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Related Concept Videos

Insertion of Single-pass Transmembrane Proteins in the RER01:26

Insertion of Single-pass Transmembrane Proteins in the RER

Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
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Conservation of Protein Domains Over Different Proteins

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Ribozymes02:47

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Protein Modifications in the RER01:26

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Bioinformatics perspective on rhomboid intramembrane protease evolution and function.

Lisa N Kinch1, Nick V Grishin

  • 1Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Biochimica Et Biophysica Acta
|July 13, 2013
PubMed
Summary
This summary is machine-generated.

Rhomboid proteases, a diverse group of intramembrane serine proteases, have established structures and mechanisms but unknown cellular roles and substrates. Evolutionary analysis aids in understanding their function and identifying potential targets.

Keywords:
BioinformaticsClassificationEvolutionIntramembrane proteolysisRhomboid proteaseStructure

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Area of Science:

  • Biochemistry
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Endopeptidase classification aids proteolytic enzyme studies.
  • Serine endopeptidases, including soluble chemotrypsins and subtilisins, are abundant and diverse.
  • Rhomboid proteases are polytopic transmembrane proteins utilizing the serine protease mechanism.

Purpose of the Study:

  • To explore the cellular roles and natural substrates of rhomboid proteases.
  • To clarify the evolutionary history and relationships among rhomboid proteases.
  • To bridge the knowledge gap between rhomboid protease biochemical functions and cellular roles.

Main Methods:

  • Classification of endopeptidases based on catalytic mechanism and evolutionary history.
  • Analysis of spatial structure, mechanism, and biochemical function of rhomboid proteases.
  • Phylogenetic profile analysis to identify co-occurring protein motifs and potential substrates.

Main Results:

  • The serine protease mechanism has evolved independently multiple times.
  • The structure, mechanism, and function of rhomboid proteases as intramembrane proteases are established.
  • Phylogenetic analysis identified a C-terminal processing motif (GlyGly-Cterm) co-occurring with bacterial rhomboid proteases.

Conclusions:

  • Understanding rhomboid protease evolution provides insights into their cellular functions.
  • Evolutionary relationships can guide experimental investigations into rhomboid proteases.
  • Bioinformatic approaches, like phylogenetic profile analysis, can aid in identifying novel substrates and functions for rhomboid proteases.