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Related Concept Videos

Conformations of Butane02:20

Conformations of Butane

14.3K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
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Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

13.8K
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...
13.8K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

992
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...
992
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.2K
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...
6.2K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

12.2K
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
12.2K
Newman Projections02:06

Newman Projections

16.9K
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...
16.9K

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T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis
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Bimodal Peptide Collision Cross Section Distribution Reflects Two Stable Conformations in the Gas Phase.

Juan Restrepo1, Daniel Szoelloesi2, Tobias Kiermeyer1

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Ion mobility spectrometry (IMS) coupled with mass spectrometry reveals peptides adopt multiple conformations. A new two-valued predictor improves peptide identification rates in proteomics by accounting for these distinct peptide structures.

Keywords:
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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biophysical Chemistry

Background:

  • High-throughput shotgun proteomics benefits from coupling ion mobility spectrometry (IMS) to mass spectrometry.
  • IMS separates biomolecules based on size and shape, adding a crucial dimension.
  • Peptide collision cross section (CCS) distributions often exhibit bimodality, hindering current machine learning predictions.

Purpose of the Study:

  • To investigate the structural basis for bimodal CCS distributions in peptides.
  • To develop an improved CCS prediction method accounting for peptide conformational flexibility.
  • To enhance peptide identification rates in data-independent acquisition proteomics.

Main Methods:

  • Molecular dynamics simulations to model peptide behavior in IMS drift tubes.
  • Analysis of peptide CCS data using a geometric model.
  • Development and implementation of a novel two-valued CCS predictor.
  • Integration of the predictor into data-independent acquisition proteomics workflows.

Main Results:

  • Molecular dynamics simulations show peptides adopt stable extended (helical) and compact (globular) conformations.
  • Peptide conformation preference is often charge-dependent, with some peptides adapting to both states.
  • A two-valued CCS predictor was developed, accommodating multiple peptide conformations.
  • Integration of the two-valued predictor increased peptide identification rates compared to single-value predictors.

Conclusions:

  • Peptide conformational heterogeneity is a key factor influencing CCS measurements in IMS.
  • A two-valued CCS prediction approach effectively models peptide conformational flexibility.
  • The novel predictor enhances peptide identification in proteomics, improving data analysis accuracy.