ArticleProtein science : a publication of the Protein Society2008
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Design of complicated all-α protein structures.Nature structural & molecular biology · 2024Article
- Rigidifying aACS catalysis · 2021Article
- De novo proteins from random sequences through in vitro evolution.Current opinion in structural biology · 2021Review
- Chimeric Claudins: A New Tool to Study Tight Junction Structure and Function.International journal of molecular sciences · 2021Article
- A novel type of colistin resistance genes selected from random sequence space.PLoS genetics · 2021Article
- Harnessing synthetic biology to enhance heterologous protein expression.Protein science : a publication of the Protein Society · 2020Article
- A Strategy for Combinatorial Cavity Design in De Novo Proteins.Life (Basel, Switzerland) · 2020Article
- Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals.Life (Basel, Switzerland) · 2019Article
- Hierarchical design of artificial proteins and complexes toward synthetic structural biology.Biophysical reviews · 2018Review
- A de novo protein confers copper resistance in Escherichia coli.Protein science : a publication of the Protein Society · 2016Article
- A protein constructed de novo enables cell growth by altering gene regulation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic.Journal of molecular biology · 2016Article
- Computational de novo design of a four-helix bundle protein--DND_4HB.Protein science : a publication of the Protein Society · 2015Article
- Hierarchical cascades of instability govern the mechanics of coiled coils: helix unfolding precedes coil unzipping.Biophysical journal · 2014Article
- Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7.Protein science : a publication of the Protein Society · 2013Article
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.PLoS computational biology · 2013Article
- Folding helical proteins in explicit solvent using dihedral-biased tempering.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Proteins from an unevolved library of de novo designed sequences bind a range of small molecules.ACS synthetic biology · 2012Article
- Relative stability of de novo four-helix bundle proteins: insights from coarse grained molecular simulations.Protein science : a publication of the Protein Society · 2011Article
- Binding of small molecules to cavity forming mutants of a de novo designed protein.Protein science : a publication of the Protein Society · 2011Article
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4 authors.
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Abstract
Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.
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