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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.

Protein Organization

Protein Organization

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: Jul 16, 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

Stochastic pairwise alignments and scoring methods for comparative protein structure modeling.

Adam C Marko¹, Kate Stafford, Troy Wymore

¹Pittsburgh Supercomputing Center, National Resource for Biomedical Supercomputing, 300 South Craig Street, Pittsburgh, Pennsylvania 15213, USA.

Journal of Chemical Information and Modeling

|March 30, 2007

Summary

Generating alignment ensembles using stochastic backtracking improves protein models. This method, utilizing the probA program and structural assessment, enhances accuracy for distantly related proteins in comparative modeling.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Area of Science:

Computational biology
Structural bioinformatics
Protein modeling

Background:

Comparative protein modeling relies on accurate target-template alignments.
Distantly related proteins pose challenges due to poor alignment quality.
Existing fold recognition algorithms struggle with distant homology.

Purpose of the Study:

To introduce and evaluate the use of alignment ensembles from stochastic backtracking for improving 3D comparative protein models.
To compare alignment ensembles with optimal alignments in protein modeling.
To assess the effectiveness of various structural assessment methods on these ensembles.

Main Methods:

Utilized stochastic backtracking to generate ensembles of pairwise alignments with the probA program.
Compared alignments from ensembles to structural alignments and optimal alignments.
Evaluated the lowest energy structures from ensembles using DFIRE, DOPE, ProsaII, and CHARMM/Generalized Born methods.

Main Results:

Ensembles generated by probA consistently produced alignments closer to structural alignments than optimal alignments in 35 cases.
Structural assessment methods identified improved models from the ensembles.
The combination of alignment ensembles and statistical potentials enhanced comparative models.

Conclusions:

Ensemble generation via stochastic backtracking is a viable strategy for improving protein model quality.
This approach effectively addresses alignment challenges in comparative modeling of distantly related proteins.
Integrating alignment ensembles with structural assessment tools offers a robust method for accurate protein structure prediction.