De Novo Design of Proteins - Peptide and Protein Design for Biopharmaceutical Applications - page 206

natural protein. In addition, there are a variety of strategies and methods for
the redesign or reengineering of naturally occurring peptides and proteins.
The ultimate goal of de novo protein design is the design from first
principles of proteins which fold in a specified way and possibly with
defined properties, e.g. enzymatic, without relying on a natural protein as
a paradigm, i.e. without starting from a natural sequence. Thus the aim is
to specify a certain 3D fold (a tertiary structure) constituted from specific
secondary structure elements and appropriate loops, turns and templates.
It is not redecoration of a natural protein but the use of general knowl-
edge about protein folding and packing to construct new proteins.
However, obviously there is no opposition here between 'natural' and
'manmade' and the same rules govern the folding of all molecules regard-
less of their heritage.
De novo design has often taken the form of - in DeGrado's words - a
'minimalist' approach, which involves design of minimalist sequences
that are simpler than their natural counterparts but retain sufficient
complexity for folding and function. The alternative, structure-based
strategy - which is not de novo design in the strict sense - begins with an
experimentally determined 3D structure of a protein. This has been useful
for the design of proteins with enhanced stability or novel functions.
However, the designed proteins have often behaved as molten globules,
i.e. with non-native states, where most of the a-helices and b-sheets have
formed but the tertiary structure is loose, showing dynamically averaging
conformations, containing poorly packed hydrophobic cores behaving
more like a liquid. Bryson and DeGrado have cautioned that '...between
the conception of a designed protein and its realization lies the molten
globule - an energy well of surprising depth and breadth that must be
overcome en route to the final goal' [4].
This chapter will describe de novo design of secondary structural
elements and tertiary structures, with an emphasis on general applicabil-
ity. The chapter is closely connected with Chapter 2 by Nikiforovich and
Marshall on computational methods and Chapter 3 by Maes and Tourw ´
on peptidomimetics.

6.2 SECONDARY STRUCTURE ELEMENTS

6.2.1 The a-helix

The most common secondary structural element is the a-helix
(Figures 6.1 and 6.2). In the a-helix, the carbonyl of residue i is hydrogen