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Related Concept Videos

Protein Folding01:22

Protein Folding

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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
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Physical Properties of Alkanes02:33

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Alkanes are nonpolar molecules due to the presence of only carbon and hydrogen atoms. The electronegativity difference between carbon and hydrogen is minimal, and hence alkanes have a zero dipole moment. This leads to the presence of only dispersion forces between the molecules. The strength of dispersion forces is dependent on the surface area of the molecules on which they act. Since the surface area increases with the molecular length for straight-chain alkanes, the dispersion forces also...
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The acidic strength of hydrocarbons follows the order: Alkynes > Alkenes > Alkanes. The strength of an acid is commonly expressed in units of pKa — the lower the pKa, the stronger the acid. Among the hydrocarbons, terminal alkynes have lower pKa values and are, therefore, more acidic. For example, the pKa values for ethane, ethene, and acetylene are 51, 44, and 25, respectively, as shown here.
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The protons in unsubstituted alkanes are strongly shielded with chemical shifts below 1.8 ppm. Methine, methylene, and methyl protons appear at approximately 1.7, 1.2 and 0.7 ppm, while the proton signal from methane appears at 0.23 ppm. An electronegative substituent, such as chlorine, withdraws the electron density from the protons, increasing their chemical shift. Progressive substitution of the hydrogens in methane by chlorine shifts the proton signals increasingly downfield, to 3.05 ppm in...
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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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How does a hydrocarbon staple affect peptide hydrophobicity?

Adelene Y L Sim1, Chandra Verma

  • 1Bioinformatics Institute (A*STAR), 30 Biopolis Street #07-01, Matrix, 138671, Singapore.

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|February 24, 2015
PubMed
Summary

Water molecules play a crucial role in protein complex formation. Modifying peptide interfaces with hydrophobic staples can stabilize water networks, influencing binding kinetics.

Keywords:
MDM2hydrationhydrophobicityp53stapled peptides

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Water is critical for protein folding and complex assembly.
  • The role of water at protein-protein/ligand interfaces is complex and depends on interface characteristics.

Purpose of the Study:

  • To investigate the dynamics of water in the interdomain region between MDM2 and p53-derived peptides.
  • To understand how peptide modifications, specifically hydrophobic stapling, affect water distribution and binding kinetics.

Main Methods:

  • Molecular dynamics simulations were employed to study water dynamics.
  • Analysis focused on interdomain water densities and hydrogen bonding networks.

Main Results:

  • Peptides exhibited bimodal water density distributions.
  • Hydrophobic stapling increased interface hydrophobicity and stabilized a water chain between peptide and MDM2.
  • This stabilization may lower the energy barrier for peptide binding.

Conclusions:

  • Water network stabilization by hydrophobic staples can kinetically regulate peptide-MDM2 binding.
  • Understanding water's role is key to designing peptides with specific binding properties.