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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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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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Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
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Structure based sequence analysis of viral and cellular protein assemblies.

Daniel J Montiel-García1, Ranjan V Mannige2, Vijay S Reddy2

  • 1Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico.

Journal of Structural Biology
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Summary
This summary is machine-generated.

Protein structure conservation varies by region, with buried core residues being most stable. Virus capsid proteins and cellular proteins represent structural extremes, with some viruses showing slower evolution.

Keywords:
BioinformaticsProtein complexesProtein-protein interactionsSequence conservationSubunit interfaceViral capsid proteins

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Area of Science:

  • Structural biology
  • Biophysics
  • Molecular evolution

Background:

  • Protein structural similarity generally correlates with amino acid sequence identity.
  • Understanding residue conservation is key to deciphering protein function and evolution.

Purpose of the Study:

  • To analyze the correlation and variation of conserved residues across different protein structural regions.
  • To compare conservation patterns between cellular complex-forming proteins and viral capsid proteins.
  • To investigate the evolutionary rates of different protein complexes.

Main Methods:

  • Analysis of high-resolution structural data for 5245 cellular proteins and 293 viral capsid proteins.
  • Categorization of proteins based on structural regions (core, interface, surface).
  • Statistical analysis to compare conservation levels and evolutionary rates.

Main Results:

  • Buried core residues exhibit the highest conservation, followed by protein-protein interface residues.
  • Solvent-exposed surface residues show greater sequence variation.
  • Cellular monomers and viral capsid proteins represent extremes in quaternary structural space, with other complexes in between.
  • A subset of icosahedral virus families displays significantly slower evolution in their capsid proteins.

Conclusions:

  • Residue conservation is spatially regulated within protein structures, reflecting functional and evolutionary constraints.
  • Viral capsid proteins and cellular protein complexes occupy distinct positions in the structural and evolutionary landscape.
  • Specific viral families exhibit unique, slower evolutionary trajectories for their capsid proteins.