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Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures.

Venkata R Sanaboyana¹, Adrian H Elcock¹

¹Department of Biochemistry & Molecular Biology, University of Iowa, USA.

Journal of Molecular Biology

|December 8, 2023

Summary

Protein structure prediction using AlphaFold2 can refine signal peptide predictions from tools like TargetP 2.0 and SignalP 6.0. Analyzing AlphaFold2 structures helps identify false positives, improving the accuracy of protein localization prediction.

Keywords:

protein localization protein targeting signal sequence subcellular location

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Published on: July 25, 2013

Area of Science:

Proteomics
Structural Biology
Bioinformatics

Background:

Proteins utilize signal or transit peptides for subcellular localization.
Sequence-based methods like TargetP 2.0 and SignalP 6.0 predict these peptides with high accuracy.
However, occasional false positive predictions can occur.

Purpose of the Study:

To investigate the utility of AlphaFold2-predicted protein structures in identifying false positive signal peptide predictions.
To assess the consistency between sequence-based predictions and structural data.

Main Methods:

Analysis of AlphaFold2-predicted structures for proteins with predicted signal peptides.
Comparison of AlphaFold2 structural data with predictions from TargetP 2.0 and SignalP 6.0 across 48 proteomes.
Evaluation of signal peptide confidence and orientation within the predicted protein structure.

Main Results:

AlphaFold2 correctly models signal peptides as external to the mature protein structure.
In 95.1% of cases, AlphaFold2 structures align with TargetP 2.0/SignalP 6.0 predictions.
A small percentage (4.9%) of predictions showed inconsistency, often with low confidence, suggesting potential false positives.

Conclusions:

AlphaFold2 structural analysis offers a complementary approach to sequence-based methods for signal peptide prediction.
Inconsistencies between predicted structures and sequence-based predictions can highlight potential false positives.
This approach can aid in developing more accurate protein localization prediction tools.