Covalent attachment of TAT peptides and thiolated alkyl molecules on GaAs surfaces

Four TAT peptide fragments were used to functionalize GaAs surfaces by adsorption from solution. In addition, two well-studied alkylthiols, mercaptohexadecanoic acid (MHA) and 1-octadecanethiol (ODT) were utilized as references to understand the structure of the TAT peptide monolayer on GaAs. The different sequences of TAT peptides were employed in recognition experiments where a synthetic RNA sequence was tested to verify the specific interaction with the TAT peptide. The modified GaAs surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). AFM studies were used to compare the surface roughness before and after functionalization. XPS allowed us to characterize the chemical composition of the GaAs surface and conclude that the monolayers composed of different sequences of peptides have similar surface chemistries. Finally, FT-IRRAS experiments enabled us to deduce that the TAT peptide monolayers have a fairly ordered and densely packed alkyl chain structure. The recognition experiments showed preferred interaction of the RNA sequence toward peptides with high arginine content.     

TAT peptide immobilization on gold surfaces: a comparison study with a thiolated peptide and alkylthiols using AFM, XPS, and FT-IRRAS

A TAT peptide was used to functionalize a gold surface by three different methods: adsorption from solution, microcontact printing, and dip-pen nanolithography (DPN). The composition and structure of the modified gold was characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform -infrared reflection absorption spectroscopy (FT-IRRAS). We used two well-studied alkylthiols, mercaptohexadecanoic acid and 1-octadecanethiol, as a comparison in order to understand the structure of the TAT peptide monolayers prepared by the three methods. AFM studies allowed us to assess the homogeneity after each modification protocol. XPS was used to characterize the chemical composition of the gold surface after each functionalization procedure. The XPS results showed that surfaces modified with the TAT peptide by the three methods exhibit similar surface chemistry. Finally, FT-IRRAS experiments allowed us to conclude that the structure of the alkyl chains of the TAT peptides is fairly disordered and different after each procedure. Regardless of the type of surface functionalization method used, the monolayer of TAT peptide formed on the surface was of "liquidlike" nature.     

α-Helix-Mimetic Foldamers for Targeting HIV-1 TAR RNA

An oligopyridylamide-based foldamer approach has been employed to target HIV TAR RNA-TAT assembly as a model system to study RNA-protein interactions. The oligopyridylamide scaffold adopts a constrained conformation which presents surface functionalities at distinct spatial locations and mimic the chemical features of the secondary structure of proteins. We have designed a library of oligopyridylamides containing diverse surface functionalities which mimic the side chain residues of the TAT protein domain. The interaction of TAR RNA and TAT plays a pivotal role in facilitating HIV replication. The library was screened using various fluorescent based assays to identify antagonists of the TAR RNA-TAT complex. A tricationic oligopyridylamide ADH-19, possessed the highest affinity towards TAR and efficiently inhibited the TAR RNA-TAT interaction with apparent K_d of 4.1±1.0 μm . Spectroscopic studies demonstrated that ADH-19 interacts with the bulge and the lower bulge regions of TAR RNA, the domains important for TAT interaction. ADH-19 demonstrated appreciable in vivo efficacy (IC₅₀=25±1 μm ) by rescuing TZM-bl cells infected with the pseudovirus HIV-1HXB-2.     

Creation of lipid partitions by deposition of amphipathic viral peptides

Phospholipid vesicles exhibit a natural characteristic to fuse and reform into a continuous single bilayer membrane on hydrophilic solid substrates such as glass, mica, and silica. The resulting solid-supported bilayer mimics physiological tendencies such as lipid flip-flop and lateral mobility. The lateral mobility of fluorescently labeled lipids fused into solid-supported bilayers is found to change upon deposition on the membrane surface of an amphipathic alpha-helical peptide (AH) derived from the hepatitis C virus (HCV) NS5A protein. The binding of the AH peptide to a phospholipid bilayer, with the helical axis parallel to the bilayer, leads to immobilization of the bilayer. We used AFM to better understand the mechanistic details of this specific interaction, and determined that the diminished fluidity of the bilayer is due to membrane thinning. Utilizing this specific interaction between AH peptides and lipid molecules, we demonstrate a novel process for the creation of lipid partition by employing AH peptides as agents to immobilize lipid molecules, thus creating a patterned solid support with partition-defined areas of freely mobile lipid bilayers. This architecture could have a wide range of applications in novel sensing, biotechnology, high-throughput screening, and biomimetic strategies.     

Investigation of RNA-protein and RNA-metal ion interactions by electron paramagnetic resonance spectroscopy. The HIV TAR-Tat motif

Electron paramagnetic resonance (EPR) spectroscopy was used to investigate changes in dynamics of spin-labeled nucleotides in the TAR RNA (U23, U25, U38, and U40) upon binding to cations, argininamide, and two peptides derived from the Tat protein. Nearly identical changes in dynamics were obtained for either calcium or sodium ions, indicating the absence of a calcium-specific structural change for the TAR RNA in solution that had previously been suggested by crystallographic data. Similar dynamic signatures were obtained for two Tat-derived peptides that have the same important binding determinant (R52) and similar binding affinities to the TAR RNA. However, U23 and U38 were substantially less mobile for the wild-type peptide (YGRKKRRQRRR) than for the mutant (YKKKKRKKKKA), demonstrating that, flanking R52, amino acids in the wild-type sequence make specific contacts to the RNA.     

Nonionic side chains modulate the affinity and specificity of binding between functionalized polyamines and structured RNA

This Communication introduces side-chain-bearing polyamines as molecules for selective recognition of folded RNA structures. The complex folded structures associated with RNA create binding pockets for proteins, and also binding sites for small molecules. Developing organic molecules that can bind RNA with high affinity and specificity is a challenge that must be overcome for RNA to be considered a viable drug target. In this work, six polyamines with different side chains were synthesized to test for effects on binding affinity and specificity to TAR RNA and RRE RNA of HIV. Binding interactions between polyamines and RNAs were examined using two footprinting assays, based on terbium-induced cleavage and magnesium-catalyzed cleavage at higher pH. The binding constants and the binding specificity were highly dependent on the side chains of the polyamines, demonstrating that this class of molecules is a very promising starting point for development of highly selective RNA-binding ligands.     

Driving in vitro selection of anti-HIV-1 TAR aptamers by magnesium concentration and temperature

In vitro selection with either DNA or RNA libraries was performed against the TAR RNA element of HIV-1. The role of the selection conditions on the outcome of the selection was evaluated by varying the magnesium concentration and the temperature. The selection stringency was demonstrated to determine i) the affinity of the best identified aptamers for the TAR target, and ii) the type of interaction between the two partners. Selections performed with a DNA library under low (4 degrees C, 10 mM magnesium) and high stringency (23 degrees C, 3 mM magnesium) led to the emergence of "kissing aptamers"; but even if the motif interacting directly with the TAR loop were identical in the two kinds of aptamers, the consensus was extended from eight to thirteen nucleotides when the Mg(2+) concentration was decreased from 10 to 3 mM. Similar kissing aptamers were selected at 23 degrees C and 37 degrees C starting with two different RNA libraries under identical ionic conditions. In addition, selection performed at 37 degrees C yielded a significant proportion of antisense sequences. Only antisense RNAs complementary to the TAR loop competitively inhibited the association of a Tat peptide with TAR.     

Cell-Penetrating Peptides: Correlation between Peptide-Lipid Interaction and Penetration Efficiency

Cell-penetrating peptides are used in the delivery of peptides and biologics, with some cell-penetrating peptides found to be more efficient than others. The exact mechanism of how they interact with the cell membrane and penetrate it, however, remains unclear. This study attempts to investigate the difference in free energy profiles of three cell-penetrating peptides (TAT, CPP1 and CPP9) with a model lipid bilayer (DOPC) using molecular dynamics pulling simulations with umbrella sampling. Potential mean force (PMF) and free energy barrier between the peptides and DOPC are determined using WHAM analysis and MM-PBSA analysis, respectively. CPP9 is found to have the smallest PMF value, followed by CPP1 and TAT, consistent with the experimental data. YDEGE peptide, however, does not give the highest PMF value, although it is a non-cell-permeable peptide. YDEGE is also found to form water pores, alongside with TAT and CPP9, suggesting that it is difficult to distinguish true water pore formation from artefacts arising from pulling simulations. On the contrary, free energy analysis of the peptide-DOPC complex at the lipid-water interface with MM-PBSA provides results consistent with experimental data with CPP9 having the least interaction with DOPC and lowest free energy barrier, followed by CPP1, TAT and YDEGE. These findings suggest that peptide-lipid interaction at the lipid-water interface has a direct correlation with the penetration efficiency of peptides across the lipid bilayer.     

Binding affinity and inhibitory potency of neomycin and streptomycin on the Tat peptide interaction with HIV-1 TAR RNA detected by on-line acoustic wave sensor

The binding of two aminoglycoside antibiotics, neomycin and streptomycin, to a segment of the transactivation responsive region (TAR) RNA of the human immunodeficiency virus, and their inhibitory potency to disrupt the interaction of the RNA with a regulatory Tat protein-derived peptide, have been studied using a flow-through acoustic wave detector system. Binding affinity is directly correlated with the inhibitory potency of these molecules and the acoustic wave detection system shows that neomycin exhibits at least a ten-fold greater affinity for TAR RNA and that it is also a more potent inhibitor than streptomycin. These results are in agreement with previous studies. However, unlike the time-consuming batch-based assays, use of the flow-through format offers considerable potential for the rapid screening of the chemistry of relatively small-molecule-nucleic acid binding events.     

Lipopolysaccharide removal by a peptide-functionalized surface

Five peptides: BPI(85-109); CAP18(106-137); endotoxin inhibitor (EI); GQ33 and GQ33C, derived from lipopolysaccharide (LPS)-binding molecules were investigated for LPS-binding ability with a view to a potential use in extracorporeal therapy. The surface plasmon resonance technique (SPR) was used to monitor the interaction between LPS in solution and the surface-immobilized peptides. The peptides were covalently bound to a model dextran surface via inherent amino groups or via terminally introduced cysteine residues. The results showed that the binding efficacy and binding stability of the peptides varied greatly. The CAP18(106-137) peptide, which exhibited the highest binding efficacy and binding stability, was also immobilized on a poly(ethylene imine)-poly(ethylene glycol) (PEI-PEG) surface through maleimide-terminal PEG. The binding efficacy of the CAP18(106-137) peptide was not significantly affected by the different immobilization methods used in the attachment to a dextran or a PEI-PEG surface. LPS bound selectively to CAP18(106-137) and showed very low unspecific binding to the PEI-PEG surface layer. The EI peptide proved to have a reasonably good binding capacity but a less stable interaction with LPS. The other peptides exhibited much poorer binding efficacy. We believe that the results presented in this work can be of practical value for the development of extracorporeal treatment of patients suffering from septic shock.     

Attachment of nanoparticles to the AFM tips for direct measurements of interaction between a single nanoparticle and surfaces

Here we report a universal method of attachment/functionalization of tips for atomic force microscope (AFM) with nanoparticles. The particles of interest are glued to the AFM tip with epoxy. While the gluing of micron size particles with epoxy has been known, attachment of nanoparticles was a problem. The suggested method can be used for attachment of virtually any solid nanoparticles. Approximately every other tip prepared with this method has a single nanoparticle terminated apex. We demonstrate the force measurements between a single approximately 50 nm ceria nanoparticle and flat silica surface in aqueous media of different acidity (pH 4-9). Comparing forces measured with larger ceria particles ( approximately 500 nm), we show that the interaction with nanoparticles is qualitatively different from the interaction with larger particles.     

Interaction between dendrons directly studied by single-molecule force spectroscopy

In this article, we have investigated the interaction between two poly(benzyl ether) dendrons directly by single-molecule force spectroscopy. For this purpose, one dendron was immobilized on an AFM tip through a poly(ethylene glycol) (PEG) spacer, and the other dendron was anchored on a gold substrate as a self-assembled monolayer. Two dendrons approached and then interacted with each other when the AFM tip and the substrate moved close together. The rupture force between dendrons was measured while the AFM tip and the substrate separated. PEG as a flexible spacer can function as a length window for recognizing the force signals and avoiding the disturbance of the interaction between the AFM tip and the substrate. The interaction between two first-generation dendrons is measured to be about 224 pN at a force loading rate of 40 nN/s. The interaction between second- and first-generation dendrons rises to 315 pN at the same loading rate. Such interactions depend on the force loading rate in the range of several to hundreds of nanonewtons per second, indicating that the rupture between dendrons is a dynamic process. The study of the interaction between surface-bound dendrons of different generations provides a model system for understanding the surface adhesion of molecules with multiple branches. In addition, this multiple-branch molecule may be used to mimic the sticky feet of geckos as a man-made adhesive.     

Immobilization and surface characterization of NeutrAvidin biotin-binding protein on different hydrogel interlayers

For a number of potential applications, it is desirable to immobilize avidin class molecules onto solid supports and exploit their ability to bind biotinylated molecules with high affinity. NeutrAvidin molecules were surface immobilized in various ways. In this study, NeutrAvidin was covalently attached by carbodiimide chemistry onto carboxyl groups of polyacrylic acid and carboxymethyl-dextran hydrogel interlayers. A third strategy involved the affinity "docking" of NeutrAvidin onto a biotinylated poly(ethylene glycol) interlayer. These three interlayers were selected for their low nonspecific binding of proteins, which was expected to minimize surface binding of NeutrAvidin by nonspecific interfacial adsorption. X-ray photoelectron spectroscopy (XPS) analyses allowed detailed characterization of the multilayer fabrication steps. An ELISA assay was used to measure NeutrAvidin activity, which varied with the surface immobilization route. Atomic force microcopy (AFM) force measurements showed that the hydrogel interlayer contributed to a repulsive force and verified the specific interaction between biotinylated AFM tips and the NeutrAvidin surfaces. When a solution of free biotin was injected into the AFM liquid cell, the force curve changed substantially and became identical to that recorded between surfaces carrying no NeutrAvidin, indicating that the free solution biotin had displaced NeutrAvidin proteins off the PEG-biotin layer.     

High-affinity tags fused to s-layer proteins probed by atomic force microscopy

Two-dimensional, crystalline bacterial cell surface layers, termed S-layers, are one of the most commonly observed cell surface structures of prokaryotic organisms. In the present study, genetically modified S-layer protein SbpA of Bacillus sphaericus CCM 2177 carrying the short affinity peptide Strep-tag I or Strep-tag II at the C terminus was used to generate a 2D crystalline monomolecular protein lattice on a silicon surface. Because of the genetic modification, the 2D crystals were addressable via Strep-tag through streptavidin molecules. Atomic force microscopy (AFM) was used to investigate the topography of the single-molecules array and the functionality of the fused Strep-tags. In high-resolution imaging under near-physiological conditions, structural details such as protein alignment and spacing were resolved. By applying molecular recognition force microscopy, the Strep-tag moieties were proven to be fully functional and accessible. For this purpose, streptavidin molecules were tethered to AFM tips via approximately 8-nm-long flexible polyethylene glycol (PEG) linkers. These functionalized tips showed specific interactions with 2D protein crystals containing either the Strep-tag I or Strep-tag II, with similar energetic and kinetic behavior in both cases.     

Peptides on GaAs surfaces: comparison between features generated by microcontact printing and dip-pen nanolithography

Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS) were employed to understand the size, composition, and conformation of lithographic patterns composed of peptide molecules. GaAs surfaces were patterned by microcontact printing (microCP) and dip-pen nanolithography (DPN) using a peptide sequence composed of 15 amino acids. The detailed surface evaluation showed that the patterns have similar chemical compositions but differ in the bonding among the molecules anchored on the GaAs substrate. Both types of patterns were crystalline-like in nature. The features created by DPN exhibited interchain hydrogen bonding, while the ones generated by microCP displayed non-hydrogen bonding. The differences in the lithographic structures can be utilized in future biorecognition experiments that take advantage of the electronic properties of the GaAs substrate and the tunable behavior of the covalently anchored biomolecules on the surface.     

Structural mimicry of retroviral tat proteins by constrained beta-hairpin peptidomimetics: ligands with high affinity and selectivity for viral TAR RNA regulatory elements

An approach is described to the design of beta-hairpin peptidomimetic ligands for bovine immunodeficiency virus (BIV) Tat protein, which inhibit binding to its transactivator response element (TAR) RNA. A library of peptidomimetics was derived by grafting onto a hairpin-inducing d-Pro-l-Pro template sequences related to the RNA recognition element in Tat. One hairpin mimetic was identified that binds tightly (K(d) approximately 150 nM) to BIV TAR, and another that binds also to HIV-1 TAR RNA (K(d) approximately 1-2 microM). (In the same assay, the wild-type BIV Tat(65-81) peptide binds to BIV TAR with K(d) approximately 50 nM.) The high-affinity BIV-Tat mimetic was shown to adopt a stable beta-hairpin conformation in free solution by NMR methods. Amino acid substitutions in this mimetic were shown to impact on the hairpin structure and to disrupt binding to the RNA. This family of conformationally constrained peptidomimetics affords insights into the structural requirements for binding to TAR RNA and provides a basis for the design of new ligands with increased inhibitory activity and specificity to both BIV and HIV TAR RNAs.     

运用功能化修饰的碳纳米管针尖测量配体-受体的作用力

电弧法自制碳纳米管原子力显微镜针尖,对其末端进行功能化修饰,然后测量配体-受体之间的作用力。运用没有功能化修饰的碳纳米管针尖与修饰有亲和素分子的基底进行接触测量时,没有粘滞力出现;而运用末端修饰生物素分子的碳纳米管针尖测量时,有粘滞力产生。功能化的碳纳米管针尖直接测得的粘滞力均大约200pN,此值符合一对配体生物素和受体亲和素之间的作用力。这一结果很难用传统的针尖获得,功能化修饰的碳纳米管针尖能够克服传统针尖在力测量中的局限,在生物学和化学领域有着广泛的应用前景。     

The role of few-asperity contacts in adhesion

The surface roughness of a few asperities and their influence on the work of adhesion is of scientific interest. Macroscale and nanoscale adhesion data have seemingly given inconsistent results. Despite the importance of bridging the gap between the two regimes, little experimental work has been done, presumably due to the difficulty of the experiment needed to determine how small amounts of surface roughness might influence adhesion data lying in between the two scales. To investigate the role of few-asperity contacts in adhesion, the pull-off force was measured between different sized atomic-force microscope (AFM) tips (with different roughnesses) and sample surfaces that had well-controlled material properties. There were seventeen tips of four different types, with radii from 200 nm to 60 microm. The samples were unpatterned single crystal silicon with a chemical silicon dioxide surface resulting from a standard silicon wafer clean. Some of the samples were treated with a few angstroms of vapor deposited diphenylsiloxane. We observed that the uncorrected (for surface roughness) pull-off force was independent of the radius of the AFM tip, which was contrary to all continuum-mechanics model predictions. To explain this behavior, we assumed that the interactions between the AFM tip and sample were additive, material properties were constant, and that the AFM tip, asperities, and sample surfaces were of uniform density. Based on these assumptions, we calculated a simple correction due to the measured root mean square (RMS) surface roughness of the AFM tips. The simple correction for the RMS surface roughness resulted in the expected dependence of the pull-off force on radius, but the magnitudes were higher than expected. Commercial and heat-treated AFM tips have minimal surface roughness and result in magnitudes that are more reliable. The relative uncertainty for the pull-off force was estimated to be 10%. In this paper, we derive how the cantilever and tip parameters contribute to the measured pull-off force and show how the corrected results compare with theory. Although much work is still needed, the work presented here should advance the understanding of adhesion between the macroscale and nanoscale regimes.