Premium
Construction and characterization of protein libraries composed of secondary structure modules
Author(s) -
Matsuura Tomoaki,
Ernst Andreas,
Plückthun Andreas
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0215102
Subject(s) - protein secondary structure , sequence (biology) , peptide sequence , alpha helix , protein structure , sequence space , beta (programming language) , protein design , chemistry , crystallography , computational biology , biology , biochemistry , gene , computer science , mathematics , pure mathematics , banach space , programming language
Only a minute fraction of all possible protein sequences can exist in the genomes of all life forms. To explore whether physicochemical constraints or a lack of need causes the paucity of different protein folds, we set out to construct protein libraries without any restriction of topology. We generated different libraries (all α‐helix, all β‐strand, and α‐helix plus β‐strand) with an average length of 100 amino acid residues, composed of designed secondary structure modules (α‐helix, β‐strand, and β‐turn) in various proportions, based primarily on the patterning of polar and nonpolar residues. We wished to explore that part of sequence space that is rich in secondary structure. The analysis of randomly chosen clones from each of the libraries showed that, despite the low sequence homology to known protein sequences, a substantial proportion of the library members containing α‐helix modules were indeed helical, possess a defined oligomerization state, and showed cooperative chemical unfolding behavior. On the other hand, proteins composed of mainly β‐strand modules tended to form amyloid‐like fibrils and were among the least soluble proteins ever reported. We found that a large fraction of members in non‐β‐strand–containing protein libraries that are distant from natural proteins in sequence space possess unexpectedly favorable properties. These results reinforce the efficacy of applying binary patterning to design proteins with native‐like properties despite lack of restriction in topology. Because of the intrinsic tendency of β‐strand modules to aggregate, their presence requires precise topologic arrangement to prevent fibril formation.