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Related Concept Videos

Protein Folding01:22

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Protein Folding01:25

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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.
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Molecular Chaperones and Protein Folding03:00

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Related Experiment Video

Updated: May 27, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Current computer modeling cannot explain why two highly similar sequences fold into different structures.

Jane R Allison1, Maike Bergeler, Niels Hansen

  • 1Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland.

Biochemistry
|November 16, 2011
PubMed
Summary
This summary is machine-generated.

Understanding protein structure is complex. Minimally different protein sequences can fold into distinct structures, challenging the sequence-structure relationship. Computer modeling reveals interdependent factors govern protein stability.

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Last Updated: May 27, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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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

Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Two proteins with minimal sequence differences (few amino acids) fold into distinct, stable structures with different functions.
  • This presents a challenge to understanding how amino acid sequence dictates protein structure and stability.

Purpose of the Study:

  • To investigate the reasons behind differing structural preferences in highly similar protein sequences.
  • To characterize native protein structures and model sequences onto alternate folds using computer simulations.

Main Methods:

  • Utilized computer modeling to analyze native structures and alternative fold simulations.
  • Performed structure analyses and compared potential energies from energy-minimized structures.
  • Employed molecular dynamics simulations and a novel free energy difference calculation method.
  • Assessed the sensitivity of analyses to different computational force fields.

Main Results:

  • Computer modeling characterized native structures and explored sequence-structure interactions.
  • Analyses supported hypotheses derived from nuclear magnetic resonance (NMR) data for 95% identical sequences.
  • Different analytical levels yielded varying predictions for favored sequence-structure combinations.

Conclusions:

  • Protein structure and stability arise from a complex interplay of interdependent factors.
  • The relationship between amino acid sequence and protein structure is not straightforward.
  • Computational approaches provide unique insights into protein folding and stability mechanisms.