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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 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...

Protein and Protein Structures

Protein and Protein Structures

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

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...

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Related Experiment Video

Updated: Jun 15, 2025

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

GTalign: spatial index-driven protein structure alignment, superposition, and search.

Mindaugas Margelevičius¹

¹Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania. mindaugas.margelevicius@bti.vu.lt.

Nature Communications

|August 24, 2024

Summary

This summary is machine-generated.

GTalign is a new algorithm for fast and accurate protein structure alignment and search. It significantly speeds up the identification of optimal protein superpositions, aiding biological research.

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Published on: July 14, 2015

Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Protein databases are rapidly expanding, necessitating efficient methods for structure alignment and search.
Existing methods struggle to keep pace with the scale of modern protein structure repositories.

Purpose of the Study:

To introduce GTalign, an innovative algorithm for rapid and accurate protein structure alignment and search.
To address the challenge of efficiently searching vast protein structure databases.

Main Methods:

Developed GTalign, an algorithm utilizing spatial structure indexing.
Parallelized superposition search across residues and protein structure pairs.
Implemented a high-speed algorithm for optimal superposition identification.

Main Results:

GTalign achieves optimal superposition at high speeds.
Demonstrated orders of magnitude speedup compared to existing methods while maintaining state-of-the-art accuracy.
Evaluated rigorously across diverse datasets, showing superior accuracy.

Conclusions:

GTalign provides a highly accurate and efficient solution for protein structure alignment and search.
Its speed and accuracy support applications in functional inference, evolutionary analysis, protein design, and drug discovery.
Facilitates advancements in understanding protein structure and function.