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arXiv · 2407.14063

Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles

John M. McBride·Aleksei Koshevarnikov·Marta Siek·Bartosz A. Grzybowski·Tsvi Tlusty
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Abstract

Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and catalysis. This paper provides a systematic survey of the universe of protein surfaces and quantifies the sizes, shapes, and curvatures of the positively/negatively charged and hydrophobic/hydrophilic surface patches as well as correlations between such patches. It then compares these statistics with the metrics characterizing nanoparticles functionalized with ligands terminated with positively and negatively charged ligands. These particles are of particular interest because they are also surface-patchy and have been shown to exhibit both antibiotic and anticancer activities - via selective interactions against various cellular structures - prompting loose analogies to proteins. Our analyses support such analogies in several respects (e.g., patterns of charged protrusions and hydrophobic niches similar to those observed in proteins), although there are also significant differences. Looking forward, this work provides a blueprint for the rational design of synthetic nanoobjects with further enhanced mimicry of proteins' surface properties.

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John M. McBride, Aleksei Koshevarnikov, Marta Siek, Bartosz A. Grzybowski, Tsvi Tlusty. 2024-07-19. Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles. https://arxiv.org/abs/2407.14063

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