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Peptide Bonds02:43

Peptide Bonds

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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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The Equilibrium Binding Constant and Binding Strength02:18

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Related Experiment Video

Updated: Mar 30, 2026

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
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Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

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A Basis Set for Peptides for the Variational Approach to Conformational Kinetics.

F Vitalini1, F Noé2, B G Keller1

  • 1Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin , Takustraße 3, D-14195 Berlin, Germany.

Journal of Chemical Theory and Computation
|November 18, 2015
PubMed
Summary
This summary is machine-generated.

This study introduces a new basis set for peptides, improving kinetic modeling by controlling discretization error. This method allows direct interpretation of slow kinetic modes and quantifies conformational changes.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Dynamics

Background:

  • Markov state models (MSMs) are vital for analyzing biomolecular kinetics.
  • Discretizing conformational space in MSMs presents a significant challenge.
  • A variational approach using basis functions offers systematic control over discretization error.

Purpose of the Study:

  • To develop and validate a peptide-specific basis set for variational kinetic modeling.
  • To enable systematic control of discretization error in peptide conformational dynamics.
  • To provide direct interpretation of slow kinetic modes without additional clustering.

Main Methods:

  • Constructed a basis set from local, residue-centered kinetic modes of amino acids.
  • Applied the basis set to model conformational kinetics of two hexapeptides (VGLAPG and VGVAPG).
  • Utilized variational approach with basis functions instead of discrete states.

Main Results:

  • Six basis functions effectively captured the slow kinetic modes of the studied hexapeptides.
  • The basis set facilitated direct interpretation of slow kinetic modes.
  • Conformational kinetic differences between leucine and valine substitutions were quantifiable.

Conclusions:

  • The developed basis set enhances variational kinetic modeling for peptides.
  • This approach offers improved accuracy and interpretability in biomolecular kinetics.
  • It provides a quantitative method to study sequence-dependent kinetic variations.