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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.
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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
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Covering complete proteomes with X-ray structures: a current snapshot.

Marcin J Mizianty1, Xiao Fan1, Jing Yan1

  • 1Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada.

Acta Crystallographica. Section D, Biological Crystallography
|November 6, 2014
PubMed
Summary

X-ray crystallography and homology modeling can determine structures for 25% of protein families, covering all Gene Ontology functions. Knowledge-based selection enhances structure determination, with the human proteome showing high potential.

Keywords:
crystallization propensityfDETECTproteome coverage

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Area of Science:

  • Structural biology
  • Genomics
  • Biochemistry

Background:

  • Structural genomics programs utilize structure-determination pipelines to visualize macromolecular interactions and understand protein functions.
  • The feasibility of determining three-dimensional protein structures and functional annotations via X-ray crystallography remains a key question.

Purpose of the Study:

  • To investigate the potential of X-ray crystallography and homology modeling to determine structures for all proteins and functional annotations.
  • To analyze crystallization propensity across diverse proteomes and assess coverage of functional annotations.

Main Methods:

  • Large-scale analysis of crystallization propensity for proteins encoded in 1953 fully sequenced genomes.
  • Application of homology modeling to predict protein structures.
  • Evaluation of coverage for Gene Ontology functional annotations.

Main Results:

  • Current methods can provide structures for 25% of modeling families, ensuring at least one structural model per Gene Ontology annotation.
  • Coverage varies by superkingdom: 19% for eukaryotes, 35% for bacteria, and 49% for archaea.
  • Knowledge-based target selection significantly improves X-ray structure production, with the human proteome exhibiting high attainable coverage.

Conclusions:

  • X-ray crystallography, augmented by homology modeling and knowledge-based selection, offers substantial potential for structural and functional annotation of proteomes.
  • Distinct crystallization propensities exist across taxonomic superkingdoms.
  • The human proteome is amenable to high structural coverage, including important targets like GPCR membrane proteins.