Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Summary

We developed computational de novo protein design methods capable of tackling several important areas of protein design. To disseminate these methods we present Protein WISDOM, an online tool for protein design (http://www.proteinwisdom.org). Starting from a structural template, design of monomeric proteins for increased stability and complexes for increased binding affinity can be performed.

Abstract

The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific properties, such as binding affinity, agonist or antagonist behavior, or stability, relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does protein design provide predictions for potentially useful drug targets, but it also enhances our understanding of the protein folding process and protein-protein interactions. Experimental methods such as directed evolution have shown success in protein design. However, such methods are restricted by the limited sequence space that can be searched tractably. In contrast, computational design strategies allow for the screening of a much larger set of sequences covering a wide variety of properties and functionality. We have developed a range of computational de novo protein design methods capable of tackling several important areas of protein design. These include the design of monomeric proteins for increased stability and complexes for increased binding affinity.

To disseminate these methods for broader use we present Protein WISDOM (http://www.proteinwisdom.org), a tool that provides automated methods for a variety of protein design problems. Structural templates are submitted to initialize the design process. The first stage of design is an optimization sequence selection stage that aims at improving stability through minimization of potential energy in the sequence space. Selected sequences are then run through a fold specificity stage and a binding affinity stage. A rank-ordered list of the sequences for each step of the process, along with relevant designed structures, provides the user with a comprehensive quantitative assessment of the design. Here we provide the details of each design method, as well as several notable experimental successes attained through the use of the methods.

Introduction

De novo protein design is the identification of protein sequences that will yield a desired tertiary structure with improved properties or function. Since the native fold of a protein is the conformation which lies at the free energy minimum, de novo protein design seeks sequences that will have a free energy minimum in the target fold. This problem was first described by Drexler¹ and Pabo² and was referred to as the "inverse folding problem." However, unlike the protein folding problem, where a sequence can yield only one folded structure solution, the de novo protein design problem exhibits degeneracy. Many different ....

Protocol

Method Overview

The de novo design framework used in Protein WISDOM consists of two stages. The first stage produces a rank-ordered list of amino acid sequences that will fold into a given template structure. The second stage validated these sequences by calculating either fold specificity or approximate binding affinity, or both. The former is primarily used when the design is of a single protein, while the latter is used when the design is of a complex (a peptide binding to a target protein). Figure 1 gives an overview of the steps involved in the framework.

Design Inputs:

Results

De Novo Design of Entry Inhibitors for HIV-1

The de novo design framework implemented in Protein WISDOM has been used for the design of inhibitor peptides for several important therapeutic systems (Tables 1 and 2). One system of note is the design of peptides to inhibit HIV-1 entry to the host cell receptor CD4, which is here used as a representative system to demonstrate the practical use of the Protein WISDOM interface. The peptides were designed to target the.......

Discussion

The de novo protein design framework consists of two stages, a sequence selection stage and a validation stage. The framework is robust enough to handle rigid and flexible design templates, and can be applied to single protein design or complex protein design. The framework has been successfully applied to numerous protein systems with applications to dozens of diseases. A number of the designs have been experimentally validated, providing the most potent inhibitors or agonists of some proteins discovered to dat.......