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Improved recognition of native-like protein structures using a family of designed sequences.

ABSTRACT: The goal of the inverse protein folding problem is to identify amino acid sequences that stabilize a given target protein conformation. Methods that attempt to solve this problem have proven useful for protein sequence design. Here we show that the same methods can provide valuable information for protein fold recognition and for ab initio protein structure prediction. We present a measure of the compatibility of a test sequence with a target model structure, based on computational protein design. The model structure is used as input to design a family of low free energy sequences, and these sequences are compared with the test sequence by using a metric in sequence space based on nearest-neighbor connectivity. We find that this measure is able to recognize the native fold of a myoglobin sequence among different globin folds. It is also powerful enough to recognize near-native protein structures among non-native models.

SUBMITTER: Koehl P

PROVIDER: S-EPMC117367 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

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Improved recognition of native-like protein structures using a family of designed sequences.

Koehl Patrice P Levitt Michael M

Proceedings of the National Academy of Sciences of the United States of America 20020108 2

The goal of the inverse protein folding problem is to identify amino acid sequences that stabilize a given target protein conformation. Methods that attempt to solve this problem have proven useful for protein sequence design. Here we show that the same methods can provide valuable information for protein fold recognition and for ab initio protein structure prediction. We present a measure of the compatibility of a test sequence with a target model structure, based on computational protein desig ...[more]

PMID: 11782533

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Project description:BackgroundAccording to structure-dependent function of proteins, two main challenging problems called Protein Structure Prediction (PSP) and Inverse Protein Folding (IPF) are investigated. In spite of IPF essential applications, it has not been investigated as much as PSP problem. In fact, the ultimate goal of IPF problem or protein design is to create proteins with enhanced properties or even novel functions. One of the major computational challenges in protein design is its large sequence space, namely searching through all plausible sequences is impossible. Inasmuch as, protein secondary structure represents an appropriate primary scaffold of the protein conformation, undoubtedly studying the Protein Secondary Structure Inverse Folding (PSSIF) problem is a quantum leap forward in protein design, as it can reduce the search space. In this paper, a novel genetic algorithm which uses native secondary sub-structures is proposed to solve PSSIF problem. In essence, evolutionary information can lead the algorithm to design appropriate amino acid sequences respective to the target secondary structures. Furthermore, they can be folded to tertiary structures almost similar to their reference 3D structures.ResultsThe proposed algorithm called GAPSSIF benefits from evolutionary information obtained by solved proteins in the PDB. Therefore, we construct a repository of protein secondary sub-structures to accelerate convergence of the algorithm. The secondary structure of designed sequences by GAPSSIF is comparable with those obtained by Evolver and EvoDesign. Although we do not explicitly consider tertiary structure features through the algorithm, the structural similarity of native and designed sequences declares acceptable values.ConclusionsUsing the evolutionary information of native structures can significantly improve the quality of designed sequences. In fact, the combination of this information and effective features such as solvent accessibility and torsion angles leads IPF problem to an efficient solution. GAPSSIF can be downloaded at http://bioinformatics.aut.ac.ir/GAPSSIF/ .

Dataset Information

Improved recognition of native-like protein structures using a family of designed sequences.

Publications

Improved recognition of native-like protein structures using a family of designed sequences.

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