Cumitech 31: Verification and Validation of Procedures in by Susan E. Sharp

By Susan E. Sharp

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By Susan E. Sharp

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Collect the cells by centrifugation. 0 ml of cold 1 x MKEI with protease inhibitors. 38 3: Methods to study actin assembly and dynamics in yeast 3. Pellet the cells in a microcentrifuge for 2 sec, aspirate the supernatant, and freeze immediately in liquid nitrogen. 4. Thaw the frozen pellet at RT, add an equal volume of 1 x MKEI (about 100 ul) with protease inhibitors, and freeze again. 5. 1 vol. of 5 mg/ml saponin) in MKEI buffer with freshly added protease inhibitors. 6. Sediment the cells in a microcentrifuge at top speed for 15 min.

Involved in binding of other ligands or in the scaffolding of the protein. A distinction between scaffolding sequences (in the interior of the protein) and surface regions can be found using other algorithms predicting hydropathy (3). In exceptional cases similar actin-binding motifs may be present in otherwise unrelated proteins. For example, protein kinase Cepsilon has a functional actin-binding sequence also present in the small actin sequestering protein thymosin B4 (4). 2 Crystal structures of actin-binding proteins and calculated models help to design mutants We found it very useful to guide our mutagenesis experiments by knowledge of the three-dimensional structure of actin-binding proteins, several of which have been solved.

Amplify the fragment using steps 2-4. 7. Purify the amplified fragment on an agarose gel, excise the two bands, and use Gene clean to extract the DNA. 8. Perform a digest on the restriction sites, incorporated via the forward and reverse primers in the PCR product, and ligate into a suitable vector. aUsing degenerate mutator oligos at one or more codons (up to six adjacent ones), one can create libraries of mutants. Non-mutated 5' and 3' flanking sequences are usually 15-18 nucleotides long, depending on the GC content.

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