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Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet.
- Source :
-
Biotechnology journal [Biotechnol J] 2013 Jul; Vol. 8 (7), pp. 855-64. Date of Electronic Publication: 2013 Jun 21. - Publication Year :
- 2013
-
Abstract
- Automated methodologies to design synthetic proteins from first principles use energy computations to estimate the ability of the sequences to adopt a targeted structure. This approach is still far from systematically producing native-like sequences, due, most likely, to inaccuracies when modeling the interactions between the protein and its aqueous environment. This is particularly challenging when engineering small protein domains (with less polar pair interactions than with the solvent). We have re-designed a three-helix bundle, domain B, using a fixed backbone and a four amino acid alphabet. We have enlarged the rotamer library with conformers that increase the weight of electrostatic interactions within the design process without altering the energy function used to compute the folding free energy. Our synthetic sequences show less than 15% similarity to any Swissprot sequence. We have characterized our sequences in different solvents using circular dichroism and nuclear magnetic resonance. The targeted structure achieved is dependent on the solvent used. This method can be readily extended to larger domains. Our method will be useful for the engineering of proteins that become active only in a given solvent and for designing proteins in the context of hydrophobic solvents, an important fraction of the situations in the cell.<br /> (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Subjects :
- Algorithms
Amino Acid Sequence
Circular Dichroism
Computer Simulation
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Sequence Data
Protein Conformation
Protein Folding
Static Electricity
Thermodynamics
Amino Acids chemistry
Computational Biology methods
Protein Engineering methods
Proteins chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1860-7314
- Volume :
- 8
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- Biotechnology journal
- Publication Type :
- Academic Journal
- Accession number :
- 23788466
- Full Text :
- https://doi.org/10.1002/biot.201200380