Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis

The controlled formation of nanoparticles with optimum characteristics and functional aspects has proven successful via peptide-mediated nanoparticle synthesis. However, the effects of the peptide sequence and binding motif on surface features and physicochemical properties of nanoparticles are not well-understood. In this study, we investigate in a comparative manner how a specific peptide known as Pd4 and its two known variants may form nanoparticles both in an isolated state and when attached to a green fluorescent protein (GFPuv). More importantly, we introduce a novel computational approach to predict the trend of the size and activity of the peptide-directed nanoparticles by estimating the binding affinity of the peptide to a single ion. We used molecular dynamics (MD) simulations to explore the differential behavior of the isolated and GFP-fused peptides and their mutants. Our computed palladium (Pd) binding free energies match the typical nanoparticle sizes reported from transmission electron microscope pictures. Stille coupling and Suzuki-Miyaura reaction turnover frequencies (TOFs) also correspond with computationally predicted Pd binding affinities. The results show that while using Pd4 and its two known variants (A6 and A11) in isolation produces nanoparticles of varying sizes, fusing these peptides to the GFPuv protein produces nanoparticles of similar sizes and activity. In other words, GFPuv reduces the sensitivity of the nanoparticles to the peptide sequence. This study provides a computational framework for designing free and protein-attached peptides that helps in the synthesis of nanoparticles with well-regulated properties.

Full-Atomistic Optimized Potentials for Liquid Simulations and Polymer Consistent Force Field Models for Biocompatible Shape-Memory Poly(ε-caprolactone)

Thermally induced shape memory poly(ε-caprolactone) (PCL)-based polymers are one of the most extensively researched families of biocompatible materials. They are degradable under physiological conditions and have high applicability in general biomedical engineering, with cross-linked PCL networks being particularly useful for tissue engineering. In this study, we used the optimized potentials for liquid simulations (OPLS) force field, which is well suited for describing intermolecular interactions in biomolecules, and the class II polymer consistent force field (PCFF) to investigate the properties of telechelic PCL with diacrylates as reactive functionalities on its end groups. PCFF has been specifically parameterized for simulating synthetic polymeric materials. We compare the findings of all-atom molecular dynamics simulations with known experimental data and theoretical assumptions to verify the applicability of both these force fields. We estimated the melt density, volume, transition temperatures, and mechanical characteristics of two-branched PCL diacrylates with a molecular weight of 2481 Da. Our findings point to the utility of the aforementioned force fields in predicting the properties of PCL-based polymers. It also opens avenues for developing PCL cross-linked polymer models and employing OPLS to investigate the interactions of synthetic polymers with biomolecules.

Protein-Nanoparticle Complex Structure Determination by Cryo-Electron Microscopy

Methods that allow the study of the structure of proteins in complex with nanomaterials promise to enhance our understanding of how biological molecules interface with inorganic materials. We used single-particle cryo-electron microscopy (cryo-EM) to demonstrate the potential for cryo-EM analysis to reveal structural details of protein-nanoparticle complexes. Two protein-nanomaterial complexes, namely, GroEL bound to platinum nanoparticles (GroEL-PtNP) and ferritin bound to an iron oxide nanoparticle, were used as model samples. For the GroEL-PtNP complex, a final reconstruction was obtained to 3.93 Å, which allowed us to fit the atomic model of GroEL into the resulting map. This sets the stage for future work and improvements on the use of cryo-EM for the study of protein-nanomaterial complexes.

Structure-guided identification of a peptide for bio-enabled gold nanoparticle synthesis

In this study, we show that maltose-binding protein (MBP) is capable of facilitating stable gold nanoparticle synthesis, and a structure of MBP in the presence of gold ions was determined by X-ray crystallography. Using this high-resolution structure of gold ion bound MBP, a peptide (AT1) was selected and synthesized and was shown to also aid in the synthesis of stable gold nanoparticles under similar experimental conditions to those used for protein facilitated synthesis. This structure-based approach represents a new potential method for the selection of peptides capable of facilitating stable nanoparticle synthesis.

Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials

The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.

In Situ Generation of Chiroptically-Active Gold-Peptide Superstructures Promoted by Iodination

Peptide-mediated routes to the synthesis of plasmonic nanoparticles have been drawing increasing attention for the development of chiroptically active nanoscale architectures. However, designing a multifunctional peptide able to drive the formation of structurally defined nanomaterials endowed with specific functionalities is still challenging. In this work, iodination has been devised as a strategy to strengthen Au-reduction capability of the amyloidogenic peptide DFNKF and combine it with its distinctive self-assembly features. Thanks to the Au-mediated C-I activation on the phenylalanine iodobenzenes, the peptides yield efficient Au-reduction ability promoting the synthesis of Au nanoparticles, and simultaneously working as templates for their spontaneous self-assembly into spherical superstructures endowed with chiroptical activities. The reaction occurs in situ through a one-pot process in aqueous media. The generality of this approach has been demonstrated using an iodinated derivative of the peptide KLVFF, which also showed reducing and templating abilities forming chiroptically active helical superstructures decorated with Au nanoparticles.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Optical Control of Nanoparticle Catalysis Influenced by Photoswitch Positioning in Hybrid Peptide Capping Ligands

Here, we present an in-depth analysis of structural factors that modulate peptide-capped nanoparticle catalytic activity via optically driven structural reconfiguration of the biointerface present at the particle surface. Six different sets of peptide-capped Au nanoparticles were prepared, in which an azobenzene photoswitch was incorporated into one of two well-studied peptide sequences with known affinity for Au, each at one of three different positions: the N- or C-terminus or mid-sequence. Changes in the photoswitch isomerization state induce a reversible structural change in the surface-bound peptide, which modulates the catalytic activity of the material. This control of reactivity is attributed to changes in the amount of accessible metallic surface area available to drive the reaction. This research specifically focuses on the effect of the peptide sequence and photoswitch position in the biomolecule, from which potential target systems for on/off reactivity have been identified. Additionally, trends associated with photoswitch position for a peptide sequence (Pd4) have been identified. Integrating the azobenzene at the N-terminus or central region results in nanocatalysts with greater reactivity in the trans and cis conformations, respectively, however, positioning the photoswitch at the C-terminus gives rise to a unique system that is reactive in the trans conformation and partially deactivated in the cis conformation. These results provide a fundamental basis for new directions in nanoparticle catalyst development to control activity in real time, which could have significant implications in the design of catalysts for multistep reactions using a single catalyst. Additionally, such a fine level of interfacial structural control could prove to be important for applications beyond catalysis, including biosensing, photonics, and energy technologies that are highly dependent on particle surface structures.

Nature of peptide wrapping onto metal nanoparticle catalysts and driving forces for size control

Colloidal metal nanocrystals find many applications in catalysis, energy conversion devices, and therapeutics. However, the nature of ligand interactions and implications on shape control have remained uncertain at the atomic scale. Large differences in peptide adsorption strength and facet specificity were found on flat palladium surfaces versus surfaces of nanoparticles of 2 to 3 nm size using accurate atomistic simulations with the Interface force field. Folding of longer peptides across many facets explains the formation of near-spherical particles with local surface disorder, in contrast to the possibility of nanostructures of higher symmetry with shorter ligands. The average particle size in TEM correlates inversely with the surface coverage with a given ligand and with the strength of ligand adsorption. The role of specific amino acids and sequence mutations on the nanoparticle size and facet composition is discussed, as well as the origin of local surface disorder that leads to large differences in catalytic reactivity.

Seed-Mediated Growth of Colloidal Metal Nanocrystals

Seed-mediated growth is a powerful and versatile approach for the synthesis of colloidal metal nanocrystals. The vast allure of this approach mainly stems from the staggering degree of control one can achieve over the size, shape, composition, and structure of nanocrystals. These parameters not only control the properties of nanocrystals but also determine their relevance to, and performance in, various applications. The ingenuity and artistry inherent to seed-mediated growth offer extensive promise, enhancing a number of existing applications and opening the door to new developments. This Review demonstrates how the diversity of metal nanocrystals can be expanded with endless opportunities by using seeds with well-defined and controllable internal structures in conjunction with a proper combination of capping agent and reduction kinetics. New capabilities and future directions are also highlighted.

Peptide-Directed Assembly of Single-Helical Gold Nanoparticle Superstructures Exhibiting Intense Chiroptical Activity

Chiral nanoparticle assemblies are an interesting class of materials whose chiroptical properties make them attractive for a variety of applications. Here, C18-(PEPAuM-ox)2 (PEPAuM-ox = AYSSGAPPMoxPPF) is shown to direct the assembly of single-helical gold nanoparticle superstructures that exhibit exceptionally strong chiroptical activity at the plasmon frequency with absolute g-factor values up to 0.04. Transmission electron microscopy (TEM) and cryogenic electron tomography (cryo-ET) results indicate that the single helices have a periodic pitch of approximately 100 nm and consist of oblong gold nanoparticles. The morphology and assembled structure of C18-(PEPAuM-ox)2 are studied using TEM, atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD) spectroscopy, X-ray diffraction (XRD), and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. TEM and AFM reveal that C18-(PEPAuM-ox)2 assembles into linear amyloid-like 1D helical ribbons having structural parameters that correlate to those of the single-helical gold nanoparticle superstructures. FTIR, CD, XRD, and ssNMR indicate the presence of cross-β and polyproline II secondary structures. A molecular assembly model is presented that takes into account all experimental observations and that supports the single-helical nanoparticle assembly architecture. This model provides the basis for the design of future nanoparticle assemblies having programmable structures and properties.

Peptide-Directed PdAu Nanoscale Surface Segregation: Toward Controlled Bimetallic Architecture for Catalytic Materials

Bimetallic nanoparticles are of immense scientific and technological interest given the synergistic properties observed when two different metallic species are mixed at the nanoscale. This is particularly prevalent in catalysis, where bimetallic nanoparticles often exhibit improved catalytic activity and durability over their monometallic counterparts. Yet despite intense research efforts, little is understood regarding how to optimize bimetallic surface composition and structure synthetically using rational design principles. Recently, it has been demonstrated that peptide-enabled routes for nanoparticle synthesis result in materials with sequence-dependent catalytic properties, providing an opportunity for rational design through sequence manipulation. In this study, bimetallic PdAu nanoparticles are synthesized with a small set of peptides containing known Pd and Au binding motifs. The resulting nanoparticles were extensively characterized using high-resolution scanning transmission electron microscopy, X-ray absorption spectroscopy, and high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Structural information obtained from synchrotron radiation methods was then used to generate model nanoparticle configurations using reverse Monte Carlo simulations, which illustrate sequence dependence in both surface structure and surface composition. Replica exchange with solute tempering molecular dynamics simulations were also used to predict the modes of peptide binding on monometallic surfaces, indicating that different sequences bind to the metal interfaces via different mechanisms. As a testbed reaction, electrocatalytic methanol oxidation experiments were performed, wherein differences in catalytic activity are clearly observed in materials with identical bimetallic composition. Taken together, this study indicates that peptides could be used to arrive at bimetallic surfaces with enhanced catalytic properties, which could be leveraged for rational bimetallic nanoparticle design using peptide-enabled approaches.

Simple and Flexible Model for Laser-Driven Antibody-Gold Surface Interactions: Functionalization and Sensing

Interactions between biomolecules and between substrates and biomolecules is a crucial issue in physics and applications to topics such as biotechnology and organic electronics. The efficiency of bio- and mechanical sensors, of organic electronics systems, and of a number of other devices critically depends on how molecules are deposited on a surface so that these acquire specific functions. Here, we tackle this vast problem by developing a coarse grained model of biomolecules having a recognition function, such as antibodies, capable to quantitatively describe in a simple manner essential phenomena: antigen-antibody and antibody substrate interactions. The model is experimentally tested to reproduce the results of a benchmark case, such as (1) gold surface functionalization with antibodies and (2) antibody-antigen immune-recognition function. The agreement between experiments and model prediction is excellent, thus unveiling the mechanism for antibody immobilization onto metals at the nanoscale in various functionalization schemes. These results shed light on the geometrical packing properties of the deposited molecules, and may open the way to a novel coarse-grained based approach to describe other processes where molecular packing is a key issue with applications in a huge number of fields from nano- to biosciences.

A Palladium-Binding Deltarhodopsin for Light-Activated Conversion of Protonic to Electronic Currents

Fusion of a palladium-binding peptide to an archaeal rhodopsin promotes intimate integration of the lipid-embedded membrane protein with a palladium hydride protonic contact. Devices fabricated with the palladium-binding deltarhodopsin enable light-activated conversion of protonic currents to electronic currents with on/off responses complete in seconds and a nearly tenfold increase in electrical signal relative to those made with the wild-type protein.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Facet selectivity in gold binding peptides: exploiting interfacial water structure

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.

Thermodynamic Study of Interactions Between ZnO and ZnO Binding Peptides Using Isothermal Titration Calorimetry

While material-specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modeling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully realized. Understanding the thermodynamic changes that occur during peptide-inorganic interactions and correlating these to structural modifications of the inorganic materials could be the key to achieving and mastering control over material formation processes. This study is a detailed investigation applying isothermal titration calorimetry (ITC) to directly probe thermodynamic changes that occur during interaction of ZnO binding peptides (ZnO-BPs) and ZnO. The ZnO-BPs used are reported sequences G-12 (GLHVMHKVAPPR), GT-16 (GLHVMHKVAPPR-GGGC), and alanine mutants of G-12 (G-12A6, G-12A11, and G-12A12) whose interaction with ZnO during solution synthesis studies have been extensively investigated. The interactions of the ZnO-BPs with ZnO yielded biphasic isotherms comprising both an endothermic and an exothermic event. Qualitative differences were observed in the isothermal profiles of the different peptides and ZnO particles studied. Measured ΔG values were between -6 and -8.5 kcal/mol, and high adsorption affinity values indicated the occurrence of favorable ZnO-BP-ZnO interactions. ITC has great potential in its use to understand peptide-inorganic interactions, and with continued development, the knowledge gained may be instrumental for simplification of selection processes of organic molecules for the advancement of material synthesis and design.

Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences.

Reductant and sequence effects on the morphology and catalytic activity of peptide-capped Au nanoparticles

The use of peptides as capping ligands for materials synthesis has been widely explored. The ambient conditions of bio-inspired syntheses using molecules such as peptides represent an attractive route for controlling the morphology and activity of nanomaterials. Although various reductants can be used in such syntheses, no comprehensive comparison of the same bio-based ligand with different reductants has been reported. In this contribution, peptides AuBP1, AuBP2, and Pd4 are used in the synthesis of Au nanoparticles. The reductant strength is varied by using three different reducing agents: NaBH4, hydrazine, and ascorbic acid. These changes in reductant produce significant morphological differences in the final particles. The weakest reductant, ascorbic acid, yields large, globular nanoparticles with rough surfaces, whereas the strongest reductant, NaBH4, yields small, spherical, smooth nanomaterials. Studies of 4-nitrophenol reduction using the Au nanoparticles as catalysts reveal a decrease in activation energy for the large, globular, rough materials relative to the small, spherical, smooth materials. These studies demonstrate that modifying the reductant is a simple way to control the activity of peptide-capped nanoparticles.

Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors

Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.

A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (¹H ²S ³S ⁴Y ⁵W ⁶Y ⁷A ⁸F ⁹N ¹⁰N ¹¹K ¹²T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular aggregates at low temperatures and disperse as random-coil at high temperatures. The specificity of the mass distribution of the self-assembly depends on the temperature and spatial lengths which are identified from the scaling of the structure factor. Analysis of energy and mobility profiles, gyration radius of peptide, and radial distribution function of the assembly provide insight into the multi-scale (intra- and inter-chain) characteristics. Thermal response of the global assembly with the simulated residue-residue interaction is consistent with that of the knowledge-based analysis despite expected quantitative differences.

Variation in structure of a protein (H2AX) with knowledge-based interactions

The structure of a protein (H2AX) as a function of temperature is examined by three knowledge-based phenomenological interactions, MJ (Miyazawa and Jernigan), BT (Betancourt and Thirumalai), and BFKV (Bastolla et al.) to identify similarities and differences in results. Data from the BT and BFKV residue-residue interactions verify finding with the MJ interaction, i.e., the radius of gyration (R_g) of H2AX depends non-monotonically on temperature. The increase in R_g is followed by a decay on raising the temperature with a maximum at a characteristic value, T_c, which depends on the knowledge-based contact matrix, T_cBFKV ≤ T_cMJ ≤ T_cBT. The range (ΔT) of non-monotonic thermal response and its decay pattern with the temperature are sensitive to interaction. A rather narrow temperature range of ΔT_MJ ≈ 0.015–0.022 with the MJ interaction expands and shifts up to ΔT_BT ≈ 0.018–0.30 at higher temperatures with the BT interaction and shifts down with the BFKV interaction to ΔT_BFKV ≈ 0.011–0.018. The scaling of the structure factor with the wave vector reveals that the structure of the protein undergoes a transformation from a random coil at high temperature to a globular conformation at low temperatures.

Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution

Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (-20 to -60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (-15 to -25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often β-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures.

Determining peptide sequence effects that control the size, structure, and function of nanoparticles

The ability to tune the size, shape, and composition of nanomaterials at length scales <10 nm remains a challenging task. Such capabilities are required to fully realize the application of nanotechnology for catalysis, energy storage, and biomedical technologies. Conversely, nature employs biomacromolecules such as proteins and peptides as highly specific nanoparticle ligands that demonstrate exacting precision over the particle morphology through controlling the biotic/abiotic interface. Here we demonstrate the ability to finely tune the size, surface structure, and functionality of single-crystal Pd nanoparticles between 2 and 3 nm using materials directing peptides. This was achieved by selectively altering the peptide sequence to change the binding motif, which in turn modifies the surface structure of the particles. The materials were fully characterized before and after reduction using atomically resolved spectroscopic and microscopic analyses, which indicated that the coordination environment prior to reduction significantly affects the structure of the final nanoparticles. Additionally, changes to the particle surface structure, as a function of peptide sequence, can allow for chloride ion coordination that alters the catalytic abilities of the materials for the C-C coupling Stille reaction. These results suggest that peptide-based approaches may be able to achieve control over the structure/function relationship of nanomaterials where the peptide sequence could be used to selectivity tune such capabilities.

Nanotechnology Meets Biology: Peptide-based Methods for the Fabrication of Functional Materials

Nature exploits sustainable methods for the creation of inorganic materials on the nanoscale for a variety of applications. To achieve such capabilities, biomolecules such as peptides and proteins have been developed that recognize and bind the different compositions of materials. While a diverse set of materials binding sequences are present in the biosphere, biocombinatorial techniques have been used to rapidly identify peptides that facilitate the formation of new materials of technological importance. Interestingly, the binding motif of the peptides at the inorganic surface is likely to control the size, structure, composition, shape, and functionality of the final materials. In order to advance these intriguing new biomimetic approaches, a complete understanding of this biotic/abiotic interface is required. In this Perspective, we highlight recent advances in the biofunctionalization of nanoparticles with potential applications ranging from catalysis and energy storage to plasmonics and biosensing. We specifically focus on the physical characterization of the peptide-based surface from which specificity and activity are likely embedded.

The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces

We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues. We found that tyrosine, methionine, and phenylalanine are strong binding residues; serine serves as an effective anchoring residue; proline acts as a dynamic anchoring point, while glycine and alanine give flexibility to the peptide backbone. We then show that our findings apply to unrelated phage-derived sequences that have been reported recently to facilitate AuNP synthesis. This new knowledge may aid in the design of new peptides for the synthesis of gold nanostructures with novel morphologies.

Control over self-assembly of diblock copolymers on hexagonal and square templates for high area density circuit boards

Self-assembled diblock copolymer melts on patterned substrates can induce a smaller characteristic domain spacing compared to predefined lithographic patterns and enable the manufacture of circuit boards with a high area density of computing and storage units. Monte Carlo simulation using coarse-grain models of polystyrene-b-polydimethylsiloxane shows that the generation of high-density hexagonal and square patterns is controlled by the ratio N(D) of the surface area per post and the surface area per spherical domain of neat block copolymer. N(D) represents the preferred number of block copolymer domains per post. Selected integer numbers support the formation of ordered structures on hexagonal (1, 3, 4, 7, 9) and square (1, 2, 5, 7) templates. On square templates, only smaller numbers of block copolymer domains per post support the formation of ordered arrays with significant stabilization energies relative to hexagonal morphology. Deviation from suitable integer numbers N(D) increases the likelihood of transitional morphologies between square and hexagonal. Upon increasing the spacing of posts on the substrate, square arrays, nested square arrays, and disordered hexagonal morphologies with multiple coordination numbers were identified, accompanied by a decrease in stabilization energy. Control over the main design parameter N(D) may allow an up to 7-fold increase in density of spherical block copolymer domains per surface area in comparison to the density of square posts and provide access to a wide range of high-density nanostructures to pattern electronic devices.

Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach

A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al. [Phys. Chem. Chem. Phys., 2011, 13, 1123-1130]). Both local (mobility, solvent-surrounding, energy profiles) and global (variation of the root mean square displacement of peptides and its gyration radius with time steps, radial distribution function, and structure factors) physical quantities are analyzed as a function of the solvent quality (i.e. the solvent-residue interaction strength). We find that the mobility of the interacting side group (lysine) decays as the number of its surrounding solvent constituents grows systematically on increasing the interaction strength. Pinning of lysine directs the underlying segmental conformation that propagates to larger scale scaffolding. The radial distribution function (a measure of the correlated peptide assembly) decays with the distance (faster with stronger solvent interaction). Scaling of the structure factor (S(q)) of peptide assembly with the wave vector q = 2π/λ (λ is the wavelength), S(q) ∝q(-1/ν) provides an insight into its multi-scale mass (N) distribution. The effective dimension D(e) = 1/ν of the peptide assembly over the spatial distribution (R) can be estimated using N∝R(D(e)). On scales larger than the size (i.e. the radius of gyration R(g)) of the peptide, D(e) ≈ 1.303 ± 0.070 to D(e) ≈ 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, D(e) ≈ 1.809 ± 0.017 to D(e) ≈ 1.978 ± 0.017, at a smaller scale R≤R(g).

Interrogating the catalytic mechanism of nanoparticle mediated Stille coupling reactions employing bio-inspired Pd nanocatalysts

To address issues concerning the global environmental and energy state, new catalytic technologies must be developed that translate ambient and efficient conditions to heavily used reactions. To achieve this, the structure/function relationship between model catalysts and individual reactions must be critically discerned to identify structural motifs responsible for the reactivity. This is especially true for nanoparticle-based systems where this level of information remains limited. Here we present evidence indicating that peptide-capped Pd nanoparticles drive Stille C-C coupling reactions via Pd atom leaching. Through a series of reaction studies, the materials are shown to be optimized for reactivity under ambient conditions where increases in temperature or catalyst concentration deactivate reactivity due to the leaching process. A quartz crystal microbalance analysis demonstrates that Pd leaching occurs during the initial oxidative addition step at the nanoparticle surface by aryl halides. Together, this suggests that peptide-based materials may be optimally suited for use as model systems to isolate structural motifs responsible for the generation of catalytically reactive materials under ambient synthetic conditions.

Biological surface effects of metallic nanomaterials for applications in assembly and catalysis

Recent experimental evidence has suggested that bioinspired techniques represent promising avenues toward the production of functional nanomaterials that possess a high degree of activity. These materials are prepared under synthetically simple and efficient conditions, thus making them attractive alternatives to many traditional methods that employ hazardous and harsh conditions. Many biomimetic methods employ peptide and amino acid binding events on the surfaces of nanostructures to generate materials that are stable in solution. The basis of both the stability and activity of these materials is likely to be controlled by the biotic/abiotic interface, which is mediated by the bioligand binding process. Unfortunately, most readily available techniques are unable to be used to study this intrinsic process; however, very recent studies have begun to shed light on this important event. In this feature article, an overview of the understanding of peptide and amino acid binding events to nanomaterials and how these motifs can be exploited for activities in nanoparticle assembly and catalytic reactivity is discussed. From both 2D surface studies and computational modeling analyses, different biomolecule binding characteristics have been elucidated. These results indicate that the amino acid sequence and peptide secondary structure play important roles in the binding capability. Furthermore, these studies suggest that the peptides are able to form specific patterns and motifs once bound to the nanoparticle surface. This attribute could affect the nanoparticle electronics and can play a significant role in their activities to generate functional materials. From these binding motifs, the ability of reagents to interact with the metallic surface is possible, thus affecting many of the properties of these materials.

Polarization at metal-biomolecular interfaces in solution

Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately -50 mJ m(-2) and decreases to -70 mJ m(-2) in the presence of charged peptides. In molecular terms, the polarization energy corresponds to -2.3 and -0.1 kJ mol(-1) for water in the first and second molecular layers on the metal surface, and to between -40 and 0 kJ mol(-1) for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10-20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (-80 kJ mol(-1) for peptide Flg-Na(3)). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies.