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Amyloid Fibrils

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...

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NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation.

Changsik Kim¹, Jiwon Choi, Seong Joon Lee

¹Sookmyung Women's University, Department of Biological Sciences, Hyochangwon-gil 52, Yongsan-gu, Seoul, Republic of Korea.

Nucleic Acids Research

|May 27, 2009

Summary

NetCSSP calculates contact-dependent secondary structure propensity (CSSP) to identify non-native structures in proteins. This tool aids in predicting protein aggregation and amyloid fibril formation by analyzing sequence changes.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Protein structure and dynamics
Bioinformatics and computational biology
Molecular biophysics

Background:

Protein secondary structure propensities are crucial for understanding protein folding and function.
Non-native secondary structures are implicated in protein aggregation diseases like amyloidosis.
Predicting conformational changes requires sensitive methods for analyzing local sequence properties.

Purpose of the Study:

To introduce NetCSSP, a web tool for calculating contact-dependent secondary structure propensity (CSSP).
To provide an interactive platform for analyzing CSSP values and predicting mutational effects.
To offer a searchable database of precalculated CSSP values for protein fragments.

Main Methods:

Implementation of the latest CSSP algorithm within the NetCSSP web tool.
Development of a Flash chart-based graphic interface for interactive CSSP calculations.
Precalculation and storage of CSSP values for over 1.4 million 7-residue fragments from PDB.

Main Results:

NetCSSP enables interactive calculation of CSSP for user-defined protein regions.
The tool quantitatively assesses the impact of mutations on secondary structure propensities.
A searchable database identifies 'chameleon' subsequences associated with amyloid formation.

Conclusions:

NetCSSP is a valuable resource for studying protein secondary structure and aggregation.
The tool facilitates research into the mechanisms of amyloid fibril formation.
Interactive analysis and precalculated data enhance the prediction of local conformational changes.