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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Organization01:13

Protein Organization

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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Related Experiment Video

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Relation between native ensembles and experimental structures of proteins.

Robert B Best1, Kresten Lindorff-Larsen, Mark A DePristo

  • 1Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom. best@helix.nih.gov

Proceedings of the National Academy of Sciences of the United States of America
|July 11, 2006
PubMed
Summary

High-sequence similarity Protein Data Bank (HSP) ensembles accurately represent protein structural heterogeneity in solution. These ensembles effectively capture native-state protein dynamics, crucial for interpreting experimental data.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Proteins exhibit structural variations even in similar sequences or experimental structures.
  • Understanding native-state structural heterogeneity is key to interpreting protein function and dynamics.

Purpose of the Study:

  • To assess if high-sequence similarity Protein Data Bank (HSP) ensembles represent native-state structural heterogeneity in solution.
  • To evaluate the ability of HSP ensembles to reproduce experimental data from Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Methods:

  • Construction of HSP ensembles from existing structural data.
  • Comparison of HSP ensemble predictions with experimental NMR measurements (order parameters, scalar couplings, residual dipolar couplings).

Main Results:

  • HSP ensembles remarkably reproduce various NMR measurements probing protein structure and dynamics in solution.
  • The observed agreement is not attributable to uncertainties in structure determination alone.
  • Even a small number of structures under varied conditions or with sequence variations capture a representative subset of the native-state ensemble.

Conclusions:

  • Native-state protein dynamics are essential for accurate comparisons with ensemble-averaged experimental data.
  • HSP ensembles are valuable tools for representing and studying protein structural heterogeneity and dynamics.
  • The study underscores the importance of considering dynamic structural ensembles in biophysical research.