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Related Concept Videos

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.
Protein Organization01:13

Protein Organization

Overview
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...
Protein and Protein Structure02:15

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 can...
Elastin is Responsible for Tissue Elasticity01:12

Elastin is Responsible for Tissue Elasticity

Elastic fiber contains the protein elastin along with lesser amounts of other proteins and glycoproteins. The main property of elastin is that it will return to its original shape after being stretched or compressed. Elastic fibers are prominent in elastic tissues found in skin and the elastic ligaments of the vertebral column.
Ligaments and tendons are made of dense regular connective tissue, but in ligaments not all fibers are parallel. Dense regular elastic tissue contains elastin fibers and...

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Related Experiment Video

Updated: Jul 2, 2026

Production of Elastin-like Protein Hydrogels for Encapsulation and Immunostaining of Cells in 3D
11:46

Production of Elastin-like Protein Hydrogels for Encapsulation and Immunostaining of Cells in 3D

Published on: May 19, 2018

Building alternate protein structures using the elastic network model.

Qingyi Yang1, Kim A Sharp

  • 1Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

Proteins
|August 16, 2008
PubMed
Summary
This summary is machine-generated.

This study presents a novel method for generating diverse, high-quality protein structures using modified elastic network models. The approach ensures good stereochemistry and steric properties, advancing protein modeling and homology studies.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Generating diverse and accurate protein structures is crucial for understanding protein function and dynamics.
  • Existing methods often struggle to produce ensembles with both significant conformational diversity and good structural quality.

Purpose of the Study:

  • To develop an efficient method for generating ensembles of all-atom protein structures with significant conformational differences.
  • To ensure generated structures possess excellent stereochemistry and steric properties.
  • To improve backbone templates for homology modeling.

Main Methods:

  • A modified elastic network model (ENM) with enhanced force parameters was used to generate backbone framework structures.
  • Perturbations along low-frequency normal modes were applied to explore conformational space.
  • Backbone structures were refined into all-atom models using the SCWRL side chain building program.

Main Results:

  • Parameterization reduced backbone violations to less than 1% and improved B-factor correlation to R = 0.77.
  • Over 100,000 protein backbones were generated, spanning a 15 Å root mean square deviation conformational space.
  • Homology modeling using improved templates resulted in better full-atom models, with 50% identifiable via blind D-Fire potential analysis.

Conclusions:

  • The developed method efficiently generates high-quality, diverse protein structural ensembles.
  • This approach significantly enhances the accuracy and utility of protein structure prediction and homology modeling.
  • The method offers a powerful tool for exploring protein conformational landscapes and improving structural biology research.