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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
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

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Unsymmetric Bending01:18

Unsymmetric Bending

Unsymmetrical bending occurs when the bending moment applied to a structural member does not align with its principal axis. This misalignment leads to complex stress distributions and deflection patterns that differ from those in symmetrical bending, and are essential for designing structures to withstand different loading conditions. In unsymmetrical bending, the neutral axis—where stress is zero—does not necessarily align with the geometric axes of the cross-section. The orientation of the...
Mechanisms of Membrane-bending01:15

Mechanisms of Membrane-bending

The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
Membrane bending can happen due to intrinsic changes in lipid composition or extrinsic association with different proteins. The proteins involved...
Deformations in a Symmetric Member in Bending01:18

Deformations in a Symmetric Member in Bending

When analyzing the deformation of a symmetric prismatic member subjected to bending by equal and opposite couples, it becomes clear that as the member bends, the originally straight lines on its wider faces curve into circular arcs, with a constant radius centered at a point known as Point C. This phenomenon helps to understand the stress and strain distribution within the member more clearly.
When the member is segmented into tiny cubic elements, it is observed that the primary stress...

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Folding and Characterization of a Bio-responsive Robot from DNA Origami
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Closed loop folding units from structural alignments: experimental foldons revisited.

Sree V Chintapalli1, Boon K Yew, Christopher J R Illingworth

  • 1Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom.

Journal of Computational Chemistry
|September 15, 2010
PubMed
Summary
This summary is machine-generated.

Short, non-overlapping closed loops are key protein structures that fold rapidly, avoiding the Leventhal paradox. This study identifies these crucial protein folding units using structural alignment, confirming their significance.

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Area of Science:

  • Protein structure and folding dynamics
  • Structural bioinformatics
  • Biophysics

Background:

  • Non-overlapping closed loops (25-35 amino acids) formed by nonlocal interactions are hypothesized as fundamental protein structure units.
  • These units could explain rapid protein folding and the nature of the folding funnel, bypassing the Leventhal paradox.
  • Previous identification relied on sequence analysis or individual protein geometry.

Purpose of the Study:

  • To explore a novel strategy for identifying closed loops using structural alignment of proteins.
  • To validate this new method against existing closed loop data and experimental findings.

Main Methods:

  • Structural alignment of 37 protein pairs to identify insertions.
  • Analysis of these insertions to determine the locations of closed loops.
  • Comparison with previously identified closed loops and experimental data (hydrogen exchange, proton-alkyl exchange).

Main Results:

  • Successfully determined closed loop locations in 37 protein pairs with excellent agreement to prior studies.
  • Demonstrated a strong correspondence between theoretically derived closed loops and experimentally determined foldons in specific proteins (cytochrome c, cytochrome b562, triosephosphate isomerase).

Conclusions:

  • The proposed method for identifying closed loops via structural alignment is effective and validated.
  • The closed loop hypothesis provides a useful framework for interpreting experimental data on protein folding units (foldons).
  • This research offers insights into protein folding mechanisms and the fundamental units of protein structure.