Abstract
Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.
Highlights
Correspondence and requests for materials should be addressed to Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software
Our results show that INTMSAlign could assign both consensus and correlation residues, and that this software could be applied to the design of functional proteins
A schematic view of the INTMSAlign algorithm is shown in Figure 1, and a more detailed description of the algorithm is provided in the supporting information (Supplementary Figures 1 and 2)
Summary
Correspondence and requests for materials should be addressed to Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software. Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. Within the top-down approach, consensus design is a representative method for creating complete sequences of functional proteins[3] One advantage of this method is that both protein engineering and consideration of protein evolution can be performed at once[3,7]. The libraries used to date contain dozens to thousands of sequences After these assignments are completed, primary sequence of full-consensus proteins can be designed by selecting fully consensus residues. Creation and biochemical analysis of full-consensus proteins may reveal the source of a protein’s extraordinary properties These features are useful in both protein engineering and prediction of protein evolution. This assignment is difficult, because correlation residues are often less conserved and cannot be revealed by conventional MSA methods
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