Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy level...
Exothermic binding to Rb was observed for the Human E2F2 peptide and E1A peptides and protein fragments harboring the LxCxE motif, while E1AE2F and E1AΔL harboring only the E1A E2F motif clearly showed an endothermic behavior. i) ITC curve of a peptide corresponding to the TAZ2 region ...
Thus, new methods for measuring secretion in high throughput are needed. We here develop an approach to evaluate the secretory potential (“secretability”) of proteins on a proteome-wide scale. SECRiFY (secretability screening of recombinant fragments in yeast) combines yeast surface display ...
It has been proposed thatprotein domainsevolved by combination of subdomain size fragments. Structural alignments between divergent pairs of proteins suggest that nature has assembled these fragments to create the structural diversity we observe today. Based on this observation, we developed a general st...
(selected to ensure primarilyβ-lactamases in the alignment). The alignment was filtered to exclude positions with more than 30% gaps and to exclude sequence fragments aligning to less than 50% of the target sequence. To account for redundancy, similar sequences in the alignment are re-weighted...
Secondary structure propensities of protein fragments are low in most of the cases studied [10], suggesting that local interactions are weak. On the other hand, site-directed mutagenesis experiments have indicated the existence of different secondary structure propensities for the 20 amino acids, both...
function, indicating that the folding fragment library at least partially contain folding information. In general, the diversity of MSTA determines the precision of folding force field and the quality of fragments, which together drive the protein fold to its final state following the native folding ...
We present a method for constructing thousands of compact protein conformations from fragments and then connecting these structures to form a network of physically plausible folding pathways. This is the first attempt to merge the previous successes in fragment assembly methods with probabilistic roadmap...
By eschewing use of fragments from existing protein structures, SCUBA-driven structure design facilitates far-reaching exploration of the designable backbone space, thus extending the novelty and diversity of the proteins amenable to de novo design....
Rosetta ab initio uses secondary structure probabilities obtained from Psipred65,66,67,68 to generate a set of candidate backbone fragments at each amino-acid position in a protein. These fragments are sampled via the Metropolis–Hastings algorithm to construct realistic candidate structures (decoys) ...