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Protein Folding

Protein Folding

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.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Protein Folding

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Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Simultaneous alignment and folding of protein sequences.

Jérôme Waldispühl¹, Charles W O'Donnell, Sebastian Will

¹1 School of Computer Science, McGill University , Montreal, Canada .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 29, 2014

Summary

partiFold-Align is a novel algorithm for simultaneous protein sequence alignment and consensus folding, excelling in low-homology cases. This computational biology tool significantly improves protein structure prediction where other methods fail.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Area of Science:

Computational biology
Bioinformatics
Structural biology

Background:

Comparative analysis of low-homology proteins is challenging.
Sequence alignment and consensus folding are key problems.
Transmembrane β-barrel proteins are difficult to analyze.

Purpose of the Study:

Introduce partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences.
Address limitations in current protein comparative analysis tools.
Improve secondary structure prediction for challenging protein families.

Main Methods:

Developed partiFold-Align, an algorithm with polynomial time and space complexity.
Exploited sparsity in super-secondary structure pairings and alignment candidates.
Achieved effectively cubic running time for simultaneous pairwise alignment and folding.

Main Results:

partiFold-Align significantly outperforms state-of-the-art alignment tools in low-homology cases.
Demonstrated efficacy on transmembrane β-barrel proteins.
Improved secondary structure prediction where current methods fail.
No prior training required for the algorithm.

Conclusions:

partiFold-Align offers a breakthrough in analyzing low-homology proteins.
The algorithm is widely applicable to diverse protein families.
partiFold-Align advances computational biology and structural prediction.