Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions

On the interactions of peptides with gold nanoparticles: effects of sequence and size

Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous media. In the present study, we use all-atom molecular dynamic (MD) simulations to study the interactions of ten short peptides (namely A3, AgBP1, AgBP2, AuBP1, AuBP2, GBP1, Midas2, Pd4, Z1, and Z2) with different gold nanoparticles (of different diameters ranging from 2 to 8 nm). Our MD simulation results imply that the gold nanoparticles have a remarkable effect on the stability and conformational properties of peptides. Moreover, the size of the gold nanoparticles and the type of peptide amino acid sequences play important roles in the stability of the peptide-AuNP complexes. Our results reveal that some amino acids such as Tyr, Phe, Met, Lys, Arg, and Gln have direct contact with the metal surface in comparison with Gly, Ala, Pro, Thr, and Val residues. The peptide adsorption on the surface of the gold nanoparticles is favorable from the energetic viewpoint, in which the van der Waals (vdW) interactions between the peptides and metal surface can be considered as one of the driving forces for the complexation process. The calculated Gibbs binding energies indicate that AuNPs have more sensitivity against the GBP1 peptide in the presence of different peptides. Overall, the results of this study can provide new insight into the peptide interaction with the gold nanoparticles from the molecular viewpoint, which can be important for designing new biomaterials based on the peptides and gold nanoparticles.Communicated by Ramaswamy H. Sarma.

Resolving Atomic-Scale Structure and Chemical Coordination in High-Entropy Alloy Electrocatalysts for Structure-Function Relationship Elucidation

The recent breakthrough in confining five or more atomic species in nanocatalysts, referred to as high-entropy alloy nanocatalysts (HEAs), has revealed the possibilities of multielemental interactions that can surpass the limitations of binary and ternary electrocatalysts. The wide range of potential surface configurations in HEAs, however, presents a significant challenge in resolving active structural motifs, preventing the establishment of structure-function relationships for rational catalyst design and optimization. We present a methodology for creating sub-5 nm HEAs using an aqueous-based peptide-directed route. Using a combination of pair distribution function and X-ray absorption spectroscopy, HEA structure models are constructed from reverse Monte Carlo modeling of experimental data sets and showcase a clear peptide-induced influence on atomic-structure and chemical miscibility. Coordination analysis of our structure models facilitated the construction of structure-function correlations applied to electrochemical methanol oxidation reactions, revealing the complex interplay between multiple metals that leads to improved catalytic properties. Our results showcase a viable strategy for elucidating structure-function relationships in HEAs, prospectively providing a pathway for future materials design.

Shape control of Au nanostructures using peptides for biotechnological applications

Metallic gold (Au) nanostructures have attracted attentions in various fields of materials science and electrical science in terms of catalysts, sensing systems, photonic devices, and drug delivery systems because of their characteristic physical, chemical, and biocompatible properties. Recently, Au nanostructures with near-infrared light absorbing properties have shown potential for applications such as biological imaging and thermotherapy in biotechnological fields. However, fabrication of Au nanostructures with complex shapes often requires the use of highly biotoxic substances such as surfactants and reducing agents. Peptides are promising compounds for controlling the shape of Au nanostructures by mineralization with several advantages for this purpose. In this highlight, we focus on the shapes with respect to the fabrication of Au nanostructures using biocompatible peptides. We classify the peptides that form Au nanostructures into three broad categories: those that bind Au ions, those that reduce Au ions, and those that control the direction of Au crystal growth. Then, we briefly summarize the correlations between peptide sequences and their roles, and propose future strategies for fabricating Au nanostructures using peptides for biotechnological applications.

Advances in the design of amino acid and peptide synthesized gold nanoparticles for their applications

The field of therapeutics and diagnostics is advanced by nanotechnology-based approaches including the spatial-temporal release of drugs, targeted delivery, enhanced accumulation of drugs, immunomodulation, antimicrobial action, and high-resolution bioimaging, sensors and detection. Various compositions of nanoparticles (NPs) have been developed for biomedical applications; however, gold NPs (Au NPs) have attracted tremendous attention due to their biocompatibility, easy surface functionalization and quantification. Amino acids and peptides have natural biological activities as such, their activities enhance several folds in combination with NPs. Although peptides are extensively used to produce various functionalities of Au NPs, amino acids have also gained similar interests in producing amino acid-capped Au NPs due to the availability of amine, carboxyl and thiol functional groups. Henceforth, a comprehensive review is needed to timely bridge the synthesis and the applications of amino acid and peptide-capped Au NPs. This review aims to describe the synthesis mechanism of Au NPs using amino acids and peptides along with their applications in antimicrobial, bio/chemo-sensors, bioimaging, cancer therapy, catalysis, and skin regeneration. Moreover, the mechanisms of various activities of amino acid and peptide capped-Au NPs are presented. We believe this review will motivate researchers to better understand the interactions and long-term activities of amino acid and peptide-capped Au NPs for their success in various applications.

Biomimetic Sequence-Templating Approach toward a Multiscale Modulation of Chromogenic Polymer Properties

Precision control via molecular structure over adaptive conjugated polymer properties in aqueous environments is critical for realizing their biomedical applications. Here, we unravel the dependence of amphiphilic peptide-polydiacetylene (PDA) conjugate properties on the characteristic steric and hydrophobic contributions within peptide segments that serve as a biomimetic template for diacetylene polymerization in water. We investigated the functional impacts of molecular volume and polarity changes brought by dipeptide substitution domains on the following peptide-PDA material properties at multiple length scales: supramolecular assembly behavior, chain conformation-dependent photophysical properties, cell-material interfacing, and for the first time, bulk electrical properties of their films processed in water. A library of peptide-PDAs with systematically varied sequences show that the contributions of steric effects predominantly influence the electronic structure and resulting trends in photophysical properties, while the interplay between size and hydrophobicity of individual residues becomes more significant for higher-order assemblies affecting bulk properties. This work demonstrates sequence-tunable molecular volume and polarity as synthetic handles to rationally modulate PDA material properties across length scales, providing insights into the programmability of biomimetic conjugated polymers with adaptive functionalities.

Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures

Assembling nanoparticles (NPs) into well-defined superstructures can lead to emergent collective properties that depend on their 3-D structural arrangement. Peptide conjugate molecules designed to both bind to NP surfaces and direct NP assembly have proven useful for constructing NP superstructures, and atomic- and molecular-level alterations to these conjugates have been shown to manifest in observable changes to nanoscale structure and properties. The divalent peptide conjugate, C₁₆-(PEP_Au)₂ (PEP_Au = AYSSGAPPMPPF), directs the formation of one-dimensional helical Au NP superstructures. This study examines how variation of the ninth amino acid residue (M), which is known to be a key Au anchoring residue, affects the structure of the helical assemblies. A series of conjugates of differential Au binding affinities based on variation of the ninth residue were designed, and Replica Exchange with Solute Tempering (REST) Molecular Dynamics simulations of the peptides on an Au(111) surface were performed to determine the approximate surface contact and to assign a binding score for each new peptide. A helical structure transition from double helices to single helices is observed as the peptide binding affinity to the Au(111) surface decreases. Accompanying this distinct structural transition is the emergence of a plasmonic chiroptical signal. REST-MD simulations were also used to predict new peptide conjugate molecules that would preferentially direct the formation of single-helical AuNP superstructures. Significantly, these findings demonstrate how small modifications to peptide precursors can be leveraged to precisely direct inorganic NP structure and assembly at the nano- and microscale, further expanding and enriching the peptide-based molecular toolkit for controlling NP superstructure assembly and properties.

Biomimetic mineralization based on self-assembling peptides

Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.

Controlling Mineralization with Protein-Functionalized Peptoid Nanotubes

Sequence-defined foldamers that self-assemble into well-defined architectures are promising scaffolds to template inorganic mineralization. However, it has been challenging to achieve robust control of nucleation and growth without sequence redesign or extensive experimentation. Here, peptoid nanotubes functionalized with a panel of solid-binding proteins are used to mineralize homogeneously distributed and monodisperse anatase nanocrystals from the water-soluble TiBALDH precursor. Crystallite size is systematically tuned between 1.4 and 4.4 nm by changing protein coverage and the identity and valency of the genetically engineered solid-binding segments. The approach is extended to the synthesis of gold nanoparticles and, using a protein encoding both material-binding specificities, to the fabrication of titania/gold nanocomposites capable of photocatalysis under visible-light illumination. Beyond uncovering critical roles for hierarchical organization and denticity on solid-binding protein mineralization outcomes, the strategy described herein should prove valuable for the fabrication of hierarchical hybrid materials incorporating a broad range of inorganic components.

Chiral-engineered supraparticles: Emerging tools for drug delivery

The handedness of chiral-engineered supraparticles (CE-SPs) influences their interactions with cells and proteins, as evidenced by the increased penetration of breast, cervical, and myeloma cell membranes by d-chirality-coordinated SPs. Quartz crystal dissipation and isothermal titration calorimetry have been used to investigate such chiral-specific interactions. d-SPs are more thermodynamically stable compared with l-SPs in terms of their adhesion. Proteases and other endogenous proteins can be shielded by the opposite chirality of d-SPs, resulting in longer half-lives. Incorporating nanosystems with d-chirality increases uptake by cancer cells and prolongs in vivo stability, demonstrating the importance of chirality in biomaterials. Thus, as we discuss here, chiral nanosystems could enhance drug delivery systems, tumor markers, and biosensors, among other biomaterial-based technologies, by allowing for better control over their features.

Achieving regioselective materials binding using multidomain peptides

The ability to integrate two disparate materials-binding domains into a single ligand to achieve regiospecific binding would be powerful to direct material assembly; however, this has proven challenging to achieve due to cross-materials binding. Accomplishing this goal might be achieved by harnessing the precision of biology to exploit the recognition between peptides and specific nanomaterials. Here, a designed bifunctional molecule termed Biomolecular Exfoliant and Assembly Motifs (BEAM) is introduced, featuring two different materials-binding peptide domains, one for graphene and one for hexagonal boron nitride (h-BN), at each end of the molecule, separated by a fatty acid spacer. The BEAM is demonstrated to bind strongly to both graphene and h-BN surfaces, and in each case the materials-binding peptide domain is shown to preferentially bind its target material. Critically, the two materials-binding domains exhibited limited cross-domain interaction. The BEAM design concept shows substantial potential to eventually guide self-organization of a range of materials in aqueous media.

Peptide modification on the interior surface of red blood cell ghosts for construction of catalytic reactors

We report in situ synthesis of gold nanoparticles (Au NPs) on the interior surfaces of red blood cell ghosts (RBCGs) with a cytoskeleton conjugated to a gold-binding peptide and reduction of 4-nitrophenol by the resulting Au NP-deposited RBCG.

Towards the identification of the gold binding region within trypsin stabilized nanoclusters using microwave synthesis routes

Elucidating the location of stabilized nanoclusters within their protein hosts is an existing challenge towards the optimized development of functional protein-nanoclusters. While nanoclusters of various metal compositions can be readily synthesized within a wide array of protein hosts and exhibit tailorable properties, the inability to identify the cluster stabilization region prevents controllable property manipulation of both metallic and protein components. Additionally, the ability to synthesize protein-nanoclusters in a consistent and high-throughput fashion is also highly desirable. In this effort, trypsin stabilized gold nanoclusters are synthesized through standard and microwave-enabled methodologies to determine the impact of processing parameters on the materials physical and functional properties. Density functional theory simulations are employed to localize high probability regions within the trypsin enzyme for Au25 cluster stabilization, which reveal that cluster location is likely within close proximity of the trypsin active region. Trypsin activity measurements support our findings from DFT, as trypsin enzymatic activity is eliminated following cluster growth and stabilization. Moreover, studies on the reactivity of Au NCs and synchrotron characterization measurements further reveal that clusters made by microwave-based techniques exhibit slight structural differences to those made via standard methodologies, indicating that microwave-based syntheses largely maintain the native structural attributes despite the faster synthetic conditions. Overall, this work illustrates the importance of understanding the connections between synthetic conditions, atomic-scale structure, and materials properties that can be potentially used to further tune the properties of metal cluster-protein materials for future applications.

Peptide-directed Pd-decorated Au and PdAu nanocatalysts for degradation of nitrite in water

In this work, a palladium binding peptide, Pd4, has been used for the synthesis of catalytically active palladium-decorated gold (Pd-on-Au) nanoparticles (NPs) and palladium–gold (Pd_xAu_100−x) alloy NPs exhibiting high nitrite degradation efficiency. Pd-on-Au NPs with 20% to 300% surface coverage (sc%) of Au showed catalytic activity commensurate with sc%. Additionally, the catalytic activity of Pd_xAu_100−x alloy NPs varied based on palladium composition (x = 6–59). The maximum nitrite removal efficiency of Pd-on-Au and Pd_xAu_100−x alloy NPs was obtained at sc 100% and x = 59, respectively. The synthesized peptide-directed Pd-on-Au catalysts showed an increase in nitrite reduction three and a half times better than monometallic Pd and two and a half times better than Pd_xAu_100−x NPs under comparable conditions. Furthermore, peptide-directed NPs showed high activity after five reuse cycles. Pd-on-Au NPs with more available activated palladium atoms showed high selectivity (98%) toward nitrogen gas production over ammonia.

In this work, a palladium binding peptide, Pd4, has been used for the synthesis of catalytically active palladium-decorated gold (Pd-on-Au) nanoparticles (NPs) and palladium–gold (Pd_xAu_100−x) alloy NPs exhibiting high nitrite degradation efficiency.

Simulating selective binding of a biological template to a nanoscale architecture: a core concept of a clamp-based binding-pocket-favored N-terminal-domain assembly

The biological template and its mutants have vital significance in next generation remediation, electrochemical, photovoltaic, catalytic, sensing and digital memory devices. However, a microscopic model describing the biotemplating process is generally lacking on account of modelling complexity, which has prevented widespread commercial use of biotemplates. Here, we demonstrate M13-biotemplating kinetics in atomic resolution by leveraging large-scale molecular dynamics (MD) simulations. The model reveals the assembly of gold nanoparticles on two experimentally-based M13 phage types using full M13-capsid structural models and with polarizable gold nanoparticles in explicit solvent. Both mechanistic and structural insights into the selective binding affinity of the M13 phage to gold nanoparticles are obtained based on a previously unconsidered clamp-based binding-pocket-favored N-terminal-domain assembly and also on surface-peptide flexibility. These results provide a deeper level of understanding of protein sequence-based affinity and open the route for genetically engineering a wide range of 3D electrodes for high-density low-cost device integration.

Valence Alignment of Mixed Ni-Fe Hydroxide Electrocatalysts through Preferential Templating on Graphene Edges for Enhanced Oxygen Evolution

Engineering the metal-carbon heterointerface has become an increasingly important route toward achieving cost-effective and high-performing electrocatalysts. The specific properties of graphene edge sites, such as the high available density of states and extended unpaired π-bonding, make it a promising candidate to tune the electronic properties of metal catalysts. However, to date, understanding and leveraging graphene edge-metal catalysts for improved electrocatalytic performance remains largely elusive. Herein, edge-rich vertical graphene (er-VG) was synthesized and used as a catalyst support for Ni-Fe hydroxides for the oxygen evolution reaction (OER). The hybrid Ni-Fe/er-VG catalyst exhibits excellent OER performance with a mass current of 4051 A g^-1 (at overpotential η = 300 mV) and turnover frequency (TOF) of 4.8 s^-1 (η = 400 mV), outperforming Ni-Fe deposited on pristine VG and other metal foam supports. Angle-dependent X-ray absorption spectroscopy shows that the edge-rich VG support can preferentially template Fe-O units with a specific valence orbital alignment interacting with the unoccupied density of states on the graphene edges. This graphene edge-metal interaction was shown to facilitate the formation of undersaturated and strained Fe-sites with high valence states, while promoting the formation of redox-activated Ni species, thus improving OER performance. These findings demonstrate rational design of the graphene edge-metal interface in electrocatalysts which can be used for various energy conversion and chemical synthesis reactions.

Entropy-Enthalpy Compensation in Peptide Adsorption on Solid Surfaces: Dependence on Surface Hydration

Although protein adsorption at the solid-water interface is of immense importance, understanding the crucial role of the water phase in mediating protein-surface interactions is lacking, particularly due to the lack of fundamental thermodynamic data. Herein, we have performed complicated free energy calculations and successfully extracted the entropy and enthalpy changes of molecular adsorption on solids. Using the gold and graphene as the surface models with distinct affinities to the water phase, we successfully unravel the sharply opposite manners of entropy-enthalpy compensation in driving water and tripeptide adsorptions on two surfaces. Though the thermodynamic features of water adsorption on surface are enthalpically dominated based on the positions of free energy barriers and minima, the favorable entropy term significantly decreases the free energy barrier and further stabilizes the adsorbate at the adsorption site on the graphene surface. For the peptide, the shape of the adsorption free energy profile is jointly determined by the enthalpy and entropy changes, which, however, alternatively act the driving force to promote the peptide adsorption on the Au surface and graphene surface. The distinct structural and dynamic properties of solid-liquid interfaces account for the special role of the interfacial water phase in regulating the competitive relationship between the entropy and enthalpy variations.

Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions

Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.

Leveraging Peptide Sequence Modification to Promote Assembly of Chiral Helical Gold Nanoparticle Superstructures

Peptide conjugate molecules comprising a gold-binding peptide (e.g., AYSSGAPPMPPF) attached to an aliphatic tail have proven to be powerful agents for directing the synthesis and assembly of gold nanoparticle superstructures, in particular chiral helices having interesting plasmonic chiroptical properties. The composition and structure of these molecular agents can be tailored to carefully tune the structure and properties of gold nanoparticle single and double helices. To date, modifications to the β-sheet region (AYSSGA) of the peptide sequence have not been exploited to control the metrics and assembly of such superstructures. We report here that systematic peptide sequence variation in a series of gold-binding peptide conjugate molecules can be leveraged not only to affect the assembly of peptide conjugates but also to control the synthesis, assembly, and optical properties of gold nanoparticle superstructures. Depending upon the hydrophobicity of a single-amino acid variant, the conjugates yield either dispersed gold nanoparticles or helical superstructures. These results provide evidence that subtle changes to peptide sequence, via single-amino acid variation in the β-sheet region, can be leveraged to program structural control in chiral gold nanoparticle superstructures.

Enhanced Hyperbox Classifier Model for Nanomaterial Discovery

Machine learning tools can be applied to peptide-mediated biomineralization, which is an emerging biomimetic technique of creating functional nanomaterials. In particular, they can be used for the discovery of biomineralization peptides, which currently relies on combinatorial enumeration approaches. In this work, an enhanced hyperbox classifier is developed which can predict if a given peptide sequence has a strong or weak binding affinity towards a gold surface. A mixed-integer linear program is formulated to generate the rule-based classification model. The classifier is optimized to account for false positives and false negatives, and clearly articulates how the classification decision is made. This feature makes the decision-making process transparent, and the results easy to interpret for decision support. The method developed can help accelerate the discovery of more biomineralization peptide sequences, which may expand the utility of peptide-mediated biomineralization as a means for nanomaterial synthesis.

Self-assembled peptide-inorganic nanoparticle superstructures: from component design to applications

Peptides have become excellent platforms for the design of peptide-nanoparticle hybrid superstructures, owing to their self-assembly and binding/recognition capabilities. Morover, peptide sequences can be encoded and modified to finely tune the structure of the hybrid systems and pursue functionalities that hold promise in an array of high-end applications. This feature article summarizes the different methodologies that have been developed to obtain self-assembled peptide-inorganic nanoparticle hybrid architectures, and discusses how the proper encoding of the peptide sequences can be used for tailoring the architecture and/or functionality of the final systems. We also describe the applications of these hybrid superstructures in different fields, with a brief look at future possibilities towards the development of new functional hybrid materials.

Fabrication of nanohybrids assisted by protein-based materials for catalytic applications

Protein units and architectures were applied as supports in the synthesis of metal and metal oxide nanoparticles for environmentally benign catalytic applications.

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.

Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements

Combinatorially selected solid-binding peptides (SBPs) provide a versatile route for synthesizing advanced materials and devices, especially when they are installed within structurally or functionally useful protein scaffolds. However, their promise has not been fully realized because we lack a predictive understanding of SBP-material interactions. Thermodynamic and kinetic binding parameters obtained by fitting quartz crystal microbalance and surface plasmon resonance (SPR) data with the Langmuir model whose assumptions are rarely satisfied provide limited information on underpinning molecular interactions. Using SPR, we show here that a technologically useful SBP called Car9 confers proteins to which is fused a sigmoidal adsorption behavior modulated by partner identity, quaternary structure, and ionic strength. We develop a two-step cooperative model that accurately captures the kinetics of silica binding and provides insights into how SBP-SBP interactions, fused scaffold, and solution conditions modulate adsorption. Because cooperative binding can be converted to Langmuir adhesion by mutagenesis, our approach offers a path to identify and to better understand and design practically useful SBPs.

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.

Direct SERS tracking of a chemical reaction at a single 13 nm gold nanoparticle

Metal nanoparticles (NPs) with decreased sizes are promising catalysts in energy and medicine. Measuring the local reactions and simultaneously acquiring molecular insights at single small NPs, however, remain an experimental challenge. Here we report on surface-enhanced Raman spectroscopic (SERS) tracking of catalytic reactions of single 13 nm gold NPs (GNPs) in situ. We designed spatially isolated (>1.5 μm of inter-dimer space) GNP dimers, each of which consisted of two GNPs with sizes of ∼200 and ∼13 nm, respectively. This design integrates the SERS and catalytic activities into a single entity, while eliminating the crosstalk between adjacent particles, which allows us to trace the redox-derived spectral evolution at single 13 nm GNPs for the first time. We also quantified the reaction kinetics of each individual GNP and analyzed the average behavior of multiple GNPs. There is a large variability among different particles, which underscores the significance of single particle analysis.

Rational screening of biomineralisation peptides for colour-selected one-pot gold nanoparticle syntheses

Biomineralisation peptides that facilitate the one-pot synthesis of gold nanoparticles (AuNPs) with selected optical properties, were screened using a coherent peptide-spotted array consisting of a AuNP binding peptide library. As the biomineralised AuNPs were captured on each peptide spot, analysis of the images provided information on their collective optical properties.

Sequence-Specific Control of Inorganic Nanomaterials Morphologies by Biomolecules

Controlling morphologies of nanomaterials such as their shapes and surface features has been a major endeavor in the field of nanoscale science and engineering, because the morphology is a major determining factor for functional properties of nanomaterials. Compared with conventional capping ligands based on organic molecules or polymers, the programmability of biomolecules makes them attractive alternatives for morphology-controlled nanomaterials synthesis. Towards the goal of predictable control of the synthesis, many studies have been performed on using different sequences of biomolecules to generate specific nanomaterial morphology. In this review, we summarize recent studies in the past few years on using DNA and peptide sequences to control inorganic nanomaterial morphologies, focusing on both case studies and mechanistic investigations. The functional properties resulting from such a sequence-specific control are also discussed, along with strengths and limitations of different approaches to achieving the goal.

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.

Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface

How the presence of Ca²⁺ ions at the aqueous TiO₂ interface influences the binding modes of two experimentally identified titania-binding peptides, Ti-1 and Ti-2, is investigated using replica exchange with solute tempering molecular dynamics simulations. The findings are compared with available experimental data, and the results are contrasted with those obtained under NaCl solution conditions. For Ti-1, Ca²⁺ ions enhance the adsorption of the negatively charged Asp8 residue in this sequence to the negatively charged surface, via Asp–Ca²⁺–TiO₂ bridging. This appears to generate a nonlocal impact on the adsorption of Lys12 in Ti-1, which then pins the peptide to the surface via direct surface contact. For Ti-2, fewer residues were predicted to adsorb directly to the surface in CaCl₂, compared with predictions made for NaCl solution, possibly due to competition between the other peptide residues and Ca²⁺ ions to adsorb to the surface. This reduction in direct surface contact gives rise to a more extensive solvent-mediated contact for Ti-2. In general, the presence of Ca²⁺ ions resulted in a loss of conformational diversity of the surface-adsorbed conformational ensembles of these peptides, compared to counterpart data predicted for NaCl solution. The findings provide initial insights into how peptide–TiO₂ interactions might be tuned at the molecular level via modification of the salt composition of the liquid medium.

Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering

In nature, specific biomolecules interacting with mineral precursors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. Herein we report the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. By engineering peptoid sequences and investigating the resulting particle formation mechanisms, we develop a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped nanoparticles. Through a combination of hyperspectral UV-Vis extinction microscopy and three-photon photoemission electron microscopy, we demonstrate that the individual coral-shaped gold nanoparticles exhibit a plasmonic enhancement as high as 10⁵-fold. This research significantly advances our ultimate vision of predictive bio-inspired materials synthesis using sequence-defined synthetic molecules that mimic proteins and peptides.

Peptoids are promising crystallization agents, as they offer the molecular recognition capabilities of proteins and peptides but with higher stability and synthetic tunability. Here, the authors show that sequence-defined peptoids can controllably template the formation and shape evolution of gold nanostructures with defined morphologies.

Probing nano-patterned peptide self-organisation at the aqueous graphene interface

The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.

Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Disappearance of the Superionic Phase Transition in Sub-5 nm Silver Iodide Nanoparticles

Bulk silver iodide (AgI) is known to show a phase transition from the poorly conducting β/γ-phases into the superionic conducting α-phase at 147 °C. Its transition temperature decreases with decreasing the size of AgI, and the α-phase exists stably at 37 °C in AgI nanoparticles with a diameter of 6.3 nm. In this Letter, we investigated the atomic configuration, the phase transition behavior, and the ionic conductivity of AgI nanoparticles with a diameter of 3.0 nm. The combination of pair distribution function (PDF) analysis and reverse Monte Carlo (RMC) modeling based on high-energy X-ray diffraction (XRD) revealed for the first time that they formed the β/γ-phases with atomic disorder. The results of extended X-ray absorption fine structure (EXAFS) analysis, differential scanning calorimetry (DSC), and AC impedance spectroscopy demonstrated that they did not exhibit the superionic phase transition and their ionic conductivity was lower than that of crystalline AgI. The disappearance of the superionic phase transition and low ionic conductivity in the very small AgI nanoparticles originates from their small size and disordered structure.

Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures

An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chemistry and the physics of the interface, which comprises two very different states of matter, in the presence of liquid water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is especially challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relationships of these interfaces have been the goals of our efforts. We have made substantial progress in developing interatomic potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes our progress in the development and deployment of interfacial force fields and molecular simulation techniques for the purpose of elucidating these insights at biomolecule-materials interfaces, using examples from our laboratories ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addition to the well-established application areas of plasmonic materials, biosensing, and the production of medical implant materials, we outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.

Tunable preparation of ruthenium nanoparticles with superior size-dependent catalytic hydrogenation properties

Ruthenium (Ru) featured with an unusual catalytic behavior is of great significance in several heterogeneous and electro-catalytic reactions. The preparation of tractable Ru nanocatalysts and the building of highly active catalytic system at ambient temperature remains a grand challenge. Herein, a facile strategy is developed for the controllable preparation of Ru nanoparticles (NPs) with the sizes ranging from 2.6 to 51.5nm. Ru NPs show superior size-dependent catalytic performance with the best kinetic rate constant as high as -1.52min^-1, which could far surpass the other traditional noble metals. Ru NPs exert exceedingly efficient low-temperature catalytic activity and good recyclability in the catalytic reduction of nitroaromatic compounds (NACs) and azo dyes. The developed catalytic system provides a distinguishing insight for the artificial preparation of Ru NPs with desired sizes, and allows for the development of rational design rules for exploring catalysts with superior catalytic performances, potentially broadening the applications of metallic NP-enabled catalytic analysis.

Peptide-templated noble metal catalysts: syntheses and applications

Noble metal catalysts have been widely used in many applications because of their high activity and selectivity. However, a controllable preparation of noble metal catalysts still remains as a significant challenge. To overcome this challenge, peptide templates can play a critical role in the controllable syntheses of catalysts owing to their flexible binding with specific metallic surfaces and self-assembly characteristics. By employing peptide templates, the size, shape, facet, structure, and composition of obtained catalysts can all be specifically controlled under the mild synthesis conditions. In addition, catalysts with spherical, nanofiber, and nanofilm structures can all be produced by associating with the self-assembly characteristics of peptide templates. Furthermore, the peptide-templated noble metal catalysts also reveal significantly enhanced catalytic behaviours compared with conventional catalysts because the electron conductivity, metal dispersion, and reactive site exposure can all be improved. In this review, we summarize the research progresses in the syntheses of peptide-templated noble metal catalysts. The applications of the peptide-templated catalysts in organic reactions, photocatalysis, and electrocatalysis are discussed, and the relationship between structure and activity of these catalysts are addressed. Future opportunities, including new catalytic materials designed by using biological principles, are indicated to achieve selective, eco-friendly, and energy neutral synthesis approaches.

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.

Effects of Metal Composition and Ratio on Peptide-Templated Multimetallic PdPt Nanomaterials

It can be difficult to simultaneously control the size, composition, and morphology of metal nanomaterials under benign aqueous conditions. For this, bioinspired approaches have become increasingly popular due to their ability to stabilize a wide array of metal catalysts under ambient conditions. In this regard, we used the R5 peptide as a three-dimensional template for formation of PdPt bimetallic nanomaterials. Monometallic Pd and Pt nanomaterials have been shown to be highly reactive toward a variety of catalytic processes, but by forming bimetallic species, increased catalytic activity may be realized. The optimal metal-to-metal ratio was determined by varying the Pd:Pt ratio to obtain the largest increase in catalytic activity. To better understand the morphology and the local atomic structure of the materials, the bimetallic PdPt nanomaterials were extensively studied by transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, and pair distribution function analysis. The resulting PdPt materials were determined to form multicomponent nanostructures where the Pt component demonstrated varying degrees of oxidation based upon the Pd:Pt ratio. To test the catalytic reactivity of the materials, olefin hydrogenation was conducted, which indicated a slight catalytic enhancement for the multicomponent materials. These results suggest a strong correlation between the metal ratio and the stabilizing biotemplate in controlling the final materials morphology, composition, and the interactions between the two metal species.

Array-based functional peptide screening and characterization of gold nanoparticle synthesis

Based on inorganic material production through biomineralization in organisms, the use of biological molecules in nanomaterial production has received increasing attention as a vehicle to synthesize inorganic materials with selected properties in ambient conditions. Among various biological molecules that interact with metallic surfaces, short peptides are putative ligand molecules as they exhibit potential to control the synthesis of nanoscale materials with tailored functions. Herein, using a spot synthesis-based peptide array, the gold nanoparticle (AuNP) binding activities of approximately 1800 peptides were evaluated and revealed various activities ranging from positive (high-affinity binding peptides) to negative (weak- or null-affinity binding peptides). Among 50 peptides showing the highest AuNP binding activity, 46 sequences showed the presence of tryptophan-based motifs including W[X_n]W, H[X_n]W, and W[X_n]H (W: tryptophan, X: any amino acid, n: 1-8 amino acid residues), whereas none of these motifs was found in the WORST50 peptides. Notably, three peptides showing the highest binding affinities possessed bi-functionality in AuNP binding and Au(III) reduction in solution and on solid surfaces. In addition, the characterization of truncated peptide derivatives revealed unique peptide motifs for their function expressions that also supported the importance of tryptophan-based motifs for peptide-AuNP binding. These findings open the door for peptide-mediated precise regulation of AuNP synthesis in ambient condition and for site dependent controlled AuNP integration onto nanotechnological devices.

STATEMENT OF SIGNIFICANCE

The development of a technique for functionally regulated nanosized material production in ambient condition is broadly required according to the expansion of nanomaterial based applications. Short peptides, which bind to metallic surfaces, have great potential for the technique development, but the realization remains a difficult challenge due to the lack of metal binding peptide varieties. Herein, approximately 1800 peptides with the gold nanoparticle (AuNP) binding activity are reported and characterized. Furthermore, by three highest binding peptides, the expression of bi-functionality in AuNP binding and Au(III) reduction was serendipitously discovered in solution and on solid surfaces. These findings will be attributed to new technique development of functional nanoparticle synthesis in mild condition, and for site-dependent AuNP integration in various nanotechnological devices.

Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles

Peptide-mediated synthesis and assembly of nanostructures opens new routes to functional inorganic/organic hybrid materials. However, understanding of the many factors that influence the interaction of biomolecules, specifically peptides, with metal surfaces remains limited. Understanding of the relationship between peptide sequence and resulting binding affinity and configurations would allow predictive design of peptides to achieve desired peptide/metal interface characteristics. Here, we measured the kinetics and thermodynamics of binding on a Au surface for a series of peptide sequences designed to probe specific sequence and context effects. For example, context effects were explored by making the same mutation at different positions in the peptide and by rearranging the peptide sequence without changing the amino acid content. The degree of peptide-surface contact, predicted from advanced molecular simulations of the surface-adsorbed structures, was consistent with the measured binding constants. In simulations, the ensemble of peptide backbone conformations showed little change with point mutations of the anchor residues that dominate interaction with the surface. Peptide-capped Au nanoparticles were produced using each sequence. Comparison of simulations with nanoparticle synthesis results revealed a correlation between the colloidal stability of the Au nanoparticles and the degree of structural disorder in the surface-adsorbed peptide structures for this family of sequences. These findings suggest new directions in the optimization and design of biomolecules for in situ peptide-based nanoparticle growth, binding, and dispersion in aqueous media.

Remote Optically Controlled Modulation of Catalytic Properties of Nanoparticles through Reconfiguration of the Inorganic/Organic Interface

We introduce here a concept of remote photoinitiated reconfiguration of ligands adsorbed onto a nanocatalyst surface to enable reversible modulation of the catalytic activity. This is demonstrated by using peptide-ligand-capped Au nanoparticles with a photoswitchable azobenzene unit integrated into the biomolecular ligand. Optical switching of the azobenzene isomerization state drives rearrangement of the ligand layer, substantially changing the accessibility and subsequent catalytic activity of the underlying metal surface. The catalytic activity was probed using 4-nitrophenol reduction as a model reaction, where both the position of the photoswitch in the peptide sequence and its isomerization state affected the catalytic activity of the nanoparticles. Reversible switching of the isomerization state produces reversible changes in catalytic activity via reconfiguration of the biomolecular overlayer. These results provide a pathway to catalytic materials whose activity can be remotely modulated, which could be important for multistep chemical transformations that can be accessed via nanoparticle-based catalytic systems.