Methods Mol Biol. 2018;1777:221-232
Authors: Jiang T, Conticello VP
Two-dimensional nanostructures offer significant promise as components for the construction of functional biomaterials. However, the controllable fabrication of these structures remains a challenge. Ideally, one desires to control the composition, structure, and surface functionality of the resultant materials with precision, in order to tailor properties for a particular application and minimize the unintended side effects. We recently reported the synthesis of triple-layer nanosheets from template-driven assembly of a negatively charged collagen-mimetic peptide CP – on a preassembled nanosheet of a positively charged collagen-mimetic peptide CP + . This process enabled the fabrication of nanosheets of defined composition, internal structure, and surface chemistry using a modified layer-by-layer approach. Herein, we describe the synthesis and purification procedures for these two 45-mer peptides, CP + and CP – , and guidelines for the directed assembly of triple-layer structures, along with routine methods of structural analysis.
PMID: 29744838 [PubMed – in process]
Interface Focus. 2017 Dec 06;7(6):20160141
Authors: Jiang T, Magnotti EL, Conticello VP
Two-dimensional peptide and protein assemblies have been the focus of increased scientific research as they display significant potential for the creation of functional nanomaterials. Soluble subunits derived from a variety of protein motifs have been demonstrated to self-assemble into structurally defined nanosheets under environmentally benign conditions in which the components often retain their native structure and function. These types of two-dimensional assemblies may have an advantage for nanofabrication in that their extended planar shapes can be more straightforwardly incorporated into the current formats of nanoscale devices. However, significant challenges remain in the fabrication of these materials, particularly in devising methods to control the size, shape and internal structure of the resultant materials. Geometrical frustration may be envisioned as a possible mechanism to exert control over these structural parameters through rational design. While this objective has yet to be realized in practice, we discuss in this article the potential role of geometrical frustration as a principle to rationalize unusual self-assembly behaviour in several examples of two-dimensional peptide assemblies.
PMID: 29147554 [PubMed]
Structurally Ordered Nanowire Formation from Co-Assembly of DNA Origami and Collagen-Mimetic Peptides.
J Am Chem Soc. 2017 10 11;139(40):14025-14028
Authors: Jiang T, Meyer TA, Modlin C, Zuo X, Conticello VP, Ke Y
We describe the co-assembly of two different building units: collagen-mimetic peptides and DNA origami. Two peptides CP++ and sCP++ are designed with a sequence comprising a central block (Pro-Hyp-Gly) and two positively charged domains (Pro-Arg-Gly) at both N- and C-termini. Co-assembly of peptides and DNA origami two-layer (TL) nanosheets affords the formation of one-dimensional nanowires with repeating periodicity of ∼10 nm. Structural analyses suggest a face-to-face stacking of DNA nanosheets with peptides aligned perpendicularly to the sheet surfaces. We demonstrate the potential of selective peptide-DNA association between face-to-face and edge-to-edge packing by tailoring the size of DNA nanostructures. This study presents an attractive strategy to create hybrid biomolecular assemblies from peptide- and DNA-based building blocks that takes advantage of the intrinsic chemical and physical properties of the respective components to encode structural and, potentially, functional complexity within readily accessible biomimetic materials.
PMID: 28949522 [PubMed – indexed for MEDLINE]
Subcell Biochem. 2017;82:575-600
Authors: Conticello V, Hughes S, Modlin C
The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.
PMID: 28101873 [PubMed – indexed for MEDLINE]
J Am Chem Soc. 2016 12 21;138(50):16274-16282
Authors: Magnotti EL, Hughes SA, Dillard RS, Wang S, Hough L, Karumbamkandathil A, Lian T, Wall JS, Zuo X, Wright ER, Conticello VP
Sequence-specific peptides have been demonstrated to self-assemble into structurally defined nanoscale objects including nanofibers, nanotubes, and nanosheets. The latter structures display significant promise for the construction of hybrid materials for functional devices due to their extended planar geometry. Realization of this objective necessitates the ability to control the structural features of the resultant assemblies through the peptide sequence. The design of a amphiphilic peptide, 3FD-IL, is described that comprises two repeats of a canonical 18 amino acid sequence associated with straight α-helical structures. Peptide 3FD-IL displays 3-fold screw symmetry in a helical conformation and self-assembles into nanosheets based on hexagonal packing of helices. Biophysical evidence from TEM, cryo-TEM, SAXS, AFM, and STEM measurements on the 3FD-IL nanosheets support a structural model based on a honeycomb lattice, in which the length of the peptide determines the thickness of the nanosheet and the packing of helices defines the presence of nanoscale channels that permeate the sheet. The honeycomb structure can be rationalized on the basis of geometrical packing frustration in which the channels occupy defect sites that define a periodic superlattice. The resultant 2D materials may have potential as materials for nanoscale transport and controlled release applications.
PMID: 27936625 [PubMed – indexed for MEDLINE]
Adv Exp Med Biol. 2016;940:29-60
Authors: Magnotti E, Conticello V
Two-dimensional nanoscale assemblies (nanosheets) represent a promising structural platform to arrange molecular and supramolecular substrates with precision for integration into devices. This nanoarchitectonic approach has gained significant traction over the last decade, as a general concept to guide the fabrication of functional nanoscale devices. Sequence-specific biomolecules, e.g., peptides and proteins, may be considered excellent substrates for the fabrication of two-dimensional nanoarchitectonics. Molecular level instructions can be encoded within the sequence of monomers, which allows for control over supramolecular structure if suitable design principles could be elaborated. Due to the complexity of interactions between protomers, the development of principles aimed toward rational design of peptide and protein nanosheets is at a nascent stage. This review discusses the known two-dimensional peptide and protein assemblies to further our understanding of how to control the arrangement of molecules in two-dimensions.
PMID: 27677508 [PubMed – indexed for MEDLINE]
J Am Chem Soc. 2015 Jun 24;137(24):7793-802
Authors: Jiang T, Vail OA, Jiang Z, Zuo X, Conticello VP
Two collagen-mimetic peptides, CP(+) and CP(-), are reported in which the sequences comprise a multiblock architecture having positively charged N-terminal (Pro-Arg-Gly)3 and negatively charged C-terminal (Glu-Hyp-Gly)3 triad extensions, respectively. CP(+) rapidly self-associates into positively charged nanosheets based on a monolayer structure. In contrast, CP(-) self-assembles to form negatively charged monolayer nanosheets at a much slower rate, which can be accelerated in the presence of calcium(II) ion. A 2:1 mixture of unassociated CP(-) peptide with preformed CP(+) nanosheets generates structurally defined triple-layer nanosheets in which two CP(-) monolayers have formed on the identical surfaces of the CP(+) nanosheet template. Experimental data from electrostatic force microscopy (EFM) image analysis, zeta potential measurements, and charged nanoparticle binding assays support a negative surface charge state for the triple-layer nanosheets, which is the reverse of the positive surface charge state observed for the CP(+) monolayer nanosheets. The electrostatic complementarity between the CP(+) and CP(-) triple helical cohesive ends at the layer interfaces promotes a (CP(-)/CP(+)/CP(-)) compositional gradient along the z-direction of the nanosheet. This structurally informed approach represents an attractive strategy for the fabrication of two-dimensional nanostructures with compositional control.
PMID: 26021882 [PubMed – indexed for MEDLINE]
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.
Nat Methods. 2015 Apr;12(4):361-365
Authors: DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits T, Cheng Y, Baker D
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.
PMID: 25707030 [PubMed – indexed for MEDLINE]
Angew Chem Int Ed Engl. 2014 Aug 04;53(32):8367-71
Authors: Jiang T, Xu C, Zuo X, Conticello VP
A collagen-mimetic peptide, NSIII, has been designed with three sequential blocks having positive, neutral, and negative charges, respectively. The non-canonical imino acid, (2S,4S)-4-aminoproline (amp), was used to specify the positive charges at the Xaa positions of (Xaa-Yaa-Gly) triads in the N-terminal domain of NSIII. Peptide NSIII underwent self-assembly from aqueous solution to form a highly homogeneous population of nanosheets. Two-dimensional crystalline sheets formed in which the length of the peptide defined the height of the sheets. These results contrasted with prior results on a similar multi-domain collagen-mimetic polypeptides in which the sheets had highly polydisperse distribution of sizes in the (x/y)- and (z)-dimensions. The structural differences between the two nanosheet assemblies were interpreted in terms of the relative stereoelectronic effects of the different aminoproline derivatives on the local triple helical conformation of the peptides.
PMID: 24961508 [PubMed – indexed for MEDLINE]
J Am Chem Soc. 2014 Mar 19;136(11):4300-8
Authors: Jiang T, Xu C, Liu Y, Liu Z, Wall JS, Zuo X, Lian T, Salaita K, Ni C, Pochan D, Conticello VP
We report the design of two collagen-mimetic peptide sequences, NSI and NSII, that self-assemble into structurally defined nanoscale sheets. The underlying structure of these nanosheets can be understood in terms of the layered packing of collagen triple helices in two dimensions. These nanosheet assemblies represent a novel morphology for collagen-based materials, which, on the basis of their defined structure, may be envisioned as potentially biocompatible platforms for controlled presentation of chemical functionality at the nanoscale. The molecularly programmed self-assembly of peptides NSI and NSII into nanosheets suggests that sequence-specific macromolecules offer significant promise as design elements for two-dimensional (2D) assemblies. This investigation provides a design rubric for fabrication of structurally defined, peptide-based nanosheets using the principles of solution-based self-assembly facilitated through complementary electrostatic interactions.
PMID: 24571053 [PubMed – indexed for MEDLINE]
J Am Chem Soc. 2013 Oct 16;135(41):15565-78
Authors: Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP
Design of a structurally defined helical assembly is described that involves recoding of the amino acid sequence of peptide GCN4-pAA. In solution and the crystalline state, GCN4-pAA adopts a 7-helix bundle structure that resembles a supramolecular lock washer. Structurally informed mutagenesis of the sequence of GCN4-pAA afforded peptide 7HSAP1, which undergoes self-association into a nanotube via noncovalent interactions between complementary interfaces of the coiled-coil lock-washer structures. Biophysical measurements conducted in solution and the solid state over multiple length scales of structural hierarchy are consistent with self-assembly of nanotube structures derived from 7-helix bundle subunits. The dimensions of the supramolecular assemblies are similar to those observed in the crystal structure of GCN4-pAA. Fluorescence studies of the interaction of 7HSAP1 with the solvatochromic fluorophore PRODAN indicated that the nanotubes could encapsulate shape-appropriate small molecules with high binding affinity.
PMID: 24028069 [PubMed – indexed for MEDLINE]
J Am Chem Soc. 2013 Jul 17;135(28):10278-81
Authors: Anzini P, Xu C, Hughes S, Magnotti E, Jiang T, Hemmingsen L, Demeler B, Conticello VP
Peptide TZ1C2 can populate two distinct orientations: a staggered (out-of-register) fibril and an aligned (in-register) coiled-coil trimer. The coordination of two cadmium ions induces a registry shift that results in a reversible transition between these structural forms. This process recapitulates the self-assembly mechanism of native protein fibrils in which a ligand binding event gates a reversible conformational transition between alternate forms of a folded peptide structure.
PMID: 23815081 [PubMed – indexed for MEDLINE]
Multiple site-selective insertions of noncanonical amino acids into sequence-repetitive polypeptides.
Chembiochem. 2013 May 27;14(8):968-78
Authors: Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP
A simple and efficient method is described for the introduction of noncanonical amino acids at multiple, defined sites within recombinant polypeptide sequences. Escherichia coli MRA30, a bacterial host strain with attenuated activity of release factor 1 (RF1), was assessed for its ability to support incorporation of a diverse range of noncanonical amino acids in response to multiple encoded amber (TAG) codons within genes derived from superfolder GFP and an elastin-mimetic protein polymer. Suppression efficiency and protein yield depended on the identity of the orthogonal aminoacyl-tRNA synthetase/tRNA(CUA) pair and the noncanonical amino acid. Elastin-mimetic protein polymers were prepared in which noncanonical amino acid derivatives were incorporated at up to 22 specific sites within the polypeptide sequence with high substitution efficiency. The identities and positions of the variant residues were confirmed by mass spectrometric analysis of the full-length polypeptides and proteolytic cleavage fragments from thermolysin digestion. The data suggest that this multisite suppression approach permits the preparation of protein-based materials in which novel chemical functionalities can be introduced at precisely defined positions within the polypeptide sequence.
PMID: 23625817 [PubMed – indexed for MEDLINE]
Biotechnol Prog. 2009 Nov-Dec;25(6):1810-8
Authors: Sallach RE, Conticello VP, Chaikof EL
The translation of highly repetitive gene sequences is often associated with reduced levels of protein expression and may be prone to mutational events. In this report, we describe a modified concatemerization strategy to construct a gene with enhanced sequence diversity that encodes a highly repetitive elastin-like protein polymer for expression in Pichia pastoris. Specifically, degenerate oligonucleotides were used to create a monomer library, which after concatemerization yielded a genetically nonrepetitive DNA sequence that encoded identical pentapeptide repeat sequences. By limiting genetic repetition, the risk of genetic deletions, rearrangements, or premature termination errors during protein synthesis is minimized.
PMID: 19827084 [PubMed – indexed for MEDLINE]
A permanent change in protein mechanical responses can be produced by thermally-induced microdomain mixing.
J Biomater Sci Polym Ed. 2009;20(11):1629-44
Authors: Sallach RE, Leisen J, Caves JM, Fotovich E, Apkarian RP, Conticello VP, Chaikof EL
Electrospinning was employed to fabricate 3-D fiber networks from a recombinant amphiphilic elastin-mimetic tri-block protein polymer and the effects of moderate thermal conditioning (60 degrees C, 4 h) on network mechanical responses investigated. Significantly, while cryo-high resolution scanning electron microscopy (cryo-HRSEM) revealed that the macroscopic and microscopic morphology of the network structure was unchanged, solid-state (1)H-NMR spectroscopy demonstrated enhanced interphase mixing of hydrophobic and hydrophilic blocks. Significantly, thermal annealing triggered permanent changes in network swelling behavior (28.75 +/- 2.80 non-annealed vs. 13.55 +/- 1.39 annealed; P < 0.05) and uniaxial mechanical responses, including Young’s modulus (0.170 +/- 0.010 MPa non-annealed vs. 0.366 +/- 0.05 MPa annealed; P < 0.05) and ultimate tensile strength (0.079 +/- 0.008 MPa vs. 0.119 +/- 0.015 MPa; P < 0.05). To our knowledge, these investigations are the first to note that mechanical responses of protein polymers can be permanently altered through a temperature-induced change in microphase mixing.
PMID: 19619402 [PubMed – indexed for MEDLINE]