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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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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 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

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Related Experiment Video

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Coarse-grained models for protein aggregation.

Chun Wu1, Joan-Emma Shea

  • 1Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.

Current Opinion in Structural Biology
|March 5, 2011
PubMed
Summary

Protein aggregation into fibrils involves complex pathways but shares universal features. Coarse-grained computational models simplify protein representation, revealing insights into aggregation mechanisms and intermediates.

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Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

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Area of Science:

  • Biochemistry
  • Biophysics
  • Computational Biology

Background:

  • Protein aggregation into fibrillar species is a complex, multi-scale process with numerous intermediate states.
  • Despite sequence diversity, proteins often form similar fibril structures and share aggregation kinetics, suggesting universal underlying principles.

Purpose of the Study:

  • To review computational approaches, specifically coarse-grained modeling, for studying protein aggregation.
  • To elucidate the mechanisms of protein aggregation and the nature of aggregation intermediates by leveraging universal aggregation features.

Main Methods:

  • Utilizing coarse-grained (simplified) protein models to represent aggregation processes.
  • Analyzing computational modeling advancements to understand protein aggregation pathways.
  • Investigating the role of monomeric protein conformations and intrinsic propensities in aggregation.

Main Results:

  • Coarse-grained models simplify the complex protein aggregation landscape.
  • These models provide new insights into the mechanisms driving fibril formation.
  • The study highlights the importance of aggregation-prone conformations and inherent protein properties.

Conclusions:

  • Coarse-grained modeling is a powerful tool for dissecting complex protein aggregation.
  • Understanding universal features simplifies the study of diverse aggregation pathways.
  • This approach sheds light on the nature of aggregation intermediates and disease-related protein misfolding.