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Protein Folding

Protein Folding

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

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Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Can computationally designed protein sequences improve secondary structure prediction?

Rajkumar Bondugula¹, Anders Wallqvist, Michael S Lee

¹Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.

Protein Engineering, Design & Selection : PEDS

|February 2, 2011

Summary

This summary is machine-generated.

Computational protein design enhances sequence-property prediction. Using designed sequences improved secondary structure prediction accuracy by nearly one percent, augmenting existing tools.

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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

Area of Science:

Protein Engineering
Computational Biology
Bioinformatics

Background:

Computational sequence design methods engineer proteins for enhanced stability and novel functions.
These algorithms can identify sequence compatibility with protein fold topologies.

Purpose of the Study:

To test if a large database of computationally designed protein sequences enhances secondary structure prediction accuracy.
To evaluate the impact of mutational constraints on prediction accuracy and sequence diversity.

Main Methods:

Performed a large-scale test using 6511 diverse protein domains and 50 designed sequences per domain.
Analyzed the accuracy of computationally designed sequences and implemented mutational constraints.
Augmented the PSIPRED program with the developed method.

Main Results:

Accuracy improved with mutational constraints, though sequence diversity was reduced.
Achieved a nearly one percentage point improvement in three-state prediction accuracy (Q(3)) over natural sequence databases alone.
Augmented the state-of-the-art PSIPRED program by one percentage point.

Conclusions:

Computationally designed sequences can enhance protein secondary structure prediction.
Mutational constraints are necessary for optimizing prediction accuracy with designed sequences.
Further improvements are possible, with a theoretical potential of 8-10 percentage points.