Scaffold For Recognition Research Articles

An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA.

RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.

Methods for Construction of Yeast Display Libraries of Four-Domain T-Cell Receptors.

Since two decades, yeast display methodology is a popular tool for discovery, stability improvement, and affinity maturation of diverse protein scaffolds, intended for antigen recognition. Yeast display is particularly well suited for the selection of heterodimeric proteins, such as antibodies and T-cell receptors (TCRs), as it allows rapid library creation via gap-repair-driven homologous recombination and subsequent construction of a combinatorial library after mating of yeast of opposite mating types. Certain properties of the TCR scaffold, such as its stability, inferior to most antibody fragments, require modifications of traditional antigen selection strategies. Their selection can be monitored and guided upon staining with the soluble versions of their original antigen, peptide-major histocompatibility complex (MHC), or clonotypic antibodies, whose binding is critically dependent on the TCR structural integrity. Overall, this chapter underlines the importance of the versatile yeast display technique for the diversification of the TCR scaffold for antigen recognition and optimization of its stability.

Yeast Surface Display and Cell Sorting of Antigen-Binding Fc Fragments.

Since the introduction of the yeast display platform, this method has increasingly gained popularity for the discovery and affinity maturation of antibodies and other protein scaffolds intended for antigen recognition. Yeast display is particularly well suited for the selection of antigen-binding Fc fragments (Fcabs) as it allows rapid combinatorial library construction via gap repair-driven homologous recombination and an efficient display of a glycosylated Fc able to interact with Fcγ receptors. Apart from expression-related normalization, isolation of properly folded Fcabs can be guided efficiently by simultaneous staining with ligands such as protein A, FcγRI, or the conformation-sensitive anti-FigCH2 antibody, whose binding is critically dependent on the integrity of the Fc structure. The particular properties of the Fcab scaffold, such as its homodimeric state which can promote binding to multiple antigen molecules, require modifications of traditional affinity maturation strategies. Preferred to equilibrium selections are kinetically driven antigen selections, designed to specifically influence the binding off-rate, which in many cases augments the desired biological effect. A simple design of a yeast-displayed heterodimeric Fc fragment is described and can be used as a general guideline for affinity selection of Fcabs with an asymmetric binding site. Overall, this chapter underlines the importance of the versatile yeast display technique for the optimization of the novel Fcab scaffold for antigen recognition.

Glycosylated Peptoid Nanosheets as a Multivalent Scaffold for Protein Recognition.

Glycoproteins adhered on the cellular membrane play a pivotal role in a wide range of cellular functions. Their importance is particularly relevant in the recognition process between infectious pathogens (such as viruses, bacteria, toxins) and their host cells. Multivalent interactions at the pathogen-cell interfaces govern binding events and can result in a strong and specific interaction. Here we report an approach to mimic the cell surface presentation of carbohydrate ligands by the multivalent display of sugars on the surface of peptoid nanosheets. The constructs provide a highly organized 2D platform for recognition of carbohydrate-binding proteins. The sugars were displayed using different linker lengths or within loops containing 2-6 hydrophilic peptoid monomers. Both the linkers and the loops contained one alkyne-bearing monomer, to which different saccharides were attached by copper-catalyzed azide-alkyne cycloaddition reactions. Peptoid nanosheets functionalized with different saccharide groups were able to selectively bind multivalent lectins, Concanavalin A and Wheat Germ Agglutinin, as observed by fluorescence microscopy and a homogeneous Förster resonance energy transfer (FRET)-based binding assay. To evaluate the potential of this system as sensor for threat agents, the ability of functionalized peptoid nanosheets to bind Shiga toxin was also studied. Peptoid nanosheets were functionalized with globotriose, the natural ligand of Shiga toxin, and the effective binding of the nanomaterial was verified by the FRET-based binding assay. In all cases, evidence for multivalent binding was observed by systematic variation of the ligand display density on the nanosheet surface. These cell surface mimetic nanomaterials may find utility in the inactivation of pathogens or as selective molecular recognition elements.

A simple, water soluble flavone-based fluorescent probe for fast detection of Cys

The important biological roles of thiols have attracted strong interest in developing useful chemical tools for detecting biothiols. In this work, a flavone-based fluorescent probe for the selective detection of Cys was developed by taking advantage of a pyridinium acrylate as a useful scaffold for fast recognition of biothiol. The probe had good solubility in aqueous solution and displayed good sensitivity and rapid response toward Cys with a large Stokes shift. Moreover, the probe could be used as a useful tool for rapid identification of endogenous Cys in living cells.

Two-Photon Macromolecular Probe Based on a Quadrupolar Anthracenyl Scaffold for Sensitive Recognition of Serum Proteins under Simulated Physiological Conditions.

The binding interaction of a biocompatible water-soluble polycationic two-photon fluorophore (Ant-PIm) toward human serum albumin (HSA) was thoroughly investigated under simulated physiological conditions using a combination of steady-state, time-resolved, and two-photon excited fluorescence techniques. The emission properties of both Ant-PIm and the fluorescent amino acid residues in HSA undergo remarkable changes upon complexation allowing the thermodynamic profile associated with Ant-PIm–HSA complexation to be accurately established. The marked increase in Ant-PIm fluorescence intensity and quantum yield in the proteinous environment seems to be the outcome of the attenuation of radiationless decay pathways resulting from motional restriction imposed on the fluorophore. Fluorescence resonance energy transfer and site-marker competitive experiments provide conclusive evidence that the binding of Ant-PIm preferentially occurs within the subdomain IIA. The pronounced hypsochromic effect and increased fluorescence enhancement upon association with HSA, compared to that of bovine serum albumin (BSA) and other biological interferents, makes the polymeric Ant-PIm probe a valuable sensing agent in rather complex biological environments, allowing facile discrimination between the closely related HSA and BSA. Furthermore, the strong two-photon absorption (TPA) with a maximum located at 820 nm along with a TPA cross section σ2 > 800 GM, and the marked changes in the position and intensity of the band upon complexation definitely make Ant-PIm a promising probe for two-photon excited fluorescence-based discrimination of HSA from BSA.

Iterative Design of a Biomimetic Catalyst for Amino Acid Thioester Condensation.

Herein, the design of a catalyst that combines lessons learned from peptide biosynthesis, enzymes, and organocatalysts is described. The catalyst features a urea scaffold for carbonyl recognition and elements of nucleophilic catalysis. In the presence of 10 mol % of the organocatalyst, the rate of peptide bond formation is accelerated by 10000-fold over the uncatalyzed reaction between Fmoc-amino acid thioesters and amino acid methyl esters.

Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition.

Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide. Several mutants were identified with low micromolar dissociation constants. After concatenation of the mutants, a 500-fold increase in the overall affinity for lysozyme was achieved leading to a peptide with an apparent dissociation constant of 65 nM. This mutant was immobilized for affinity chromatography experiments, and the on/off nature of the molecular recognition was demonstrated as the target is captured from a mixture in the presence of calcium and is released in the absence of calcium as the RTX peptides lose their β-roll structure. This work presents the design of a new stimulus-responsive scaffold that can be used for environmentally responsive specific molecular recognition and self-assembly.

Evaluation of Nanobody Conjugates and Protein Fusions as Bioanalytical Reagents.

Enzyme-linked immunosorbent assay (ELISA), flow cytometry, and Western blot are common bioanalytical techniques. Successful execution traditionally requires the use of one or more commercially available antibody-small-molecule dyes or antibody-reporter protein conjugates that recognize relatively short peptide tags (<15 amino acids). However, the size of antibodies and their molecular complexity (by virtue of post-translational disulfide formation and glycosylation) typically require either expression in mammalian cells or purification from immunized mammals. The preparation and purification of chemical dye- or reporter protein-antibody conjugates is often complicated and expensive and not commonplace in academic laboratories. In response, researchers have developed comparatively simpler protein scaffolds for macromolecular recognition, which can be expressed with relative ease in E. coli and can be evolved to bind virtually any target. Nanobodies, a minimalist scaffold generated from camelid-derived heavy-chain IgGs, are one such example. A multitude of nanobodies have been evolved to recognize a diverse array of targets, including a short peptide. Here, this peptide tag (termed BC2T) and BC2 nanobody-dye conjugates or reporter protein fusions are evaluated in ELISA, flow cytometry, and Western blot experiments and compared to analogous experiments using commercially available antibody-conjugate/peptide tag pairs. Collectively, the utility and practicality of nanobody-based reagents in bioanalytical chemistry is demonstrated.

Computational design of model scaffold for anion recognition based on the 'Cα NN' motif.

The 'novel phosphate binding 'Cα NN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'Cα NN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'Cα NN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'Cα NN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.

Externally controllable glycan presentation on nanoparticle surfaces to modulate lectin recognition.

Nature dynamically controls carbohydrate expression on cells rather than static presentation. Here we report synthetic glycosylated nanoparticles that contain polymeric 'gates' to enable external control (via temperature changes) of glycan surface expression, as an alternative to enzymatic control in nature. This approach offers a new dynamic multivalent scaffold for glycan recognition.

A new lawsone azo-dye for optical sensing of Fe3+ and Cu2+ and their DFT study

A new lawsone-based azo-dye 2-hydroxy-3-((pyridin-2-ylmethyl)diazenyl)naphthalene-1,4-dione (1) was synthesized and applied for sensing of metal ions. Receptor 1 showed selective fluorescent and colorimetric response for the detection of Cu2+ and Fe3+ over other tested metal ions. The fluorescence intensity of 1 was significantly quenched allowing detection of Fe3+ and Cu2+ down to 0.61 and 6.06 μM, respectively. The binding has been established by fluorescence spectroscopic method. Receptor 1 provided a 1 : 1 binding scaffold for recognition of Fe3+ and Cu2+ ions with the association constant of 3.33 × 106 and 3.33 × 105 M−1, respectively. The B3LYP/6-31G/LANL2DZ method was employed for the optimization of 1 and 1·Fe3+ and 1·Cu2+.

Size-selective recognition by a tubular assembly of phenylene-pyrimidinylene alternated macrocycle through hydrogen-bonding interactions.

Study of artificial tubular assemblies as a useful host scaffold for size-selective recognition and release of guest molecules is an important subject in host-guest chemistry. We describe well-defined self-assembled nanotubes (NT6mer) formed from π-conjugated m-phenylene-pyrimidinylene alternated macrocycle 16mer that exhibit size-selective recognition toward a specific aromatic acid. In a series of guest molecules, a size-matched trimesic acid (G3) gives inclusion complexes (NT6mer⊃G3) in dichloromethane resulting in an enhanced and red-shifted fluorescence. (1)H nuclear magnetic resonance (NMR) titration experiments indicated that the complex was formed in a 1:1 molar ratio. Density functional theory (DFT) calculations and the binding constant value (K = 1.499 × 10(5) M(-1)) of NT6mer with G3 suggested that the complex involved triple hydrogen-bonding interactions. The encapsulated guest G3 molecules can be readily released from the tubular channel through the dissociation of hydrogen bonding by the addition of a polar solvent such as dimethylsulfoxide (DMSO). In contrast, 16mer could not form self-assembled nanotubes in CHCl3 or tetrahydrofuran (THF) solution, leading to weak or no size-selective recognizability, respectively.

Anion recognition by cyclic peptides.

Anion binding selectivity can often be controlled by judicious arrangement of recognition moieties around an anion of interest. Indeed, nature takes advantage of large peptides/proteins to provide highly efficient and selective anion receptors using a small number of amino acid building blocks placed in a precise arrangement. Cyclic peptides are ideal synthetic scaffolds to position binding residues in a similarly preorganised manner as their synthetic versatility and rigidified structure allows precise control over their size and shape. This review summarises the recent use of such cyclic peptide scaffolds as receptors for various anionic species.

Super LCST thermo-responsive nanoparticle assembly for ATP binding through the Hofmeister effect.

The present investigation reports the development of a super LCST thermo-responsive amphiphilic nanoparticle assembly for the detection of adenosine triphosphate (ATP) through the Hofmeister effect. For this purpose, a new diblock molecule was designed based on hydrophilic polyethylene glycol and the renewable resource 3-pendadecylphenol as the hydrophobic unit. The amphiphile self-assembled as a 150 nm micellar nanoparticle and showed a super lower critical solution temperature (LCST) above 90 °C. The amphiphile followed the Hofmeister effect for the anion series and exhibited high selectivity for the recognition of ATP over its adenosine precursors such as ADP, AMP and inorganic phosphate (Pi). The preferential binding for ATP is attributed to the encapsulation in the hydrophobic pocket and modification of the hydration shell at the periphery of the amphiphilic nanoparticles. Electron and atomic force microscopes and dynamic light scattering techniques confirmed the size and shape of the amphiphilic assembly and its ATP complexes. Isothermal calorimetric experiments were carried out to determine the binding constants for the amphiphilic nanoparticle binding to ATP. The binding of the amphiphilic nanoparticle to ATP was found to be an endothermic process with a binding constant three times higher compared to its precursor Pi. This investigation provides the first insight into the development of a thermo-responsive scaffold for recognition of ATP.

Calix[4]arene based molecular probe for sensing copper ions

A novel calix[4]arene based molecular probe for metal ions has been designed, synthesized and evaluated. Studies on its binding with different metal ions reveal a noticeable naked eye color change, bathochromic shift in absorption spectrum and remarkable enhancement in fluorescence emission in the presence of Cu2+ only. The role of calix[4]arene scaffold for selective recognition of Cu2+ has been demonstrated by repeat evaluation and analysis of an appropriate reference molecule. A rational explanation for fluorescence enhancement in 3 on interaction with copper has been suggested.

Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment

BackgroundAnalysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464–5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor.ResultsHere we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1–3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5.ConclusionsTogether these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high-affinity interaction involving an antibody from the VH1-69 germline segment.

TRNA Binding, Structure, and Localization of the Human Interferon-Induced Protein IFIT5

Interferon-induced proteins, including the largely uncharacterized interferon-induced tetratricopeptide repeat (IFIT) protein family, provide defenses against pathogens. Differing from expectations for tetratricopeptide repeat (TPR) proteins and from human IFIT1, IFIT2, and IFIT3, we show that human IFIT5 recognizes cellular RNA instead of protein partners. In vivo and in vitro, IFIT5 bound to endogenous 5'-phosphate-capped RNAs, including transfer RNAs. The crystal structure of IFIT5 revealed a convoluted intramolecular packing of eight TPRs as a fold that we name the TPR eddy. Additional, non-TPR structural elements contribute to an RNA binding cleft. Instead of general cytoplasmic distribution, IFIT5 concentrated in actin-rich protrusions from the apical cell surface colocalized with the RNA-binding retinoic acid-inducible gene-I (RIG-I). These findings establish compartmentalized cellular RNA binding activity as a mechanism for IFIT5 function and reveal the TPR eddy as a scaffold for RNA recognition.

Synthesis and spectral investigation of a Turn-On fluorescence sensor with high affinity to Cu2+

Abstract Three anthracene derivatives ( 1a , 1b and 1c ) containing a Schiff base moiety were synthesized and investigated as chemosensors for the detection of Cu 2+ . 1a displayed extremely high selectivity to Cu 2+ over other 12 interference ions with 120-fold fluorescence enhancement at 468 nm in the acetonitrile media. The nitrogen atom in Schiff base and sulfur atom of 1a provided a binding scaffold for recognition of Cu 2+ with high affinity ( K a = 4.35 × 10 4 M −1 ). The formation of 1a –Cu 2+ complex caused a decrease of electron density on nitrogen atom and sequentially led to fluorescence enhancement based on the photoinduced electron transfer (PET) mechanism. The design used for these three molecules afforded a new model for construction of fluorescence sensors based on PET mechanism.

Designed Ankyrin Repeat Proteins as Scaffolds for Multivalent Recognition

Ankyrin repeat (AR) proteins are composed of tandem repeats of a basic structural motif of ca. 33 amino acid residues that form a β-turn followed by two antiparallel α-helices. Multiple repeats stack together in a modular fashion to form a scaffold that is ideally suited for the presentation of multiple functional groups and/or recognition elements. Here we describe a biosynthetic strategy that takes advantage of the modular nature of these proteins to generate multivalent ligands that are both chemically homogeneous and structurally well-defined. Glycosylated AR proteins cluster the tetrameric lectin concanavalin A (Con A) at a rate that is comparable to the rate of Con A aggregation mediated by globular protein conjugates and variable density linear polymers. Thus, AR proteins define a new class of multivalent ligand scaffolds that have significant potential application in the study and control of a variety of multivalent interactions.