Abstract
Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design application-tailored proteins and catalysts for a wide range of applications. Several enzymes exploit the unique features of metal cofactors to achieve catalytic activity otherwise unattainable through the use of only natural amino acid residues. One of the major bottlenecks in ab initio design of novel proteins relies on long-range and epistatic effects that severely limit the possibility of a rational design. Within this framework there is an ongoing effort to reduce protein length and complexity to unlock the full potential of in silico protein design. In this work we specifically address this problem designing and investigating the dynamic features of 10 in silico designed minimal metallo-proteins. In particular, in this paper we investigate whether and to what extent it is possible to design a minimal metallo-enzyme made of only residues involved in metal binding. In this research we address these questions by investigating the ability of 10 different “mini-proteins” with a length shorter than 15 residues. Molecular dynamics studies clearly show that it is possible to design a minimal protein able to bind a metal atom with the correct geometry. It is noteworthy that designed mini-proteins cannot achieve the formation of a canonical hydrophobic core, rather the metal ion provides a “metal core” around which the entire protein is organized. This opens the possibility of designing synthetic enzymes composed of only functional residues organized around a “metal core” which acts as both structural and functional determinat.
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Fig. S1
The picture shows the three-dimensional structure of protein 002. In orange the ion copper. Figure created with Chimera software (20) (DOC 163 kb)
Table S1
Relative distance between Glu 6 and His 8 of two independent simulations of protein 010 with copper ion. Glu6_a and Glu6_b indicate, respectively, the two tritratable position of the glutamate residue. Distances are in angstrom (DOC 41 kb)
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Mazzucco, N., Zanconato, S., De Lucrezia, D. et al. Design and dynamic simulation of minimal metallo-proteins. J Mol Model 17, 2919–2925 (2011). https://doi.org/10.1007/s00894-011-0993-8
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DOI: https://doi.org/10.1007/s00894-011-0993-8