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Related Concept Videos

Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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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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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Protein Folding01:22

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Atomic density distributions in proteins: structural and functional implications.

Sotirios Touliopoulos1, Nicholas M Glykos1

  • 1Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100, Alexandroupolis, Greece.

Journal of Molecular Graphics & Modelling
|November 22, 2025
PubMed
Summary

Atomic packing significantly impacts protein stability and function. This study analyzed 21,255 protein structures, revealing distinct packing groups and factors influencing atomic density, like protein size and type.

Keywords:
Clustering structuresHydrophobic corePacking densityProtein structureProtein structure/function relationships

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Atomic packing is crucial for protein structure, stability, evolution, and function.
  • Protein packing is not uniform, with denser cores and looser surfaces, and can be affected by internal cavities.
  • Existing methods for measuring protein packing quality have limitations.

Purpose of the Study:

  • To analyze atomic density distributions across a large dataset of protein structures.
  • To identify distinct groups of proteins based on their packing characteristics.
  • To investigate factors influencing atomic packing, including protein size, type, and stability indicators.

Main Methods:

  • Analysis of atomic density distributions from 21,255 non-redundant protein structures.
  • Inclusion of hydrogen atoms and solvation for in vitro representation.
  • Hierarchical clustering to group proteins with similar atomic density patterns.

Main Results:

  • Statistically significant differences in atomic density distributions were observed among protein structures.
  • Hierarchical clustering identified distinct groups, some associated with specific structures (coiled-coils, cytochromes) or classification families (hydrolases, transferases).
  • Larger proteins showed a narrower density range but were more loosely packed; packing density correlated with stability indicators like water molecules and B-factors.

Conclusions:

  • Protein structures exhibit diverse atomic packing behaviors beyond simple core-surface differences.
  • Specific structural motifs and protein families are associated with characteristic packing densities.
  • Atomic packing is intrinsically linked to protein size and stability, offering insights into protein biophysics.