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Related Concept Videos

Habitat Fragmentation02:31

Habitat Fragmentation

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Habitat fragmentation describes the division of a more extensive, continuous habitat into smaller, discontinuous areas. Human activities such as land conversion, as well as slower geological processes leading to changes in the physical environment, are the two leading causes of habitat fragmentation. The fragmentation process typically follows the same steps: perforation, dissection, fragmentation, shrinkage, and attrition.
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Mass Spectrometry: Alkene Fragmentation00:59

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Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
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Mass Spectrometry: Cycloalkane Fragmentation01:05

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In mass spectrometry, cycloalkanes exhibit distinct fragmentation patterns due to the inherent stability of their molecular ions compared to linear or branched alkanes. The ring structure of cycloalkanes provides additional stability to the molecular ions, often resulting in prominent ion peaks in the mass spectrum.
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Mass Spectrometry: Cycloalkene Fragmentation00:54

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The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels–Alder reaction.
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Mass Spectrometry: Alkyne Fragmentation00:53

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The fragmentation of alkynes preferentially occurs at the carbon–carbon bond between the α and β carbon of the alkyne bond to generate a 3-propynyl cation (or propargyl cation). In terminal alkynes, there is the only type of fragmentation that yields the 3-propynyl cation. The unsubstituted 3-propynyl cation exhibits a peak at a mass-to-charge ratio of 39. In internal alkynes, the 3-propynyl cation is substituted. For example, 2-pentyne fragments into methyl-substituted 3-propynyl cation,...
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Mass Spectrometry: Alcohol Fragmentation01:03

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Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. ⍺-cleavage and dehydration. During ⍺-cleavage, the bond at the ⍺-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular...
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Bacterial Inner-membrane Display for Screening a Library of Antibody Fragments
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Supersecondary Structures and Fragment Libraries.

Raphael Trevizani1, Fábio Lima Custódio2

  • 1Fiocruz-Fundação Oswaldo Cruz, Eusébio, Brazil. raphael.trevizani@fiocruz.br.

Methods in Molecular Biology (Clifton, N.J.)
|April 5, 2019
PubMed
Summary

Profrager is a new tool that generates protein structural fragments to improve protein models. It helps create better models by simplifying and increasing the quality of local protein motifs.

Keywords:
Fragment libraryProtein motifsProtein structure predictionSmotifsSupersecondary structures

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein modeling

Background:

  • Protein structure modeling is crucial for understanding protein function.
  • Existing methods for generating protein models can be complex and time-consuming.
  • Motifs and fragment libraries are valuable for improving model quality and simplification.

Purpose of the Study:

  • To present Profrager, a novel tool for automated generation of protein structural fragments.
  • To enable the reproduction of local protein motifs from a target sequence.
  • To offer a customizable solution for enhancing protein modeling workflows.

Main Methods:

  • Profrager automatically generates putative structural fragments based on a target protein sequence.
  • The tool allows users to customize fragment library size and fragment ranking methods.
  • It supports the generation of fragments of various sizes and can exclusively output small motifs (smotifs).

Main Results:

  • Profrager successfully generates structural fragments that can reproduce local protein motifs.
  • The tool's customization options provide flexibility for different modeling needs.
  • The ability to output smotifs offers a specialized approach for certain applications.

Conclusions:

  • Profrager is an effective tool for simplifying and enhancing the quality of protein models.
  • The automated generation of structural fragments aids in reproducible and efficient protein structure prediction.
  • Profrager's features, including smotif output, contribute to advancing computational protein design and analysis.