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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Mismatch Repair01:36

Mismatch Repair

Overview
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Protein Folding01:22

Protein Folding

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Related Experiment Video

Updated: Jun 13, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Residue patterning in helix interiors.

Brent Wathen1, Zongchao Jia

  • 1Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6, Canada.

Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire
|May 11, 2010
PubMed
Summary

Alpha-helix structure and stability are key to protein folding. New analysis reveals non-amphipathic patterns and neighbor preferences, suggesting hydrophobicity

Area of Science:

  • Protein Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Alpha-helices are crucial for protein folding and structure.
  • Fundamental properties governing helix formation and stability remain unclear despite extensive research.
  • Existing studies often focus on amphipathic distributions and thermodynamic/evolutionary factors.

Purpose of the Study:

  • To investigate statistical patterns of polar and apolar residue distribution within helical interiors.
  • To compare these patterns with those in other protein structural environments.
  • To explore the role of residue neighbors and hydrophobicity in helix formation.

Main Methods:

  • Statistical analysis of residue patterning in a large, non-redundant dataset of alpha-helices.

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Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins

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  • Comparison of helical interior patterns with other structural contexts.
  • Analysis of immediate (i, i+1) helical neighbor interactions and correlations.

    • Main Results:

    • Identified significant differences in polar and apolar residue distributions compared to familiar amphipathic patterns.
    • Observed non-amphipathic signals within residue distributions.
    • Found clear neighboring preferences (e.g., hydrophobics near Gly, Pro) and a negative correlation between residue propensity and neighboring hydrophobicity, suggesting inherent helix directionality.

    Conclusions:

    • Neighboring residue preferences and hydrophobicity correlations challenge simple thermodynamic or evolutionary explanations based on tertiary interactions.
    • The observed patterns suggest that the mechanism of helix formation itself may play a significant role.
    • Hydrophobicity's influence on alpha-helix formation might be more critical than currently appreciated.