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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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Updated: Jun 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Directionality in protein fold prediction.

Jonathan J Ellis¹, Fabien P E Huard, Charlotte M Deane

¹Department of Statistics, Macquarie University, Sydney, NSW 2109, Australia.

BMC Bioinformatics

|April 9, 2010

Summary

This summary is machine-generated.

Protein folding directionality matters. Folding from the N-terminus to C-terminus yields more accurate predictions, especially for proteins with cotranslational folding evidence. This suggests a sequential approach may improve protein structure prediction.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

The traditional view holds that amino acid sequence dictates protein folding.
Recent studies suggest cotranslational folding influences folding pathways, particularly for ancient protein folds.
This work investigates the impact of cotranslational folding on protein structure prediction.

Purpose of the Study:

To incorporate cotranslational folding into protein structure prediction algorithms.
To compare the accuracy of folding predictions based on translation directionality.
To assess the influence of cotranslation on folding pathway fidelity.

Main Methods:

Adapted the Rosetta program to simulate protein folding during nascent chain elongation.
Developed an algorithm to fold proteins sequentially from both N-terminus to C-terminus and C-terminus to N-terminus.
Performed pairwise comparisons of folding accuracy between the two directional approaches.

Main Results:

Folding from N-terminus to C-terminus improved prediction accuracy by 94% compared to the reverse direction.
The N-to-C terminus advantage was more pronounced in proteins with stronger evidence of cotranslational folding.
The developed algorithm achieved prediction accuracy comparable to, and sometimes exceeding, standard Rosetta.

Conclusions:

A significant directionality effect exists in protein fold prediction.
Current prediction methods are too imprecise to fully leverage this directionality.
Future advancements in prediction techniques may enable effective utilization of sequential folding approaches.