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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.
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Caspase, a family of cysteine proteases, serve as effectors in apoptosis. The ced3 gene in C.elegans was first identified to be involved in apoptosis. This gene encodes the ced-3 caspase that is similar to the interleukin-1-beta converting enzyme or ICE in mammals. In addition to apoptosis, caspases also function in the inflammatory response. Inflammatory caspases are essential in activating pro-inflammatory cytokines that recruit immune cells and block the replication of pathogens inside cells.
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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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

Protein structure prediction: challenging targets for CASP10.

Ashish Runthala1

  • 1Biological Sciences, Faculty Division III, Birla Institute of Technology & Science, Pilani, Rajasthan, India. ashishr@bits-pilani.ac.in

Journal of Biomolecular Structure & Dynamics
|June 27, 2012
PubMed
Summary

Accurately predicting protein structures from sequences remains challenging due to technical limitations. Focusing on key issues in protein structure prediction challenges like CASP is crucial for developing reliable methodologies.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure determination faces resource and technical limitations, hindering functional characterization.
  • Accurate protein structure prediction from amino acid sequences is a key goal in molecular biology.
  • The Critical Assessment of Structure Prediction (CASP) evaluates protein modeling methodologies.

Purpose of the Study:

  • To highlight limitations in current protein structure prediction methods.
  • To identify key issues impeding accurate prediction for upcoming CASP assessments.
  • To propose improvements for developing consistent and accurate protein structure prediction methodologies.

Main Methods:

  • Analysis of limitations in experimental structure determination.
  • Review of algorithmic developments in protein structure prediction.
  • Evaluation of current protein structure prediction modeling methodologies.

Main Results:

  • Current protein structure prediction methodologies are insufficient.
  • Technical gaps impede accurate prediction of native protein states.
  • Divergence between predicted and actual protein models is a significant issue.

Conclusions:

  • There is a critical need to address specific challenges in protein structure prediction.
  • Improvements in CASP assessment criteria are necessary for reliable methodology development.
  • Bridging current gaps will pave the way for accurate, sequence-based protein structure prediction.