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Related Concept Videos

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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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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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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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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Automated Robotic Liquid Handling Assembly of Modular DNA Devices
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Biological Assembly Comparison with VAST.

Thomas Madej1, Aron Marchler-Bauer2, Christopher Lanczycki2

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. madej@ncbi.nlm.nih.gov.

Methods in Molecular Biology (Clifton, N.J.)
|February 2, 2020
PubMed
Summary
This summary is machine-generated.

The VAST+ algorithm efficiently compares biological assembly structures by clustering protein alignments. This method refines alignments to reveal conformational differences in protein, RNA, and DNA molecules.

Keywords:
Molecular assemblyProtein complexSecondary structure elementStructure alignmentStructure comparison

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Comparing atomic structures of biological assemblies is crucial for understanding their function.
  • Existing methods may lack efficiency or simplicity in handling complex assemblies.

Purpose of the Study:

  • To introduce the VAST+ algorithm as an efficient and simple solution for comparing biological assembly structures.
  • To enable the detection of biologically relevant conformational differences.

Main Methods:

  • Input: Pairwise structural alignments of component proteins within two assemblies.
  • Clustering of rotation matrices from pairwise superpositions to identify alignable subsets.
  • Optional Monte Carlo refinement of alignments to detect conformational variations.

Main Results:

  • VAST+ provides a robust method for comparing protein, RNA, and DNA assemblies.
  • The algorithm effectively clusters structural alignments, identifying potentially superposable regions.
  • Refinement step aids in observing conformational differences.

Conclusions:

  • VAST+ offers an efficient, simple, and extensible approach to structural comparison of biological assemblies.
  • The algorithm facilitates the identification of conformational changes relevant to biological function.