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Related Concept Videos

Amyloid Fibrils03:03

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining, normally used to...
Amyloid Fibrils03:03

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining, normally used to...
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 Folding01:22

Protein Folding

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Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Amyloid fibril structure modeling using protein threading and molecular dynamics simulations.

Jun-Tao Guo1, Ying Xu

  • 1Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, 30602, USA.

Methods in Enzymology
|October 19, 2006
PubMed
Summary

Computational modeling aids in understanding amyloid fibril structures. This approach uses protein threading and molecular dynamics to predict and assess the stability of amyloid structures, like Abeta.

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Last Updated: Jul 19, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Amyloid and the Cross-Beta Architecture
09:06

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Published on: February 13, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Published on: January 10, 2018

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Amyloid fibrils are protein aggregates implicated in various diseases.
  • Understanding amyloid structure is crucial for developing therapeutic interventions.
  • Current methods for structural elucidation can be challenging.

Purpose of the Study:

  • To present a computational approach for modeling amyloid fibril structures.
  • To demonstrate the utility of protein threading and molecular dynamics simulations in this context.
  • To provide a framework for assessing the stability of predicted amyloid structures.

Main Methods:

  • Utilizing protein threading to align amyloid sequences against known structural templates.
  • Generating initial structural models based on threading alignments.
  • Employing molecular dynamics simulations to evaluate the stability of the generated models.

Main Results:

  • The study successfully applied computational techniques to model amyloid fibril structures.
  • The methods allow for the assessment of the stability of these models.
  • Abeta amyloid fibril modeling was used as a specific example.

Conclusions:

  • Computational modeling offers a viable strategy for elucidating amyloid fibril structures.
  • This approach can guide the development of novel inhibitors of fibril formation.
  • Further refinement of these computational methods holds promise for amyloid-related disease research.