Laleh Samii

The Tumbleweed: Towards a synthetic protein motor

Biomolecular motors have inspired the design and construction of artificial nanoscale motors and machines based on nucleic acids, small molecules, and inorganic nanostructures. However, the high degree of sophistication and efficiency of biomolecular motors, as well as their specific biological function, derives from the complexity afforded by protein building blocks. Here, we discuss a novel bottom‐up approach to understanding biological motors by considering the construction of synthetic protein motors. Specifically, we present a design for a synthetic protein motor that moves along a linear track, dubbed the “Tumbleweed.” This concept uses three discrete ligand‐dependent DNA‐binding domains to perform cyclically ligand‐gated, rectified diffusion along a synthesized DNA molecule. Here we describe how de novo peptide design and molecular biology could be used to produce the Tumbleweed, and we explore the fundamental motor operation of such a design using numerical simulations. The construction of this and more sophisticated protein motors is an exciting challenge that is likely to enhance our understanding of the structure‐function relationship in biological motors.

Construction and Characterization of Kilobasepair Densely Labeled Peptide-DNA

Directed assembly of biocompatible materials benefits from modular building blocks in which structural organization is independent of introduced functional modifications. For soft materials, such modifications have been limited. Here, long DNA is successfully functionalized with dense decoration by peptides. Following introduction of alkyne-modified nucleotides into kilobasepair DNA, measurements of persistence length show that DNA mechanics are unaltered by the dense incorporation of alkynes (∼1 alkyne/2 bp) and after click-chemistry attachment of a tunable density of peptides. Proteolytic cleavage of densely tethered peptides (∼1 peptide/3 bp) demonstrates addressability of the functional groups, showing that this accessible approach to creating hybrid structures can maintain orthogonality between backbone mechanics and overlaid function. The synthesis and characterization of these hybrid constructs establishes the groundwork for their implementation in future applications, such as building blocks in modular approaches to a range of problems in synthetic biology.

Design and construction of a one-dimensional DNA track for an artificial molecular motor

DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences from which the ideal sequence must be chosen. In order to find a suitable DNA sequence, we have adapted a genetic algorithm which is well suited for a large but sparse search space. This algorithm readily identifies long DNA sequences that include all the necessary elements to both facilitate DNA track construction and to present appropriate binding sites for the molecular motor. We have successfully experimentally incorporated the sequence identified by the algorithm into a long DNA track meeting the criteria for observation of the molecular motors activity.

Design and Construction of the Lawnmower, An Artificial Burnt-Bridges Motor

Molecular motors of the cell are protein-based, nanoscale machines, which use a variety of strategies to transduce chemical energy into mechanical work in the presence of a large thermal background. The design and construction of artificial molecular motors is one approach to better understand their basic physical principles. Here, we propose the concept of a protein-based, burnt-bridges ratchet, inspired by biological examples. Our concept, the lawnmower, utilizes protease blades to cleave peptide substrates, and uses the asymmetric substrate-product interface arising from productive cleavage to bias subsequent diffusion on the track (lawn). Following experimental screening to select a protease to act as the motors blades, we chemically couple trypsin to quantum dots and demonstrate activity of the resulting lawnmower construct in solution. Accompanying Brownian dynamics simulations illustrate the importance for processivity of correct protease density on the quantum dot and spacing of substrates on the track. These results lay the groundwork for future tests of the protein-based lawnmowers motor performance characteristics.

Motor Properties of Molecular Spiders

Molecular spiders are synthetic molecular motors featuring multiple legs such that each leg can interact with a substrate through binding and cleavage. Experimental studies of molecular spiders suggest that the motion of the spider on both a substrate matrix [R. Pei et al., J. Amer. Chem. Soc.128, 12693 (2006)] and a two dimensional substrate track [K. Lund et al, Nature 465, 206 (2010)] is biased towards uncleaved substrates. We first investigated the origin of the spiders biased motion by using Monte Carlo simulations of bipedal spiders on a 1D track based on a realistic chemical kinetic model [L. Samii et al., Phys. Rev. E81, 021106-1 (2010)], and found that substrate cleavage and spider detachment from the track both contribute to biased motion of the spider population. In the work reported here, we extend these studies by investigating how experimental parameters such as number of legs, leg length and substrate cleavage rate can be tuned to optimize the motor properties of the spider. We find that each of these parameters affect properties such as binding time to the track, processivity and speed in different ways. To evaluate further the motor properties of the spider, we calculated the thermodynamic efficiencies of multi-pedal molecular spiders, and found that they are both force and time dependent. By comparing our results with biological molecular motors such as kinesin, we were able to comment on the effect of tight versus loose mechano-chemical coupling on thermodynamic efficiency.