Cooperatively folded proteins in random sequence libraries

  title={Cooperatively folded proteins in random sequence libraries},
  author={Alan R. Davidson and K. Lumb and Robert T. Sauer},
  journal={Nature Structural Biology},
The structural properties of proteins recovered from random sequence libraries can be used to investigate the relationship between folding and sequence information. Here, we show that helical proteins displaying cooperative thermal denaturation transitions can be easily recovered from a library containing 80-residue proteins predominantly composed of glutamine, leucine, and arginine, with an average hydophobicity level similar to that of natural proteins. The native structure of one of these… 

Searching for folded proteins in vitro and in silico.

These efforts to identify novel proteins using a phage-display selection strategy from a 'mini-exon' shuffling library generated from the yeast genome and from completely random sequence libraries are described.

Sequence space, folding and protein design.

De novo proteins from designed combinatorial libraries

This review describes how focused libraries can be constructed by designing the binary pattern of polar and nonpolar amino acids to favor proteins that contain abundant secondary structure, while simultaneously burying hydrophobic side chains and exposing hydrophilic side chains to solvent.

Functional rapidly folding proteins from simplified amino acid sequences

It is shown that a small β-sheet protein, the SH3 domain, can be largely encoded by a five letter amino acid alphabet but not by a three letter alphabet, which supports the idea that the interactions which stabilize the native state induce a funnel shape to the free energy landscape sufficient to guide the folding polypeptide chain to the proper structure.

High solubility of random-sequence proteins consisting of five kinds of primitive amino acids.

A library of random-sequence proteins consisting of only five amino acids, Ala, Gly, Val, Asp and Glu, which are believed to have been the most abundant in the prebiotic environment are constructed and support the reduced-alphabet hypothesis of the primordial genetic code.



Folded proteins occur frequently in libraries of random amino acid sequences.

  • A. DavidsonR. Sauer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1994
The properties of the QLR proteins demonstrate that they possess folded structures with some native-like properties, in being remarkably resistant to denaturant-induced and thermal-induced unfolding and in being relatively insoluble in the absence of denaturants.

Cooperative deformation of a de novo designed protein.

Measurements indicate that the folding is significantly cooperative as expected, but that the protein is still loosely packed.

Identifying determinants of folding and activity for a protein of unknown structure.

  • J. BowieR. Sauer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1989
An extensive genetic map of functionally allowed and/or structurally allowed amino acid substitutions in Arc repressor, a DNA binding protein of unknown structure, identifies residues that are likely to be involved in protein function and identifies side chains that play important structural roles, including residues likely to form the hydrophobic core.

A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil.

The results suggest that, whereas nonspecific hydrophobic interactions contribute to protein stability, the requirement to satisfy the hydrogen bonding potential of buried polar residues in the generally hydrophilic environment of the protein interior can impart specificity (structural uniqueness) to protein folding and design.

Structural and genetic analysis of protein stability.

Substantial progress is being made in quantitating the interactions that determine and stabilize protein structures and in developing methods to engineer proteins of enhanced stability.

Thermodynamic analysis of the chemotactic protein from Escherichia coli, CheY.

The thermodynamic characterization of the wild-type CheY at different pH values and in different buffers and denaturation conditions is reported, showing that temperature-induced unfolding of CheY is not a two-state process and proceeds through a highly populated intermediate state, corresponding to protein dimers, as was subsequently confirmed by direct cross-linking experiments.

Thermodynamic genetics of the folding of the B1 immunoglobulin‐binding domain from streptococcal protein G

A method has been developed to select proteins that are thermodynamically destabilized yet still folded and functional and mutants that are folded but destabilized compared with wild‐type Strp G, which have been physically characterized by circular dichroism and nuclear magnetic resonance.