Strategies and rationales for the de novo design of a helical hairpin peptide

Abstract

The de novo design of a t a , a helical hairpin peptide, is described. a t a (u-helix/turn/a-helix) was developed to provide a model system for protein folding at the level of secondary structure association and stabilization. According t o the prevailing models of protein folding, the second step in the folding process is the association and stabilization of secondary structural elements or microdomains. A brief description of the design, along with CD and NMR evidence confirming the conformation of the peptide in solution, has been published (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675-3679). The present work includes a full description of the design process, including the trade-offs that were made during the development of the peptide, a discussion of recent experimental results that were not available at the time of the original design, indications of areas where, in retrospect, the design might have been done differently, and a discussion of how the present work fits into the field of de novo protein design.Keywords: diffusion-collision model; molten globule; NMR; peptide; secondary structure; tertiary structure a t a is a de novo designed 38-amino acid peptide that has been shown by CD and two-dimensional NMR to exhibit in solution the designed aspects of secondary and tertiary structure (Fezoui et al., 1994). The purpose of the present paper is to present a full description of the process that led to the sequence of the peptide. Although the paper cited above contains a brief description of the design, space limitations precluded a complete discussion of the design process. In addition, the original peptide design was completed in the fall of 1990. Since then, there has been considerable progress made in the understanding of peptide conformation and the intervening work would have a bearing on any subsequent design.The goal of the design was to produce a peptide containing two interacting helices connected by a turn region. Such a peptide was desired as an experimental model of secondary structure association that could be used to investigate the early stages of protein folding as envisioned in the diffusion-collision model (Karplus & Weaver, 1976 protein folding are transiently folded elements of secondary structure (microdomains) that associate by diffusion and collision and become mutually stabilizing during the second stage of folding (Karplus & Weaver, 1976.Because the helix-forming properties of isolated monomeric helices had received considerable attention (reviewed by Scholtz & Baldwin, 1992), it seemed reasonable to extend the range of inquiry into the mechanisms of protein folding by studying connected helices. Connected and interacting helices might be expected to be stabilized by both short-range and tertiary interactions. The relative contributions to helix stability among the various short-range and tertiary interactions could be investigated with a helical hairpin peptide. Rationale, goals, definition of success, and approachThe first consideration in un...

Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model α‐helical hairpin peptide

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Dynamic properties of pH-dependent structural organization of the amyloidogenic β-protein (1-40)

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Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide

“…The protein that we investigate is an ␣-helical hairpin peptide which is similar to the de novo designed protein of Fezoui et al 22,23 The designed sequence forms a two-helix bundle in the native state, as shown in Fig. 1.…”