Computational protein design with electrostatic focusing: Experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Issue 7 (21st June 2013)

• Record Type: Journal Article
• Authors: Suárez‐Diez, Maria; Pujol, Anaïs M.; Matzapetakis, Manolis; Jaramillo, Alfonso; Iranzo, Olga
• Is Part Of: Biotechnology journal. Volume 8:Issue 7(2013:Jul.)
• Page Start: 855
• Page End: 864
• Publication Date: 2013-06-21
• Subjects: Computational protein design -- Electrostatic focusing -- Physical effective energy functions -- Reduced alphabet; Biotechnology -- Periodicals; 660.605
• DOI: 10.1002/biot.201200380
• Languages: English
• ISSNs: 1860-6768

Abstract

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. Abstract : Automated methodologies allow the design of proteins with tailor‐made characteristics. The authors present a method, based on first principles, for the engineering of protein domains that fold, and thus become functional, only in a given solvent. To test the approach, the authors re‐designed, synthesized and experimentally characterized a three‐helix bundle; however the current methodology can be readily extended to larger domains and proteins.