A review from the group leading recent rapid progress in de novo protein design describes the successes, identifies the remaining challenges, and heralds the advance “from the Stone Age to the Iron Age” in protein design.
Archive for the 'Computational nanotechnology' Category
Ten designs spanning three types of icosahedral architectures produce atomically precise multi-megadalton protein cages to deliver biological cargo or serve as scaffolds for organizing various molecular functions.
Atomically precise chevron-shaped graphene nanoribbons were purified after solution synthesis, cleanly placed by dry contact transfer on a hydrogen-passivated Si surface, imaged and manipulated by scanning tunneling microscopy, and covalently bonded to depassivated surface positions.
Computational recombination of small elements of structure from known protein structures generates a vast library of designs that balance protein stability with the potential for new functions and novel interactions.
A trimeric protein was designed to self assemble into a 60 unit icosahedron with a roomy interior that might find use to ferry molecular cargo into cells or as a chemical reactor.
Recent research documents a structure-based rational design strategy combining molecular dynamics and single molecule imaging to improve the performance of a DNA tweezers that accurately positions an enzyme and its cofactor.
Precise matching of STM images and theoretical calculations provides exact lattice locations of dopant atoms, advancing the prospects for silicon-based quantum computers.
Combining computational nanotechnology with a noncontact-atomic force microscope probe tipped by a single CO molecule allowed researchers to visualize the dance of individual chemical bonds during a complex organic reaction on a silver surface.
Chains of monomers joined by non-biological peptoid bonds follow different rules of self-assembly and form structures not found in chains joined by the peptide bonds used to form proteins.
An engineered protein controls the assembly of C60 fullerene molecules into an atomically precise lattice that conducts electricity while neither component alone would.
Atomic resolution measurement of quasi-particle tunneling maps of spin-resolved states reveals interference processes that allow simulation of processes important for developing quantum computers based on atomically precise doping of silicon.
Computational design of an enzyme that carboligates three one-carbon molecules to form one three-carbon molecule, an activity that does not exist in nature, provides proof-of-principle for a novel metabolic pathway for carbon fixation.
Thousands of amateurs playing the online RNA folding game Eterna, backed up by a real-world automated lab testing their predictions, have provided insights to improve the algorithms computers use to design RNA molecules.
New families of protein structures, barrel proteins for positioning small molecules, self-assembling protein arrays, and precision sculpting of protein architectures highlight de novo protein design advances.
Computational design of proteins satisfying predetermined geometric constraints produced stable proteins with the designed structure that are not found in nature.
A fully automated design protocol generates dozens of designs for proteins based on helix-loop-helix-loop repeat units that are very stable, have crystal structures that match the design, have very different overall shapes, and are unrelated to any natural protein.
Prof. William Goddard presented four advances from his research group that enable going from first principles quantum mechanics calculations to realistic nanosystems of interest with millions or billions of atoms.
Prof. Gerhard Klimeck described the success of nanoHUB.org, a science and engineering gateway providing online simulations through a web browser for nanotechnology research and education.
The positions of 3769 tungsten atoms in a tungsten needle segment were determined to a precision of 19 pm (0.019 nm), including the position of a single atom defect in the interior of the sample, by using aberration-corrected scanning transmission electron microscopy and computerized tomography.
Building on previous work on single atom transistors and single atom qubits, Australian researchers have incorporated a quantum error correction code to make possible a scalable 3D silicon chip architecture that could lead to operational quantum computers.