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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....

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...

Protein and Protein Structures

Protein and Protein Structures

Potential Energy

Potential Energy

The energy stored by a structure and location of matter in space is called potential energy. For instance, raising a kettlebell changes its spatial location and increases its potential energy. Similarly, a stretched rubber band contains potential energy which, under certain conditions, can be converted into other forms of energy, such as kinetic energy.
Chemical bonds that form attractive forces between atoms also contain potential energy, called chemical energy. When a chemical reaction...

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...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Dec 12, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Protein energy landscape exploration with structure-based models.

Sridhar Neelamraju¹, David J Wales², Shachi Gosavi³

¹Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore 560 065, India; University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK.

Current Opinion in Structural Biology

|August 16, 2020

Summary

This study combines structure-based models (SBMs) with discrete path sampling (DPS) to simplify protein energy landscapes. This approach efficiently maps protein folding pathways and calculates key kinetic and thermodynamic properties.

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Last Updated: Dec 12, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

Computational biology
Biophysics
Protein dynamics

Background:

Investigating the multi-dimensional energy landscape of proteins is computationally intensive.
Understanding protein folding pathways, transition rates, and energy barriers is crucial for molecular biology.

Purpose of the Study:

To simplify the complexity of protein energy landscapes using coarse-grained models.
To detail protein folding pathways and landscape features through computational analysis.

Main Methods:

Utilizing coarse-grained structure-based models (SBMs) to approximate protein free energy landscapes.
Integrating SBMs with discrete path sampling (DPS) for enhanced landscape exploration.

Main Results:

The combined SBMs and DPS approach provides a simplified yet detailed view of protein energy landscapes.
This method enables efficient sampling of the protein free energy landscape.
Accurate calculation of kinetic and thermodynamic quantities related to protein folding.

Conclusions:

Combining SBMs and DPS offers an efficient computational framework for studying protein folding.
This integrated approach facilitates a deeper understanding of protein conformational dynamics and stability.