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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

86.3K
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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Protein Folding01:25

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
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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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Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

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In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.8K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.8K

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An Inexpensive Adaptation of a Commercial Microwave Reactor for Solid Phase Peptide Synthesis
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An Inexpensive Adaptation of a Commercial Microwave Reactor for Solid Phase Peptide Synthesis

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Peptide Bond Isomerization in High-Temperature Simulations.

Chris Neale1, Régis Pomès2,3, Angel E García1

  • 1Center for NonLinear Studies (CNLS), MS B258, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

Journal of Chemical Theory and Computation
|February 12, 2016
PubMed
Summary
This summary is machine-generated.

High-temperature molecular simulations reveal that common protein force fields allow rapid peptide bond isomerization and even atom inversion, challenging their accuracy beyond design specifications. Further validation is needed for these widely used computational tools.

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Area of Science:

  • Computational chemistry and biophysics
  • Molecular dynamics simulations
  • Protein structure and dynamics

Background:

  • Macromolecular force fields are typically optimized for ambient conditions.
  • Elevated temperatures are often used in simulations to improve sampling.
  • This practice pushes force fields beyond their intended design parameters.

Purpose of the Study:

  • To evaluate the performance of classical atomistic force fields at high temperatures.
  • To quantify peptide bond isomerization rates in various peptides and a protein.
  • To assess the accuracy of force fields for simulating extreme conditions.

Main Methods:

  • High-temperature molecular dynamics simulations of three octameric peptides and a small protein.
  • Analysis of cis/trans peptide bond isomerization rates.
  • Investigation of chiral inversion at the Cα atom.
  • Use of temperature replica exchange for sampling.

Main Results:

  • Peptide octamers showed cis/trans isomerization every 1-5 ns at 800 K with AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L force fields.
  • Isomerization of nonprolyl peptide bonds occurred at ≥500 K, and prolyl peptide bonds at ≥400 K.
  • OPLS-AA/L force field exhibited Cα chiral inversion at 800 K.
  • Temperature replica exchange allowed cis peptide bonds formed at 540 K to return to the 300 K ensemble.

Conclusions:

  • Current protein force fields may not accurately represent high-temperature dynamics, including peptide bond isomerization and chiral inversion.
  • The observed phenomena challenge the reliability of these force fields for simulations exceeding their design specifications.
  • Further research is necessary to validate and potentially refine force fields for high-temperature molecular simulations.