Protein packed
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These studies suggest that protein packing is influenced by factors such as protein size, secondary structure, amino acid composition, and the precise packing of nonpolar side chains, which are crucial for stabilizing the three-dimensional structure and guiding sequence evolution.
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Protein Packing: Insights from Recent Research
High Packing Density in Proteins
Proteins exhibit a high average packing density, comparable to crystalline solids. However, when examining the distribution of free volumes within proteins, they resemble liquids and glasses more than crystals. This is due to the broad distribution of free volumes and the scaling of volume-to-surface ratios, indicating that proteins are more like randomly packed spheres near their percolation threshold rather than tightly fitting jigsaw puzzles. Interestingly, larger proteins tend to be packed more loosely than smaller ones, and the enthalpies of folding per amino acid are independent of packing density, suggesting that van der Waals interactions are not the primary forces in protein folding.
Factors Influencing Protein Packing
Protein packing varies significantly based on protein size, secondary structure, and amino acid composition. The occluded surface algorithm has shown that both buried and exposed residues contribute to packing, unlike the Voronoi method which focuses on buried residues. Variations in packing are conserved within protein families despite sequence differences, indicating that packing assessments should consider homologous proteins. This is crucial for accurate modeling of protein structures based on templates.
Packing Rules for Alpha-Helices and Beta-Sheets
The packing of alpha-helices and beta-sheets follows specific rules that, along with primary and secondary structures, determine the three-dimensional structure of proteins. These rules are essential for understanding how proteins fold and maintain their structure.
Cavities and Constraints in Protein Packing
The presence of cavities and the constraints they impose are critical for understanding protein structure, stability, and folding. Recent studies have highlighted the importance of packing in these processes, showing that mutations affecting packing can significantly alter protein stability and function. This knowledge aids in rational protein design and modeling.
Energetics of Side-Chain Packing
The energetics of side-chain packing, particularly in the hydrophobic core, are crucial for protein stability. Mutations that create cavities in the core, such as converting leucine or isoleucine to alanine, significantly reduce the free energy of folding. This demonstrates that interior packing is vital for maintaining the three-dimensional structure of proteins.
Hydrophobic Core Packing and Evolution
The packing of hydrophobic cores is a key factor in protein evolution. Studies on staphylococcal nuclease and its homologs have shown that the most common side chains in the core (isoleucine, leucine, valine) are not necessarily the most stable but have the best interaction energies. This suggests that packing interactions guide the sequence evolution of protein cores.
Protein Core Packing Models
Properly modeling the packing of residues in protein cores requires representing amino acids with calibrated atom sizes and including hydrogen atoms. Protein cores have a packing fraction of approximately 0.56, which is less than previously thought. This packing is similar to disordered jammed packings of particles, indicating that protein cores are densely packed.
Membrane Protein Packing
Precise packing of nonpolar side chains is crucial for the stability of membrane proteins. Research on the natural protein phospholamban has revealed a steric packing code that can be used to design stable membrane proteins. This code emphasizes the importance of apolar packing in membrane protein folding and stability.
Protein-Water Interface Packing
The packing efficiency at the protein-water interface is lower than in the protein core. Atoms on the protein surface occupy larger volumes due to voids between them, resulting in looser packing. This looser packing is compensated by smaller volumes of nearby water molecules, which are more tightly packed than in bulk solvent. The extent of this packing is influenced by the structural location of the atoms, with more exposed atoms having larger volumes.
Conclusion
Protein packing is a complex and multifaceted aspect of protein structure and stability. It is influenced by factors such as protein size, secondary structure, and amino acid composition. Understanding the rules and energetics of packing, as well as the differences between core and surface packing, is essential for accurate protein modeling and design. Recent research continues to uncover the intricate details of how proteins achieve their densely packed structures, providing valuable insights for the fields of biochemistry and molecular biology.
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