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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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 form...
Protein Folding01:25

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 Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

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Conserved Binding Sites01:49

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 analyses the...
Protein Organization01:24

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.

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Related Experiment Video

Updated: Jun 4, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

Discovering conformational sub-states relevant to protein function.

Arvind Ramanathan1, Andrej J Savol, Christopher J Langmead

  • 1Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.

Plos One
|February 8, 2011
PubMed
Summary
This summary is machine-generated.

Protein conformational sub-states are crucial for function but hard to find. Quasi-anharmonic analysis (QAA) is a new computational method to identify these functionally relevant protein dynamics and transitions.

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Last Updated: Jun 4, 2026

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Proteins exhibit internal motions, exploring diverse conformations near their native state.
  • The functional relevance of these conformational fluctuations and sub-states is a key area of research.
  • Identifying low-population, transient sub-states poses significant computational challenges.

Purpose of the Study:

  • To develop a novel computational technique for identifying functionally relevant protein conformational sub-states.
  • To characterize the dynamics and transitions between these sub-states.

Main Methods:

  • Developed quasi-anharmonic analysis (QAA), a computational technique utilizing higher-order statistics.
  • Applied QAA to equilibrium simulations of human ubiquitin, T4 lysozyme, and cyclophilin A.
  • Integrated QAA with reaction pathway sampling for isomerization studies.

Main Results:

  • QAA successfully identified functionally relevant conformational sub-states in ubiquitin and T4 lysozyme.
  • Characterized protein motions critical for molecular recognition and enzyme catalysis (e.g., cis/trans peptidyl-prolyl isomerization).
  • Revealed critical structural and dynamical features of sub-states relevant to protein function.

Conclusions:

  • Quasi-anharmonic analysis (QAA) offers a powerful new framework for studying protein conformational diversity.
  • Provides an intuitive understanding of the biophysical basis linking conformational dynamics to protein function.