specific ORF within a work group. However, multiple new records can also be created simultaneously using
Create Protein Records found in the Work Groups menu of the work group view. Open the appropriate work group, highlight the ORFs
for which records should be created and use the Create Protein Records function. A pop up box will appear allowing the user to add
information to the records to be created. The new records are automatically be linked to both the ORF and work group record used
to create them. Note that when the new records are created they are not automatically saved and that the user must save each record individually.
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| As with all other record types, a protein record can be linked to other record types to create an electronic papertrail. Details can be found
on the Linking Records page.
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