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Protein Folding

Protein Folding

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 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 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....

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Related Experiment Video

Updated: Jul 11, 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 conformational ensembles in function: roles and mechanisms.

Ruth Nussinov^1,2,3, Yonglan Liu³, Wengang Zhang³

¹Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA NussinoR@mail.nih.gov.

RSC Chemical Biology

|November 3, 2023

Summary

Proteins function through dynamic conformational ensembles, not single structures. Changes in these ensembles, driven by conformational propensities, are essential for cellular life and biological activity.

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

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Area of Science:

Molecular Biology
Biophysics
Structural Biology

Background:

The traditional sequence-structure-function paradigm assumes a single, static protein structure.
Cellular function necessitates dynamic protein structures that interconvert between states.
Modern molecular biology utilizes the energy landscape concept and conformational ensembles.

Purpose of the Study:

To propose an updated sequence-conformational ensemble-function paradigm.
To highlight the role of dynamic conformational ensembles in protein function.
To explore the significance of conformational propensities in cellular processes.

Main Methods:

Discussion of the conformational ensemble framework from physics and chemistry.
Analysis of protein dynamics and interconversion between conformational states.
Examination of examples including protein kinases, lipid kinases, and Ras GTPases.

Main Results:

Proteins exist as dynamic ensembles of conformations with varying energies.
Changes in the populations of these conformational states are crucial for cellular function.
Active protein function is determined by the population of molecules in active states.

Conclusions:

The sequence-conformational ensemble-function paradigm reframes protein behavior.
Dynamic conformational propensities, not rigid structures, are key to cellular life.
Understanding protein ensembles offers broad insights into cellular mechanisms.