Tuesday, 7 June 2011

Cytochrome bc1 Complex (Ubiquinol Ferricytochrome C Oxidoreductase)

Cytochrome bc1 Facts:
  • Is a ubiquinol:ferricytochrome c oxidoreductase.
  • Cytochrome bc1 is a dimeric protein.
  • Each half of the dimer protein is composed of 11 protein chains as well as cofactors.
  • The cofactors include hemes & an iron-sulfur cluster.
  • The complex binds to ubiquinol, found in the inner mitochondrial membrane.
  • Cytochrome bc1's connection to cytochrome c passes through an iron-sulfur cluster & then to heme.
  • Is found in mitochondria, photosynthetic bacteria & other prokaryotes
Tags: Cytochrome BC1 - Cytochrome C - Dimeric Protein - Heme - Mitochondria - Oxidoreductase - Prokaryote - Ubiquinol
Posted by Medicalchemy
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Saturday, 4 December 2010

Shotgun Proteomics

Shotgun Proteomics General Details:
  • "'Shotgun proteomics' refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture." (Wu et al, 2002)
  • The approach is enhanced by the use of multidimensional protein identification technology (MudPIT).
  • MudPIT uses multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) & database-searching algorithms.
  • Various algorithms can be used to increase the rate of confident peptide identifications, i.e. Percolator algorithm. (Käll L et al, 2007)
  • Shotgun proteomics can also aid discovery of novel protein-coding genes, alternative splicing, & “resurrected” pseudogenes. (Florens & Washburn, 2006)

References:
  • Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T (2011). Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Res. 2011. 21: 756-767 [Full Text]
  • Ding Y, Choi H, Nesvizhskii A. 2008. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res 7: 4878–4889.
  • Florens L, Washburn MP. 2006. Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol. 2006;328:159-75.
  • Käll L, Canterbury J, Weston J, Noble W, MacCoss M. 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4: 923–925.
  • Wu CC, MacCoss MJ. 2002. Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Ther. 2002 Jun;4(3):242-50.

Tags: Algorithm - Database Searching - HPLC - MudPIT - Proteomics - Shotgun Proteomics - Tandem Mass Spectrometry
Posted by Medicalchemy
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Proteomics - The Study Of Proteins, Particularly Structure and Function


Proteomics - General Facts:
  • The term "Proteome" comes from the blending of the words "Protein" & "Genome".
  • An organism's proteome consists of it's entire complement of proteins.
  • Proteomics deals with the large-scale study of proteins, especially structure & functions.
  • After genomics, proteomics is considered the next essential area of study to facilitate the understanding of biological systems.
Proteomics - History:
  • The term "proteomics" was first coined by Marc Wilkins in 1994, whilst a PhD student.[1]
Proteomics - Study Approaches:
  • See Table.
  • Broad-based approach - understand proteome as a whole.
  • Focused approach - understand specific protein information.
Post-translational Modification Of Proteins:
  • Acetylation
  • Glycosylation
  • Methylation
  • Nitrosylation
  • Oxidation
  • Phosphorylation
  • Ubiquitination
References:
[1] - UNSW Staff Bio: Professor Marc Wilkins (link)

Image: Table showing pros & cons of broad-based vrs focused approach to proteomics.
Image Credit: By Mccrearym on Wikipedia (public domain)
Tags: Acetylation - Genome - Genomics - Glycosylation - Methylation - Nitrosylation - Oxidation - Phosphorylation - Protein - Proteomics - Ubiquitination
Posted by Medicalchemy
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