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Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Massive non-natural proteins structure prediction using grid technologies.

Giovanni Minervini1, Giuseppe Evangelista, Laura Villanova

  • 1Department of Biology, University Roma Tre, Viale G, Marconi 446, Rome, I-00146, Italy. gminervini@uniroma3.it

BMC Bioinformatics
|June 19, 2009
PubMed
Summary
This summary is machine-generated.

"Never born proteins" (NBPs) can form stable, soluble structures, similar to natural proteins. NBPs show more helical content and aromatic amino acids, offering evolutionary insights into protein selection.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Science

Background:

  • Natural proteins represent a small subset of all possible protein sequences.
  • The study investigates whether natural proteins possess unique properties or are products of contingency and selection.
  • Understanding the structural properties of "never born proteins" (NBPs) can elucidate the selection pressures on natural protein sequences.

Purpose of the Study:

  • To computationally investigate the structural properties of NBPs.
  • To compare the structural characteristics of NBPs with those of natural proteins.
  • To infer evolutionary implications regarding protein structure and sequence selection.

Main Methods:

  • Generated a library of 2x10^4 random protein sequences, excluding those similar to natural proteins.
  • Predicted protein structures using the Rosetta computational modeling suite.
  • Analyzed structural features including secondary structure content, net charge, and hydrophobic core composition.

Main Results:

  • The majority of NBPs predicted by Rosetta exhibit compact 3D structures with high secondary structure content.
  • NBPs show comparable compactness and surface polarity to natural proteins, suggesting similar stability and solubility.
  • NBPs display a higher proportion of alpha-helical structures and aromatic amino acids compared to natural proteins.

Conclusions:

  • The ability of polypeptides to form ordered, soluble structures appears to be an intrinsic property.
  • The propensity of random sequences to form alpha-helical structures suggests their early emergence in prebiotic evolution.
  • The lower abundance of aromatic residues in natural proteins may relate to enhanced tolerance to mutations.