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Related Concept Videos

Protein Denaturation01:28

Protein Denaturation

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The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...
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Protein Folding01:22

Protein Folding

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Overview
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Protein Folding01:25

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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.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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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...
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Force and Potential Energy in One Dimension01:13

Force and Potential Energy in One Dimension

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Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
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Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
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Related Experiment Video

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Ensemble Force Spectroscopy by Shear Forces
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Ensemble Force Spectroscopy by Shear Forces

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How force unfolding differs from chemical denaturation.

Guillaume Stirnemann1, Seung-gu Kang, Ruhong Zhou

  • 1Chemistry Department, Columbia University, New York, NY 10027.

Proceedings of the National Academy of Sciences of the United States of America
|February 20, 2014
PubMed
Summary

Single-molecule force spectroscopy reveals distinct protein unfolding pathways compared to chemical denaturation. Force unfolds proteins into extended states, while chemical denaturants leave residual structures and nonnative contacts.

Keywords:
atomic force microscopymolecular dynamics simulationsworm-like chain model

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Single-molecule force spectroscopy probes protein folding/unfolding dynamics.
  • Force-induced unfolding explores configurations distinct from chemical/thermal denaturation.
  • Understanding these differences is crucial for interpreting folding mechanisms and kinetics.

Purpose of the Study:

  • To compare chemically induced and force-induced unfolded state ensembles of ubiquitin.
  • To elucidate differences in protein configurations, secondary structure, and dihedral angle distributions.

Main Methods:

  • Extensive all-atom molecular dynamics simulations.
  • Simulating ubiquitin unfolding via applied force and urea denaturation.
  • Analysis of macromolecular structure, residual secondary structure, and backbone dihedral angles.

Main Results:

  • Force-unfolded ubiquitin is fully extended with no contacts; urea-denatured ubiquitin shows partial extension with nonnative contacts.
  • Significant alpha-helices present in urea-denatured states, absent in force-unfolded states (except transiently at 30 pN).
  • Striking differences observed in backbone dihedral angle distributions between force and chemically unfolded states.

Conclusions:

  • Unfolded protein ensembles differ significantly depending on the unfolding method (force vs. chemical).
  • Force unfolding limits secondary structure formation and leads to distinct dihedral angle distributions.
  • A simple peptide model explains these differences and the worm-like chain behavior under force.