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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Conjugated Proteins02:50

Conjugated Proteins

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Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with non-protein moieties.
Nucleoproteins are protein complexes that contain nucleic acids, categorized as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs) respectively. The nucleosome is a typical example of a DNP where nuclear DNA is associated with histone proteins. The major antigen for the Covid-19 virus SARS-CoV is an RNP that is critical...
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Conjugated Proteins02:50

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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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Conservation of Protein Domains02:26

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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PepShell: visualization of conformational proteomics data.

Elien Vandermarliere1,2, Davy Maddelein1,2, Niels Hulstaert1,2

  • 1†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.

Journal of Proteome Research
|March 3, 2015
PubMed
Summary
This summary is machine-generated.

PepShell simplifies analyzing mass spectrometry data for protein dynamics. This tool visualizes peptide changes, aiding structural biology research into protein conformational changes.

Keywords:
Comparison of peptidesPepShellconformational proteomicsprotein structurevisualization of peptides

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Area of Science:

  • Structural biology
  • Proteomics
  • Biochemistry

Background:

  • Proteins are dynamic molecules exhibiting conformational changes crucial for function.
  • Conventional structural biology methods often fail to capture protein dynamics.
  • Mass spectrometry (MS)-based approaches like limited proteolysis and hydrogen-deuterium exchange are used to study protein dynamics, but data interpretation is challenging.

Purpose of the Study:

  • To present PepShell, an interactive tool for analyzing MS-based conformational proteomics data.
  • To enable visualization of identified peptides at both sequence and structure levels.
  • To facilitate comparison of protein dynamics under various experimental conditions.

Main Methods:

  • Development of PepShell software for data analysis.
  • Utilizing mass spectrometry-based techniques (limited proteolysis, hydrogen-deuterium exchange, stable-isotope labeling).
  • Interactive visualization of peptide data and structural information.

Main Results:

  • PepShell provides interactive visualization of MS-based conformational proteomics data.
  • The tool allows for detailed analysis of identified peptides, integrating sequence and structural information.
  • PepShell enables effective comparison of experimental conditions, such as varying proteolysis times or substrate/inhibitor binding.

Conclusions:

  • PepShell offers a streamlined approach to interpreting complex MS data in conformational proteomics.
  • The tool enhances the characterization of protein dynamics and conformational changes.
  • PepShell facilitates a deeper understanding of protein function by integrating structural and dynamic information.