Atomic force microscopy analysis of the Huntington protein nanofibril formation.

Background: Huntington's disease is an autosomal dominant progressive neurodegenerative disease associated with dramatic expansion of a polyglutamine sequence in exon 1 of the huntingtin protein htt that leads to cytoplasmic, and even nuclear aggregation of fibrils.

Methods: We have studied the in vitro fibril formation of mutant exon 1, and the shorter wild-type exon 1, with use of atomic force microscopy (AFM).

Results: Large aggregates are formed spontaneously after cleavage of the glutathione-S-transferase fusion protein of the mutant exon 1 protein.

Protein design by binary patterning of polar and nonpolar amino acids.

The design of large libraries of well-folded de novo proteins is a powerful approach toward the ultimate goal of producing proteins with novel structures and functions for use in industry or medicine. A method for library design that incorporates both rational design and combinatorial diversity relies on the "binary patterning" of polar and nonpolar amino acids. Binary patterning is based on the premise that the appropriate arrangement of polar and nonpolar residues can direct a polypeptide chain to fold into amphipathic elements of secondary structure that anneal together to form a desired tertiary structure.

De novo proteins from binary-patterned combinatorial libraries.

Combinatorial libraries of well-folded de novo proteins can provide a rich source of reagents for the isolation of novel molecules for biotechnology and medicine. To produce libraries containing an abundance of well-folded sequences, we have developed a method that incorporates both rational design and combinatorial diversity. Our method specifies the "binary patterning" of polar and nonpolar amino acids, but allows combinatorial diversity of amino acid side chains at each polar and nonpolar site in the sequence.

Gibbs sampling and helix-cap motifs.

Protein backbones have characteristic secondary structures, including alpha-helices and beta-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design.