Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from ...naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
We demonstrate arrays of opioid biosensors based on chemical vapor deposition grown molybdenum disulfide (MoS2) field effect transistors (FETs) coupled to a computationally redesigned, water-soluble ...variant of the μ-opioid receptor (MOR). By transferring dense films of monolayer MoS2 crystals onto prefabricated electrode arrays, we obtain high-quality FETs with clean surfaces that allow for reproducible protein attachment. The fabrication yield of MoS2 FETs and biosensors exceeds 95%, with an average mobility of 2.0 cm2 V–1 s–1 (36 cm2 V–1 s–1) at room temperature under ambient (in vacuo). An atomic length nickel-mediated linker chemistry enables target binding events that occur very close to the MoS2 surface to maximize sensitivity. The biosensor response calibration curve for a synthetic opioid peptide known to bind to the wild-type MOR indicates binding affinity that matches values determined using traditional techniques and a limit of detection ∼3 nM (1.5 ng/mL). The combination of scalable array fabrication and rapid, precise binding readout enabled by the MoS2 transistor offers the prospect of a solid-state drug testing platform for rapid readout of the interactions between novel drugs and their intended protein targets.
Computational design of a protein crystal Lanci, Christopher J; MacDermaid, Christopher M; Kang, Seung-gu ...
Proceedings of the National Academy of Sciences - PNAS,
05/2012, Letnik:
109, Številka:
19
Journal Article
Recenzirano
Odprti dostop
Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given ...the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement backbone root mean square deviation (rmsd) with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.
► Computational protein design of protein structure, sequence and function. ► Design of combinatorial protein libraries. ► Design of novel enzymes. ► Design of protein-cofactor assemblies. ► Designed ...membrane proteins.
Computational and theoretical methods are advancing protein design as a means to create and investigate proteins. Such efforts further our capacity to control, design and understand biomolecular structure, sequence and function. Herein, the focus is on some recent applications that involve using theoretical and computational methods to guide the design of protein sequence ensembles, new enzymes, proteins with novel cofactors, and membrane proteins.
We report a novel class of amphiphilic conjugated block copolymers composed of poly(3-octylthiophene) and poly(ethylene oxide) (POT-b-PEO) that exhibit highly tunable photoluminescence colors ...spanning from blue to red. POT-b-PEO self-assembles into various well-defined core/shell-type nanostructures as a result of its amphiphilicity. The self-assembly structure can be readily controlled by altering the solvent composition or by other external stimuli. The color change was completely reversible, demonstrating that the strategy can be used to manipulate the light-emission properties of conjugated polymers in a highly controllable manner without having to synthesize entirely new sets of molecules.
The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including ...chemical recognition (of enzyme substrates or adhesive ligands
, for instance), exquisite nanostructures (composed of peptides
, proteins
or nucleic acids
), and unusual mechanical properties (such as silk-like strength
, stiffness
, viscoelasticity
and resiliency
). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.
Mimicking the hierarchical assembly of natural fiber materials is an important design challenge in the manufacturing of nanostructured materials with biomolecules such as peptides. Here, we produce ...nanofibers with control of structure over multiple length scales, ranging from peptide molecule assembly into supramolecular building blocks called “bundlemers,” to rigid-rod formation through a covalent connection of bundlemer building blocks, and, ultimately, to uniaxially oriented fibers made with the rigid-rod polymers. The peptides are designed to physically assemble into coiled-coil bundles, or bundlemers, and to covalently interact in an end-to-end fashion to produce the rigid-rod polymer. The resultant rodlike polymer exhibits a rigid, cylindrical nanostructure confirmed by transmission electron microscopy (TEM) and, correspondingly, exhibits shear-thinning behavior at low shear rates observed in many nanoscopic rod systems. The rigid-rod chains are further organized into final fiber materials via electrospinning processing, all the while preserving their unique rodlike structural characteristics. Morphological and structural investigations of the nanofibers through scanning electron microscopy, transmission electron microscopy, and X-ray scattering, as well as molecular characterization via Fourier transform infrared (FTIR) and Raman spectroscopy, show that continuous nanofibers are composed of oriented rigid-rod chains constituted by α-helical peptides within bundle building blocks. Mechanical properties of electrospun fibers are also presented. The ability to produce nanofibers from the oriented rigid-rod polymer reveals bundlemer chains as a viable tool for the development of new fiber materials with targeted structure and properties.
Theoretical and computational protein design Samish, Ilan; MacDermaid, Christopher M; Perez-Aguilar, Jose Manuel ...
Annual review of physical chemistry,
01/2011, Letnik:
62
Journal Article
Recenzirano
From exponentially large numbers of possible sequences, protein design seeks to identify the properties of those that fold to predetermined structures and have targeted structural and functional ...properties. The interactions that confer structure and function involve intermolecular forces and large numbers of interacting amino acids. As a result, the identification of sequences can be subtle and complex. Sophisticated methods for characterizing sequences consistent with a particular structure have been developed, assisting the design of novel proteins. Developments in such computational protein design are discussed, along with recent accomplishments, ranging from the redesign of existing proteins to the design of new functionalities and nonbiological applications.
Supercharged proteins exhibit high solubility and other desirable properties, but no engineered superpositively charged enzymes have previously been made. Superpositively charged variants of proteins ...such as green fluorescent protein have been efficiently encapsulated within Archaeoglobus fulgidus thermophilic ferritin (AfFtn). Encapsulation by supramolecular ferritin can yield systems with a variety of sequestered cargo. To advance applications in enzymology and green chemistry, we sought a general method for supercharging an enzyme that retains activity and is compatible with AfFtn encapsulation. The zinc metalloenzyme human carbonic anhydrase II (hCAII) is an attractive encapsulation target based on its hydrolytic activity and physiologic conversion of carbon dioxide to bicarbonate. A computationally designed variant of hCAII contains positively charged residues substituted at 19 sites on the protein’s surface, resulting in a shift of the putative net charge from −1 to +21. This designed hCAII(+21) exhibits encapsulation within AfFtn without the need for fusion partners or additional reagents. The hCAII(+21) variant retains esterase activity comparable to the wild type and spontaneously templates the assembly of AfFtn 24mers around itself. The AfFtn–hCAII(+21) host–guest complex exhibits both greater activity and thermal stability when compared to hCAII(+21). Upon immobilization on a solid support, AfFtn–hCAII(+21) retains enzymatic activity and exhibits an enhancement of activity at elevated temperatures.
Alkyl halide side groups are selectively incorporated into monodispersed, computationally designed coiled-coil-forming peptide nanoparticles. Poly2-(dimethylamino)ethyl methacrylate (PDMAEMA) is ...polymerized from the coiled-coil periphery using photoinitiated atom transfer radical polymerization (photoATRP) to synthesize well-defined, thermoresponsive star copolymer architectures. This facile synthetic route is readily extended to other monomers for a range of new complex star-polymer macromolecules.
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