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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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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Globular Proteins01:27

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In organisms, proteins are the most abundant macromolecules. They act as the building blocks of life and play various crucial roles in the body. Proteins can be broadly classified into two distinct subtypes based on their shape and solubilities: globular proteins and fibrous proteins.
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Protein Complex Assembly02:41

Protein Complex Assembly

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Updated: Jul 27, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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Establishing comprehensive quaternary structural proteomes from genome sequence.

Edward Alexander Catoiu1, Nathan Mih1, Maxwell Lu2

  • 1Department of Bioengineering, University of California, San Diego, La Jolla, CA 92101.

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Summary
This summary is machine-generated.

This study introduces a computational platform to map the structural proteome of organisms, revealing protein structures and variations at angstrom-level precision for a deeper understanding of cellular functions.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Genomics

Background:

  • Recent advances in protein microscopy, modeling, and genomic data have enabled new computational approaches.
  • Understanding the structural proteome is crucial for deciphering cellular functions.

Approach:

  • Developed a computational platform to compute the oligomeric structural proteome from genomic data.
  • Mapped multi-strain alleleomic variation to define species-level structural proteomes.
  • Calculated precise 3D protein orientations within subcellular compartments.

Key Points:

  • Computed the complete quaternary structural proteome for E. coli K-12 MG1655.
  • Identified consequential mutations using structure-guided analyses.
  • Integrated with genome-scale models for a draft 3D visualization of the proteome in a functioning cell.

Conclusions:

  • The platform resolves genome-scale structural proteomes with angstrom-level precision.
  • Enables a comprehensive understanding of whole-cell functions through integrated computational and genomic data.