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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
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.
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 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.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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Published on: July 25, 2013

Beta-sheet preferences from first principles.

Jan Rossmeisl1, Iben Kristensen, Misha Gregersen

  • 1Center for Atomic-scale Materials Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.

Journal of the American Chemical Society
|December 25, 2003
PubMed
Summary
This summary is machine-generated.

Amino acids show preferences for protein structures. Computational analysis reveals these beta-sheet propensities correlate with binding energies and local strand flexibility.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Natural amino acids exhibit distinct preferences for specific secondary protein structures.
  • Understanding these preferences is crucial for predicting protein folding and function.

Purpose of the Study:

  • To investigate the relationship between amino acid sequence and secondary structure preference.
  • To computationally determine the factors governing beta-sheet propensities.

Main Methods:

  • Density functional theory (DFT) calculations were employed.
  • Simulations were conducted on periodic model beta-sheets comprising 14 different amino acids.
  • The generalized gradient approximation (GGA) was used for electronic structure calculations.

Main Results:

  • A strong correlation was observed between statistically determined beta-sheet propensities and calculated binding energies.
  • Analysis indicated that local flexibility within individual polypeptide strands is a key determinant of beta-sheet propensities.

Conclusions:

  • The study provides a computational basis for understanding amino acid preferences in beta-sheet formation.
  • Local polypeptide flexibility emerges as a critical factor influencing secondary structure adoption.