Biomimetic spatial and temporal (4D) design and fabrication

We imagine the built environment of the future as a ‘bio-hybrid machine for living in’ that will sense and react to activities within the space in order to provide experiences and services that will elevate quality of life while coexisting seamlessly with humans and the natural environment. The study of Hierarchical design in biological materials has the potential to alter the way designers/ engineers/ crafts-men of the future engage with materials in order to realise such visions. We are ex-ploring this design approach using digital manufacturing technologies such as jac-quard weaving and 3D printing

Identification of an expanded set of translationally active methionine analogues in Escherichia coli

Amino acid incorporation into proteins in vivo is controlled most stringently by the aminoacyl-tRNA synthetases. Here we report the incorporation of several new methionine analogues into protein by increasing the rate of their activation by the methionyl-tRNA synthetase (MetRS) of Escherichia coli. cis-Crotylglycine (4), 2-aminoheptanoic acid (7), norvaline (8), 2-butynylglycine (11), and allylglycine (12) will each support protein synthesis in methionine-depleted cultures of E. coli when MetRS is overexpressed and the medium is supplemented with the analogue at millimolar concentrations. These investigations suggest important opportunities for protein engineering, as expansion of the translational apparatus toward other amino acid analogues by similar strategies should also be possible

Artificial Polypeptide Scaffold for Protein Immobilization

An artificial polypeptide scaffold composed of surface anchor and protein capture domains was designed and expressed in vivo. By using a mutant E. coli phenylalanyl−tRNA synthetase, the photoreactive amino acid para-azidophenylalanine was incorporated into the surface anchor domain. Octyltrichlorosilane-treated surfaces were functionalized with this polypeptide by spin coating and photocrosslinking. The resulting protein films were shown to immobilize recombinant proteins through association of coiled coil heterodimer

Dynamics of Phase Behavior of a Polymer Blend Under Shear Flow

We study the dynamics of the phase behavior of a polymer blend in the presence of shear flow. By adopting a two fluid picture and using a generalization of the concept of material derivative, we construct kinetic equations that describe the phase behavior of polymer blends in the presence of external flow. A phenomenological form for the shear modulus for the blend is proposed. The study indicates that a nonlinear dependence of the shear modulus of the blend on the volume fraction of one of the species is crucial for a shift in the stability line to be induced by shear flow.Comment: 16 pages, late

Synthesis and Cell Adhesive Properties of Linear and Cyclic RGD Functionalized Polynorbornene Thin Films

Described herein is the efficient synthesis and evaluation of bioactive arginine-glycine-aspartic acid (RGD) functionalized polynorbornene-based materials for cell adhesion and spreading. Polynorbornenes containing either linear or cyclic RGD peptides were synthesized by ring-opening metathesis polymerization (ROMP) using the well-defined ruthenium initiator [(H_(2)IMes)(pyr)_(2)(Cl)_(2)Ru═CHPh]. The random copolymerization of three separate norbornene monomers allowed for the incorporation of water-soluble polyethylene glycol (PEG) moieties, RGD cell recognition motifs, and primary amines for postpolymerization cross-linking. Following polymer synthesis, thin-film hydrogels were formed by cross-linking with bis(sulfosuccinimidyl) suberate (BS^3), and the ability of these materials to support human umbilical vein endothelial cell (HUVEC) adhesion and spreading was evaluated and quantified. When compared to control polymers containing either no peptide or a scrambled RDG peptide, polymers with linear or cyclic RGD at varying concentrations displayed excellent cell adhesive properties in both serum-supplemented and serum-free media. Polymers with cyclic RGD side chains maintained cell adhesion and exhibited comparable integrin binding at a 100-fold lower concentration than those carrying linear RGD peptides. The precise control of monomer incorporation enabled by ROMP allows for quantification of the impact of RGD structure and concentration on cell adhesion and spreading. The results presented here will serve to guide future efforts for the design of RGD functionalized materials with applications in surgery, tissue engineering, and regenerative medicine

Engineering Cooperativity in Biomotor-Protein Assemblies

A biosynthetic approach was developed to control and probe cooperativity in multiunit biomotor assemblies by linking molecular motors to artificial protein scaffolds. This approach provides precise control over spatial and elastic coupling between motors. Cooperative interactions between monomeric kinesin-1 motors attached to protein scaffolds enhance hydrolysis activity and microtubule gliding velocity. However, these interactions are not influenced by changes in the elastic properties of the scaffold, distinguishing multimotor transport from that powered by unorganized monomeric motors. These results highlight the role of supramolecular architecture in determining mechanisms of collective transport

From Dyck Paths to Standard Young Tableaux

We present nine bijections between classes of Dyck paths and classes of standard Young tableaux (SYT). In particular, we consider SYT of flag and rectangular shapes, we give Dyck path descriptions for certain SYT of height at most 3, and we introduce a special class of labeled Dyck paths of semilength n that is shown to be in bijection with the set of all SYT with n boxes. In addition, we present bijections from certain classes of Motzkin paths to SYT. As a natural framework for some of our bijections, we introduce a class of set partitions which in some sense is dual to the known class of noncrossing partitions

Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells

Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide–alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria

Mechanisms of diffusion in associative polymer networks: evidence for chain hopping

Networks assembled by reversible association of telechelic polymers constitute a common class of soft materials. Various mechanisms of chain migration in associative networks have been proposed; yet there remains little quantitative experimental data to discriminate among them. Proposed mechanisms for chain migration include multichain aggregate diffusion as well as single-chain mechanisms such as “walking” and “hopping”, wherein diffusion is achieved by either partial (“walking”) or complete (“hopping”) disengagement of the associated chain segments. Here, we provide evidence that hopping can dominate the effective diffusion of chains in associative networks due to a strong entropic penalty for bridge formation imposed by local network structure; chains become conformationally restricted upon association with two or more spatially separated binding sites. This restriction decreases the effective binding strength of chains with multiple associative domains, thereby increasing the probability that a chain will hop. For telechelic chains this manifests as binding asymmetry, wherein the first association is effectively stronger than the second. We derive a simple thermodynamic model that predicts the fraction of chains that are free to hop as a function of tunable molecular and network properties. A large set of self-diffusivity measurements on a series of model associative polymers finds good agreement with this model

Mechanisms of diffusion in associative polymer networks: evidence for chain hopping

Networks assembled by reversible association of telechelic polymers constitute a common class of soft materials. Various mechanisms of chain migration in associative networks have been proposed; yet there remains little quantitative experimental data to discriminate among them. Proposed mechanisms for chain migration include multichain aggregate diffusion as well as single-chain mechanisms such as “walking” and “hopping”, wherein diffusion is achieved by either partial (“walking”) or complete (“hopping”) disengagement of the associated chain segments. Here, we provide evidence that hopping can dominate the effective diffusion of chains in associative networks due to a strong entropic penalty for bridge formation imposed by local network structure; chains become conformationally restricted upon association with two or more spatially separated binding sites. This restriction decreases the effective binding strength of chains with multiple associative domains, thereby increasing the probability that a chain will hop. For telechelic chains this manifests as binding asymmetry, wherein the first association is effectively stronger than the second. We derive a simple thermodynamic model that predicts the fraction of chains that are free to hop as a function of tunable molecular and network properties. A large set of self-diffusivity measurements on a series of model associative polymers finds good agreement with this model