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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 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 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-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...

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Related Experiment Video

Updated: Jul 8, 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

Recent Advances and Challenges in Protein Structure Prediction.

Chun-Xiang Peng¹, Fang Liang¹, Yu-Hao Xia¹

¹College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China.

Journal of Chemical Information and Modeling

|December 18, 2023

Summary

Artificial intelligence, particularly AlphaFold2, now predicts protein structures with experimental accuracy. This breakthrough aids biological understanding and drug discovery but faces challenges in complex protein predictions.

Keywords:

Protein structure prediction artificial intelligence multidomain protein multiple conformational states protein complex protein folding pathways

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Area of Science:

Computational biology
Structural biology
Artificial intelligence in life sciences

Background:

Recent AI advancements have revolutionized protein structure prediction.
DeepMind's AlphaFold2 achieves accuracy comparable to experimental methods for unknown protein structures.

Purpose of the Study:

To review recent progress in AI-driven protein structure prediction.
To identify and discuss current challenges and future directions in the field.

Main Methods:

Review of artificial intelligence models, focusing on end-to-end approaches like AlphaFold2.
Analysis of the capabilities and limitations of current AI in predicting protein structures.

Main Results:

AI models, exemplified by AlphaFold2, can predict 3D protein structures with high accuracy.
This accuracy accelerates research in protein function, drug discovery, and biological applications.

Conclusions:

AI has significantly advanced protein structure prediction, opening new research avenues.
Future work must address challenges in predicting complex protein structures, complexes, and dynamics.