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Related Concept Videos

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

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
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...

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Related Experiment Video

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Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Hydrodynamic interactions in protein folding.

Marek Cieplak1, Szymon Niewieczerzał

  • 1Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland. mc@ifpan.edu.pl

The Journal of Chemical Physics
|April 2, 2009
PubMed
Summary
This summary is machine-generated.

Hydrodynamic interactions (HIs) accelerate protein folding and HIV-1 protease flap closing dynamics in simulations. These interactions impact protein dynamics near the native state but not overall structure fluctuations.

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Area of Science:

  • Computational biophysics
  • Protein dynamics
  • Molecular modeling

Background:

  • Protein folding is crucial for biological function.
  • Understanding protein dynamics aids in drug design.
  • Hydrodynamic interactions influence molecular motion.

Purpose of the Study:

  • To investigate the role of hydrodynamic interactions (HIs) in protein folding and dynamics.
  • To analyze the effect of HIs on HIV-1 protease flap closing.
  • To assess the impact of HIs on protein structure fluctuations.

Main Methods:

  • Incorporation of Rotne-Prager hydrodynamic tensor into a coarse-grained, structure-based protein model.
  • Simulation studies on small proteins and HIV-1 protease.

Main Results:

  • Hydrodynamic interactions were shown to facilitate protein folding.
  • HIs accelerate the flap closing dynamics of HIV-1 protease.
  • HIs affect time correlation functions near the native state without altering same-time structure fluctuations.

Conclusions:

  • Hydrodynamic interactions play a significant role in accelerating protein folding and specific dynamic processes like HIV-1 protease flap closure.
  • The findings highlight the importance of including HIs in molecular simulations for accurate protein dynamics prediction.
  • HIs influence temporal aspects of protein dynamics near the native state.