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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...
Protein Folding01:22

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Molecular Chaperones and Protein Folding03:00

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Protein Organization01:13

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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

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure

Qingwu Yang1, Sing-Hoi Sze

  • 1Department of Computer Science, Texas A&M University, College Station, TX 77843, USA. qingwu-yang@neo.tamu.edu

BMC Bioinformatics
|July 25, 2008
PubMed
Summary
This summary is machine-generated.

Computational methods can now efficiently predict protein folding pathways for large proteins by reducing conformational space. This mesoscopic-level approach accurately models complex folding dynamics, distinguishing even subtle differences between similar protein structures.

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Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Experimental determination of protein folding pathways is challenging.
  • Current computational methods are often too resource-intensive for large proteins.

Purpose of the Study:

  • To develop an efficient computational method for predicting protein folding pathways.
  • To enable the study of folding pathways for large proteins.

Main Methods:

  • Representing intermediate protein conformations as collections of interacting secondary structure elements.
  • Reducing conformational space by assuming known native protein structures.
  • Mesoscopic-level simulation of protein folding.

Main Results:

  • Successfully predicted energetically favorable folding pathways for large proteins (e.g., 416-residue phosphoglycerate kinase).
  • Distinguished folding pathways for structurally similar proteins (e.g., protein G, protein L, NuG1, NuG2).
  • Validated predictions against experimentally determined intermediate folding states for multiple proteins.

Conclusions:

  • The developed technique efficiently predicts folding pathways for both large and small proteins at the mesoscopic level.
  • This strategy is a feasible approach for analyzing the folding of large proteins.
  • A software program (SSFold) implementing this method is publicly available.