Principles for designing ideal protein structures

Abstract

Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features—for example kinked α-helices, bulged β-strands, strained loops and buried polar groups—that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.

A toolbox for protein design

“…Researchers from the same laboratory as Koga et al had previously reported 4 the impressive preparation of Top7 -a 93-residue α/β-protein designed to adopt a tertiary structure not found in nature, and which incidentally satisfies the newly established design principles 1 . But the success of Koga and colleagues' protocol, and its incorporation of negative design, is a big step forward compared with that earlier work.…”

“…It would be immensely useful to be able to predict native structures from amino-acid sequences, but our understanding of how such sequences determine the three-dimensional arrangements of proteins is limited. On page 222 of this issue, Koga et al 1 describe a set of rules that relate secondary protein-structure patterns -α-helices and β-sheets -to tertiary features. They also show how these principles can be used to design amino-acid sequences that fold into predefined topologies.…”

“…For each topology, the authors calculated the thermodynamic stability of possible sequences and conformations to find the ones that had the lowest energies. To refine these sequences, they incorporated large, 1 have defined fundamental rules that describe how local interactions in secondary structures relate to the assembly of simple tertiary motifs (compact, three-dimensional structures that consist of a few adjacent secondary structures, such as the βα-and αβ-motifs shown). In this example, different connecting loops direct the α-helix to pack against different sides of the β-strand.…”

Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability

“…More general methods such as RosettaDesign 13 are based on minimizing an effective energy function, which has been, for large parts, derived from molecular mechanics force fields 4 . It has been shown that RosettaDesign can achieve high success rates for idealized target structures 10 . However, success rates of automated design with common targets has remained low 14,15 .…”

“…These progresses have been driven by underlying computational or rule-based design methods, which can be stringently calibrated through the de novo design of amino acid sequences that fold into desired three-dimensional structures 4,[8][9][10] . In this regard, rule-based designs have attained some remarkable successes 7,11,12 , albeit limited to particular types of target structures or structure motifs.…”