Hydrolytic zinc metallopeptides using a computational multi-state design approach

Abstract

Combination of multi-state design and long-timescale conformational dynamics as a powerful strategy to obtain metalloenzymes.

Manually curated dataset of catalytic peptides for ester hydrolysis

“…We provided a list in CSV format (raw data reposited in Mendeley data ), containing 101 positive and negative entries of catalytic peptides active towards the p-NPA and p-NPP substrates [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] . In addition, activities towards other alkyl-based substrates including p-NPB (p-nitrophenyl butyrate), p-NPO (p-nitrophenyl octanoate), p-NPMA (p-nitrophenyl methoxyacetate), p-NPH (p-nitrophenyl hexanoate), p-NPS (p-nitrophenyl salicylate), p-NPProp (p-nitrophenyl propionate), p-NPPalm (p-nitrophenyl palmitate), indoxyl acetate, HPNPP (2-hydroxypropyl-4-nitrophenylphosphate) and BNPP (Bis(4-nitrophenyl)phosphate), were added when available.…”

“…Other important features included in the dataset are N- and C- termini modifications, self-assembly propensity and mechanism of action. Data source location The data was sourced from publicly available articles [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] found through academic search engines. Data accessibility Repository name: Mendeley Data Data identification number: 10.17632/6s9kxj2ndr.2 Direct URL to data: https://data.mendeley.com/datasets/6s9kxj2ndr …”

Catalytic Peptides: the Challenge between Simplicity and Functionality

“…The zinc finger is a common structural motif explored to accommodate a catalytic zinc center and the villin headpiece C-terminal subdomain for metal-binding and catalytic activity (0.1 M À 1 s À 1 ) towards an ester substrate. [31] In another example, an artificial carbonic anhydrase was created using the Zinc-finger as a scaffold having αββ topology. [32] The active site Zn(His) 3 O and the substrate binding site were grafted on the αββ protein, which was optimized through computational methodologies for zinc binding, substrate binding and hydrolase activity, with the observed catalytic constant of 2.5 M À 1 s À 1 .…”

“…The cooperative folding of scaffolds is fundamental for the spatial display of crucial amino acids. The zinc finger is a common structural motif explored to accommodate a catalytic zinc center and the villin headpiece C‐terminal subdomain for metal‐binding and catalytic activity (0.1 M −1 s −1 ) towards an ester substrate [31] . In another example, an artificial carbonic anhydrase was created using the Zinc‐finger as a scaffold having αββ topology [32] .…”

Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

“…Several fundamental aspects of metal cofactor assembly and functions have been clarified by studying natural metalloproteins and their site-directed mutants [ 11 , 12 ]. In addition, numerous model systems have been developed by engineering metal-binding sites into artificial protein scaffolds [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. They represent useful platforms for structure–activity relationship studies, allowing for a fast and easy screening of several mutants [ 21 , 22 ].…”