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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

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...
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...
Thermal Sigmatropic Reactions: Overview01:16

Thermal Sigmatropic Reactions: Overview

Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in 1,5-hexadiene, referred to as...
Translocation of Proteins into the Mitochondria01:19

Translocation of Proteins into the Mitochondria

Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Jun 16, 2026

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Published on: June 20, 2014

Interpolation schemes for peptide rearrangements.

Marianne S Bauer1, Birgit Strodel, Szilard N Fejer

  • 1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

The Journal of Chemical Physics
|February 9, 2010
PubMed
Summary
This summary is machine-generated.

This study compares seven coordinate systems for polypeptide rearrangement, finding that aligning methylene hydrogens by dihedral angle sign improves connection success and speed. Natural internal coordinates with internal alignment offer superior performance in molecular modeling.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biophysics

Background:

  • Polypeptide rearrangements are crucial in molecular dynamics simulations.
  • Efficient interpolation and alignment methods are needed for accurate simulations.
  • Existing methods using Cartesian or internal coordinates have limitations.

Purpose of the Study:

  • To evaluate seven different coordinate systems for interpolation and alignment in polypeptide rearrangement.
  • To identify optimal methods for improving connection times and reducing failures in molecular simulations.
  • To compare the performance of Cartesian, CHARMM internal, and natural internal coordinates.

Main Methods:

  • Tested seven combinations of internal and Cartesian coordinates for interpolation and alignment.
  • Interfaced coordinate systems with the OPTIM code for united-atom force fields.
  • Compared alignment strategies focusing on dihedral angle sign versus distance minimization.

Main Results:

  • Aligning methylene hydrogens by preserving the local dihedral angle sign significantly improved connection times and reduced failures.
  • Natural internal coordinate methods demonstrated superiority when used with internal alignment.
  • Utilizing potential energy checks for interpolated structures further reduced failures and connection times.

Conclusions:

  • The choice of coordinate system and alignment strategy critically impacts the efficiency of polypeptide rearrangement simulations.
  • Preserving dihedral angle signs and employing natural internal coordinates are key improvements.
  • Potential energy evaluation serves as an effective criterion for selecting interpolation coordinate systems.