+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

Computational design of chimeric protein libraries for directed evolution

, : Computational design of chimeric protein libraries for directed evolution. Methods in Molecular Biology 673: 175-188

The best approach for creating libraries of functional proteins with large numbers of nondisruptive amino acid substitutions is protein recombination, in which structurally related polypeptides are swapped among homologous proteins. Unfortunately, as more distantly related proteins are recombined, the fraction of variants having a disrupted structure increases. One way to enrich the fraction of folded and potentially interesting chimeras in these libraries is to use computational algorithms to anticipate which structural elements can be swapped without disturbing the integrity of a protein's structure. Herein, we describe how the algorithm Schema uses the sequences and structures of the parent proteins recombined to predict the structural disruption of chimeras, and we outline how dynamic programming can be used to find libraries with a range of amino acid substitution levels that are enriched in variants with low Schema disruption.


PMID: 20835798

DOI: 10.1007/978-1-60761-842-3_10

Other references

Przepiórski, J.; Goliszewski, J.; Swiatczak, B., 1977: Dilatation of descending ureteral branch of the left renal artery. Polski Przeglad Chirurgiczny 49(6a): 767-768

Schrauzer, Gn, 1998: Selenomethionine and selenium yeast: appropriate forms of selenium for use in infant formulas and nutritional supplements. Journal of medicinal food(3): 201-206

Briere, J.; Runtz, M., 2015: Dissociation in individuals denying trauma exposure: findings from two samples. A number of studies suggest that dissociation is reliably related to trauma exposure, and that inadequate regulation of posttraumatic distress may be a significant factor. We examined whether affect dysregulation predicts dissociation in those den...

Sagar, P.; Taylor, B., 1993: Adjuvant therapy and quality of life. Lancet 341(8841): 376-376

Glaser, V.; Holobar, A., 2017: On the impact of spike segmentation on motor unit identification in dynamic surface electromyograms. We discuss the adaptation of preexisting Convolution Kernel Compensation (CKC) surface electromyogram (EMG) decomposition technique to dynamic muscle contractions. In particular, three different algorithms for segmentation of motor unit (MU) spike...

Green, T.R.; Fisher, J.; Stone, M.; Wroblewski, B.M.; Ingham, E., 1999: Polyethylene particles of a 'critical size' are necessary for the induction of cytokines by macrophages in vitro. Particulate wear debris from total hip prosthetic components can stimulate macrophages to produce mediators of osteolysis which may cause aseptic implant loosening. This study evaluated the in vitro response of murine peritoneal macrophages to pol...

Anderson G.D.; Larson D.B., 1978: Shock wave compression of Nugget Sandstone. Eos, Transactions, American Geophysical Union 58(6): 491

Walkden Brown, S.W.; Singh, R., 1986: An effort to improve the carcass of culled female goats in Fiji. From a herd of 480 breeding female Anglo-Nubian goats 40 were selected for culling immediately after weaning of their young. Goats selected for culling were slaughtered after 2 days or grazed for 84 days on a Dicanthium caricosum/Desmodium heterop...

Ascani, A.; Iorio, A.; Agnelli, G., 1999: Withdrawal of warfarin after deep vein thrombosis: effects of a low fixed dose on rebound thrombin generation. The optimal procedure for withdrawal of warfarin in patients with deep vein thrombosis (DVT) is still not defined. Rebound thrombin generation, which occurs after the withdrawal of warfarin, has been said to be associated with early recurrence of...

Stöffler, G., 1969: Immunologic studies with antisera against isolated ribosomal proteins from 30S and 50S-subunits from E. coli. Hoppe-Seyler's Zeitschrift für Physiologische Chemie 350(10): 1166-1166