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Related Concept Videos

Phosphorylation01:02

Phosphorylation

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The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
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Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
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Conjugated Proteins02:50

Conjugated Proteins

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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.
Nucleoproteins are protein complexes that contain nucleic acids, categorized as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs) respectively. The nucleosome is a typical example of a DNP where nuclear DNA is associated with histone proteins. The major antigen for the Covid-19 virus SARS-CoV is an RNP that is critical...
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Leaky Scanning02:28

Leaky Scanning

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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...
5.0K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

6.7K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
6.7K
Nucleic Acid Structure01:25

Nucleic Acid Structure

5.9K
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.
DNA Structure
DNA...
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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
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Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.

Stefan Loonen1, Lina van Steenis1, Marianne Bauer1

  • 1Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands.

Proteins
|May 16, 2025
PubMed
Summary

Phosphorylation of the SARS-CoV-2 nucleocapsid protein (N-protein) increases its structural dynamics and reduces RNA binding. This suggests phosphorylation regulates N-protein function in the viral life cycle.

Keywords:
SARS‐CoV‐2intrinsically disordered proteinsmolecular dynamicsnucleocapsid proteinphosphorylationprotein–nucleic acid interactions

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Area of Science:

  • Molecular virology
  • Structural biology
  • Biophysics

Background:

  • The SARS-CoV-2 nucleocapsid protein (N-protein) is crucial for viral RNA replication and packaging.
  • The N-protein's phosphorylation state is hypothesized to regulate its distinct functions.
  • Understanding N-protein dynamics and RNA interactions is key to deciphering viral mechanisms.

Purpose of the Study:

  • To investigate the dynamic behavior of non-phosphorylated and phosphorylated N-protein homodimers.
  • To elucidate the impact of phosphorylation on N-protein:RNA binding affinity.
  • To explore the role of secondary structure in N-protein's interaction with viral RNA.

Main Methods:

  • Atomistic molecular dynamics simulations were employed to model N-protein behavior.
  • Comparative analysis of phosphorylated versus non-phosphorylated N-protein homodimers.
  • Assessment of N-protein:RNA interactions, focusing on the 5' UTR.

Main Results:

  • Phosphorylation significantly increases the dynamic flexibility of the N-protein structure.
  • Binding affinity between the N-protein and RNA is reduced upon phosphorylation.
  • Secondary structure elements are critical for specific RNA element binding to the N-terminal domain.

Conclusions:

  • Phosphorylation acts as a regulatory switch, modulating N-protein dynamics and function.
  • Altered N-protein dynamics and reduced RNA binding affinity support its role in regulating viral processes.
  • Detailed molecular insights confirm phosphorylation's importance in SARS-CoV-2 N-protein regulation.