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Related Concept Videos

Viral Structure00:56

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Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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Size and Structure of Viral Genomes01:26

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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with non-protein moieties.
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The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This...
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Coronaviruses spike glycoprotein endodomains: The sequence and structure-based comprehensive study.

Prateek Kumar1, Aparna Bhardwaj1, Bodhidipra Mukherjee1

  • 1School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India.

Protein Science : a Publication of the Protein Society
|October 13, 2023
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Summary

Viral protein flexibility aids function. This study analyzes coronavirus spike protein endodomains, revealing varying disorder, crucial for understanding pathogenicity and developing therapeutics.

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coronavirusesintrinsic disorder regions (IDRs)molecular dynamics simulationsmolecular recognition features (MoRFs)post-translational modifications

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Area of Science:

  • Virology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein flexibility enables interactions with biomolecules, essential for viral functions despite small genomes.
  • Flexible regions in viral proteins are key targets for understanding pathogenicity and developing therapeutics.
  • Previous work analyzed the disordered regions of the SARS-CoV-2 spike protein's cytoplasmic tail (CTR).

Purpose of the Study:

  • To investigate the disordered potential of the endodomain in the spike proteins of six additional coronaviruses.
  • To compare the disorder propensity across different coronavirus spike protein endodomains.
  • To identify potential therapeutic targets within these flexible viral regions.

Main Methods:

  • Bioinformatics approaches for sequence and structural analysis.
  • Molecular dynamics simulations.
  • Comparative analysis of endodomain disorder propensity.

Main Results:

  • Significant variations in disorder propensity were observed in the endodomains of spike proteins across different coronaviruses.
  • The sequence and structural composition contribute to the differing disorder levels.
  • Identified flexible regions with potential roles in viral interactions and pathogenicity.

Conclusions:

  • The spike protein endodomain's disorder is a conserved yet variable feature across coronaviruses.
  • Understanding these disordered regions is vital for elucidating viral mechanisms.
  • These findings offer insights for developing targeted therapeutic interventions against coronaviruses.