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Related Concept Videos

Protein Organization01:13

Protein Organization

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Protein Folding01:22

Protein Folding

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Protein Folding01:22

Protein Folding

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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.
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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.
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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.
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Related Experiment Video

Updated: Jul 17, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Ab initio folding of multiple-chain proteins.

J A Saunders1, K D Gibson, H A Scheraga

  • 1Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|April 4, 2002
PubMed
Summary

This study extends ab initio protein structure prediction to multiple-chain proteins using modified united-residue (UNRES) force fields and Conformational Space Annealing (CSA) optimization. Promising results were achieved for multi-helix protein structures in the CASP3 exercise.

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Last Updated: Jul 17, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Published on: April 10, 2012

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Accurate prediction of protein structures is crucial for understanding biological function.
  • Existing ab initio methods often struggle with multi-chain protein complexes.
  • The united-residue (UNRES) force field and Conformational Space Annealing (CSA) are established computational tools.

Purpose of the Study:

  • To extend the existing ab initio protein structure prediction methodology to handle multiple-chain proteins.
  • To adapt the UNRES force field and CSA global optimization procedure for multi-chain systems.
  • To evaluate the performance of the modified methodology on benchmark protein targets.

Main Methods:

  • Modification of the UNRES force field to incorporate inter-chain interactions.
  • Adaptation of the CSA global optimization algorithm for exploring conformational space of multi-chain proteins.
  • Application of the enhanced methodology to predict structures of multi-helix proteins from the CASP3 dataset.

Main Results:

  • Successful prediction of structures for a four-helix and a three-helix protein.
  • Demonstrated capability of the modified UNRES-CSA approach to model multi-chain protein assembly.
  • Validation against known structures from the Critical Assessment of protein Structure Prediction (CASP3) exercise.

Conclusions:

  • The extended ab initio methodology effectively predicts structures of multiple-chain proteins.
  • The adapted UNRES force field and CSA procedure provide a robust framework for multi-chain protein modeling.
  • This advancement has implications for understanding protein complex formation and function.