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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
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...
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Globular Proteins01:27

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In organisms, proteins are the most abundant macromolecules. They act as the building blocks of life and play various crucial roles in the body. Proteins can be broadly classified into two distinct subtypes based on their shape and solubilities: globular proteins and fibrous proteins.
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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 polypeptide...
Protein-Protein Interfaces02:04

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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 polypeptide...

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Related Experiment Video

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

Published on: July 16, 2017

Global dynamics of proteins: bridging between structure and function.

Ivet Bahar1, Timothy R Lezon, Lee-Wei Yang

  • 1Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA. bahar@pitt.edu

Annual Review of Biophysics
|March 3, 2010
PubMed
Summary
This summary is machine-generated.

Biomolecular dynamics are dictated by protein structure topology. Computational elastic network models accurately predict protein motion, correlating with experimental functional changes and allosteric mechanisms.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Biomolecular systems exhibit unique dynamic properties essential for biological function.
  • These dynamics are significantly influenced by the topology of native contacts within the molecular structure.

Purpose of the Study:

  • To explore the relationship between protein structure, dynamics, and function.
  • To evaluate the utility of computational methods in predicting functional changes and allosteric mechanisms.

Main Methods:

  • Utilizing elastic network models (ENMs) in conjunction with normal mode analyses.
  • Analyzing collective dynamics and global modes of motion inherent to protein structures.
  • Correlating computational predictions with experimentally observed functional changes in protein structures.

Main Results:

  • Elastic network models effectively elucidate intrinsic collective dynamics under native conditions.
  • Global modes of motion are robustly defined by the overall protein architecture.
  • A strong correspondence exists between experimentally observed functional changes and ENM-predicted global motions.

Conclusions:

  • Computational methods, particularly ENMs, are valuable for assessing structure-function relationships.
  • These methods can predict and aid in understanding allosteric mechanisms favored by native protein folds.
  • The findings support the use of computational approaches to investigate protein dynamics and function.