Controlling protein assembly on inorganic crystals through designed protein interfaces

Abstract

The ability of proteins and other macromolecules to interact with inorganic surfaces is critical to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains [1][2][3][4][5] , but the structures of most protein-inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein-mineral interfaces guided by the example of ice-binding proteins, which present arrays of threonine residues matched to the ice lattice that order clathrate waters into an ice-like structure 6 . We designed proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the K + sublattice on muscovite mica (001). At low [K + ] individual molecules bind independently to mica in the designed orientations, while at high [K + ], the designs form 2D liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimeters. Incorporation of designed protein-protein interactions preserving the match between the proteins and the K + lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micron long single protein-diameter wires, and a designed trimeric interface yielded extensive honeycomb arrays. The nearest neighbor distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nm with 2.1 nm selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein-Reprints and permissions information is available at www.nature.com/reprints.Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http:// www.nature.com/authors/editorial_policies/license.html#terms Correspondence and requests for materials should be addressed to D.B.

De NovoDesigned Peptide and Protein Hairpins Self-assemble into Sheets and Nanoparticles

“…Specifically, the proximal pin allows splaying of the helical termini, which in turn leads to curved arrays that can close, whereas the distal pins give a more tightly constrained hairpin structure, consistent with building blocks required to make flat sheets. As noted earlier, others have developed similar self-assembling peptide and protein based nanoparticles [22][23][24][25][26][27][28][29][30] or sheets, [12][13][14][15][16][17][18] so what are the differences and advantages to our hairpin system? First, by including two points (loop and pin) that define the relative positions and rotational freedom of the two coiled-coil components, we are able to control the topology of the self-assembled structures by design in a single system to render closed nanoparticles or extended sheets.…”

“…10 The toolbox of useful self-assembling protein structures has been expanded by either mutating natural protein interfaces to induce controlled self-assembly, or by de novo design. 11 Such structures are usually computationally driven towards forming closely packed 2D arrays [12][13][14][15][16][17][18] , tubes [19][20][21] or 3D icosahedral particles. [22][23][24][25][26][27][28][29][30] However, these beautifully ordered near crystalline assemblies may not be amenable to decoration with large cargos, or be very permeable to small molecules due to their close packed nature.…”

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

“…One leading structure prediction and design software suite is Rosetta, a collection of algorithms for protein structure prediction, docking, and design (10,(12)(13)(14) as well as protein interactions with small molecules (15), nucleic acids (16), carbohydrates, or in a lipid bilayer (17). Rosetta has been a scientific leader in several blind structure prediction challenges (18)(19)(20)(21) and has shown proof-of-principle for many design goals, including de novo folds (22)(23)(24), loop design, interface design (25)(26)(27)(28), symmetric assembly (29,30), and mineral binding (31,32). In addition to its success in science and engineering, Rosetta is suited for teaching structure prediction and design for several reasons.…”

Direct investigation of current transport in cells by conductive atomic force microscopy

“…Since its invention, Atomic Force Microscopy (AFM) has been a powerful and versatile approach to visualise and characterise surface properties at the nanometre scale, especially in biology (Binnig et al, 1986;Kada et al, 2008;Cai et al, 2012;Liu et al, 2012;Shan & Wang, 2015;Liu et al, 2016;Pyles et al, 2019). Multiple modes of AFM, such as CAFM, are suitable for use in the investigation of electrical properties in biology.…”