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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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Networks

Protein Networks

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....

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Related Experiment Video

Updated: Apr 19, 2026

Author Spotlight: Unveiling the Structural and Dynamic Aspects of Glycan Molecular Recognition

Author Spotlight: Unveiling the Structural and Dynamic Aspects of Glycan Molecular Recognition

Published on: May 17, 2024

Carbohydrate-protein interactions: molecular modeling insights.

Serge Pérez¹, Igor Tvaroška²

¹Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.

Advances in Carbohydrate Chemistry and Biochemistry

|December 7, 2014

Summary

Computational methods are crucial for understanding protein-carbohydrate interactions. This review covers quantum mechanics, molecular dynamics, and docking to predict these interactions and their biological roles.

Keywords:

Chemokines Density-functional theory Glycosyl hydrolases Glycosyltransferases Lectins Molecular docking Molecular dynamics Monoclonal antibodies Quantum mechanics methods Quantum mechanics/molecular mechanics

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Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Area of Science:

Computational chemistry and structural biology
Glycobiology and molecular recognition

Background:

Protein-carbohydrate interactions are vital in biological processes.
Understanding these interactions is key to deciphering carbohydrate functions.

Purpose of the Study:

To review computational methods for characterizing and predicting protein-carbohydrate interactions.
To assess the current status and limitations of these computational tools.

Main Methods:

Critical assessment of quantum-mechanical methods (molecular orbitals, density-functional theory).
Evaluation of semiempirical and empirical methods including QM/MM, molecular dynamics, free-energy calculations, and molecular docking.
Analysis of docking-validation studies in structural glycobiology.

Main Results:

Computational methods offer insights into structural, energetic, and mechanistic aspects of carbohydrate-protein recognition.
Molecular docking is a valuable tool in structural glycobiology.
Selected examples demonstrate the utility and limitations of computational approaches.

Conclusions:

Computational methods are essential for elucidating the structural basis of carbohydrate-protein interactions.
These methods aid in understanding the diverse biological roles of carbohydrates.
Applications span carbohydrate biosynthesis, glycosyltransferases, glycoside hydrolases, and various protein interactions.