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Kollman, Justin M.

Publications and source records attributed to Kollman, Justin M..

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.

36 MATERIALS SCIENCE↗

Modular repeat protein sculpting using rigid helical junctions

The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.

59 BASIC BIOLOGICAL SCIENCES↗

A Mechanistic Understanding of Nonclassical Crystal Growth in Hydrothermally Synthesized Sodium Yttrium Fluoride Nanowires

Sodium yttrium fluoride (NaYF 4 ) is an important upconverting material with many potential uses in chemistry, materials science, and biology, which can be synthesized hydrothermally in both cubic (α) and hexagonal (β) crystallographic polymorphs. Understanding the mechanisms underlying the phase conversion between the cubic and hexagonal polymorphs is of great interest to help inform future synthetic efforts, for example in the design of atomically precise quantum materials with well-defined sizes and morphologies. In this work, we use a combination of analytical transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), powder X-ray diffraction (XRD), in situ liquid cell TEM, atom probe tomography (APT), and extended X-ray absorption fine structure (EXAFS) measurements to show that the hexagonal NaYF 4 nanowires form through a nonclassical crystal growth mechanism involving the formation and subsequent oriented attachment of mesocrystals consisting of cubic (α) phase units. Additionally, EXAFS measurements suggest that substitutional Yb 3+ point defects within NaYF 4 are distributed evenly throughout the crystal lattice without clustering and also that they may exhibit selective substitution into one of the two possible trivalent yttrium sites in the unit cell for hydrothermally synthesized β-NaYF 4 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗