Assembly of alpha-helical peptide coatings on hydrophobic surfaces

The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules. Here we present data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. Small linear peptides composed of alternating leucine and lysine residues were synthesized, and their adsorption onto porous polystyrene surfaces was studied using a combination of solid-state NMR techniques. Using conventional solid-state NMR experiments and newly developed double-quantum techniques, their helical structure was verified. Large-amplitude dynamics on the NMR time scale were not observed, suggesting irreversible adsorption of the peptides. Their association, adsorption, and structure were examined as a function of helix length and sequence periodicity, and it was found that, at higher solution concentrations, peptides as short as seven amino acids adsorb with defined secondary structures. Two-dimensional double-quantum experiments using (13)C-enriched peptide sequences allow high-resolution determination of secondary structure in heterogeneous environments where the peptides are a minor component of the material. These results shed light on how polymeric surfaces may be surface-modified by structured peptides and demonstrate the level of molecular structural and dynamic information solid-state NMR can provide.     

Structure of peptides on metal oxide surfaces probed by NMR

Peptides that bind inorganic surfaces and template the formation of nanometer-sized inorganic particles are of great interest for the self- or directed assembly of nanomaterials for sensors and diagnostic applications. These surface-recognizing peptides can be identified from combinatorial phage-display peptide libraries, but little experimental information is available for understanding the relationship between the peptide sequence, structure at the nanoparticle surface, and function. We have developed NMR methods to determine the structures of peptides bound to inorganic nanoparticles and report on the structure of three peptides bound to silica and titania surfaces. Samples were prepared under conditions leading to rapid peptide exchange at the surface such that solution-based nuclear Overhauser experiments can be used to determine the three-dimensional structure of the bound peptide. The binding motif is defined by a compact "C"-shaped structure for the first six amino acids in the 12-mer. The orientation of the peptide on the nanoparticle surface was determined by magnetization transfer from the nanoparticle surface to the nearby peptide protons. These methods can be applied to a wide variety of abiotic interfaces to provide an insight into the relationship between the primary sequence of peptides and their functionality at the interface.     

Determination of peptide backbone torsion angles using double-quantum dipolar recoupling solid-state NMR spectroscopy

Several approaches for utilizing dipolar recoupling solid-state NMR (ssNMR) techniques to determine local structure at high resolution in peptides and proteins have been developed. However, many of these techniques measure only one torsion angle or are accurate for only certain classes of secondary structure. Additionally, the efficiency with which these dipolar recoupling experiments suppress the deleterious effects of chemical shift anisotropy (CSA) at high magnetic field strengths varies. Dipolar recoupling with a windowless sequence (DRAWS) has proven to be an effective pulse sequence for exciting double-quantum (DQ) coherences between adjacent carbonyl carbons along the peptide backbone. By allowing this DQ coherence to evolve, it is possible to measure the relative orientations of the CSA tensors and subsequently use this information to determine the Ramachandran torsion angles phi and psi. Here, we explore the accuracies of the assumptions made in interpreting DQ-DRAWS data and demonstrate their fidelity in measuring torsion angles corresponding to a variety of secondary structures irrespective of hydrogen-bonding patterns. It is shown how a simple choice of isotopic labels and experimental conditions allows accurate measurement of backbone secondary structures without any prior knowledge. This approach is considerably more sensitive for determining structure in helices and has comparable accuracy for beta-sheet and extended conformations relative to other methods. We also illustrate the ability of DQ-DRAWS to distinguish between structures in heterogeneous samples.     

Folding induced assembly of polypeptide decorated gold nanoparticles

Reversible assembly of gold nanoparticles controlled by the homodimerization and folding of an immobilized de novo designed synthetic polypeptide is described. In solution at neutral pH, the polypeptide folds into a helix-loop-helix four-helix bundle in the presence of zinc ions. When immobilized on gold nanoparticles, the addition of zinc ions induces dimerization and folding between peptide monomers located on separate particles, resulting in rapid particle aggregation. The particles can be completely redispersed by removal of the zinc ions from the peptide upon addition of EDTA. Calcium ions, which do not induce folding in solution, have no effect on the stability of the peptide decorated particles. The contribution from folding on particle assembly was further determined utilizing a reference peptide with the same primary sequence but containing both D and L amino acids. Particles functionalized with the reference peptide do not aggregate, as the peptides are unable to fold. The two peptides, linked to the nanoparticle surface via a cysteine residue located in the loop region, form submonolayers on planar gold with comparable properties regarding surface density, orientation, and ability to interact with zinc ions. These results demonstrate that nanoparticle assembly can be induced, controlled, and to some extent tuned, by exploiting specific molecular interactions involved in polypeptide folding.     

Revealing protein structures in solid-phase peptide synthesis by 13C solid-state NMR: evidence of excessive misfolding for Alzheimer's β

Solid-phase peptide synthesis (SPPS) is a widely used technique in biology and chemistry. However, the synthesis yield in SPPS often drops drastically for longer amino acid sequences, presumably because of the occurrence of incomplete coupling reactions. The underlying cause for this problem is hypothesized to be a sequence-dependent propensity to form secondary structures through protein aggregation. However, few methods are available to study the site-specific structure of proteins or long peptides that are anchored to the solid support used in SPPS. This study presents a novel solid-state NMR (SSNMR) approach to examine protein structure in the course of SPPS. As a useful benchmark, we describe the site-specific SSNMR structural characterization of the 40-residue Alzheimer's β-amyloid (Aβ) peptide during SPPS. Our 2D (13)C/(13)C correlation SSNMR data on Aβ(1-40) bound to a resin support demonstrated that Aβ underwent excessive misfolding into a highly ordered β-strand structure across the entire amino acid sequence during SPPS. This approach is likely to be applicable to a wide range of peptides/proteins bound to the solid support that are synthesized through SPPS.     

Investigation of the core-shell interface in gold@silica nanoparticles: a silica imprinting approach

The nature of the self-assembled core-shell interface in gold@silica nanoparticles synthesized via a 3-aminopropyltrimethoxysilane (APTMS) route is investigated using materials synthesis as a sensitive tool for elucidating interfacial composition and organization. Our approach involves condensation of the gold@silica nanoparticles within a silica framework for synthesis of a composite gold-silica material containing approximately 30 wt % gold. This material contains one of the highest gold loadings reported, but maintains gold core isolation as ascertained via a single surface plasmon resonance absorption band frequency corresponding to that of gold nanoparticles in dilute aqueous solution. The immobilized gold cores are subsequently etched using cyanide anion for the synthesis of templated porosity, which corresponds to the space that was occupied by the gold. Characterization of immobilized amines is performed using probe molecule binding experiments, which demonstrate a lack of accessible amines after gold removal. Solid-state 13C CPMAS NMR spectroscopy on these materials demonstrates that the amount of amine immobilization must be less than 10% of the expected yield, assuming that all of the APTMS becomes bound to the gold nanoparticle template. These results require a core-shell interface in the gold@silica nanoparticles that is predominantly occupied by inorganic silicate species, such as Si-O-Si and Si-OH, rather than primary amines. Such a result is likely a consequence of the weak interaction between primary amines and gold in aqueous solution. Our method for investigating the core-shell interface of gold@silica nanoparticles is generalizable for other interfacial structures and enables the synthesis of bulk imprinted silica using colloidal templates.     

Detection of peptide-phospholipid interaction sites in bilayer membranes by 13C NMR spectroscopy: observation of 2H/31P-selective 1H-depolarization under magic-angle spinning

We have developed a solid-state NMR method for observing the signals due to 13C spins of a peptide in the close vicinity of 31P and 2H spins in deuterated phospholipid bilayers. The signal intensities in 13C high-resolution NMR spectra directly indicate the depolarization of 1H by 1H-31P and 1H-2H dipolar couplings under multiple-contact cross-polarization. This method was applied to a fully 13C-, 15N-labeled 14-residue peptide, mastoparan-X (MP-X), bound to phospholipid bilayers whose fatty acyl chains are deuterated. The 13C NMR spectra for the depolarization were simulated from the chemical shifts and structure of membrane-bound MP-X previously determined and the distribution of 2H and 31P spins in lipid bilayers. The minimization of RMSD between the simulated and the experimental spectra showed that the amphiphilic alpha-helix of MP-X was located in the interface between the water layer and the hydrophobic domain of the bilayer, with nonpolar residues facing the phosphorus atoms and alkyl chains of the lipids.     

Alpha-helix-inducing dimerization of synthetic polypeptide scaffolds on gold

Designed, synthetic polypeptides that assemble into four-helix bundles upon dimerization in solution were studied with respect to folding on planar gold surfaces. A model system with controllable dimerization properties was employed, consisting of negatively and positively charged peptides. Circular dichroism spectroscopy and surface plasmon resonance based measurements showed that at neutral pH, the peptides were able to form heterodimers in solution, but unfavorable electrostatic interactions prevented the formation of homodimers. The dimerization propensity was found to be both pH- and buffer-dependent. A series of infrared absorption-reflection spectroscopy experiments of the polypeptides attached to planar gold surfaces revealed that if the negatively charged peptide was immobilized from a loading solution where it was folded, its structure was retained on the surface provided it had a cysteine residue available for anchoring to gold. If it was immobilized as random coil, it remained unstructured on the surface but was able to fold through heterodimerization if subsequently exposed to a positively charged polypeptide. When the positively charged peptide was immobilized as random coil, heterodimerization could not be induced, probably because of high-affinity interactions between the charged primary amine groups and the gold surface. These observations are intended to pave the way for future engineering of functional surfaces based on polypeptide scaffolds where folding is known to be crucial for function.     

Sequence, structure, and function of peptide self-assembled monolayers

Cysteine is commonly used to attach peptides onto gold surfaces. Here we show that the inclusion of an additional linker with a length of four residues (-PPPPC) and a rigid, hydrophobic nature is a better choice for forming peptide self-assembled monolayers (SAMs) with a well-ordered structure and high surface density. We compared the structure and function of the nonfouling peptide EKEKEKE-PPPPC-Am with EKEKEKE-C-Am. Circular dichroism, attenuated total internal reflection Fourier transform IR spectroscopy, and molecular dynamics results showed that EKEKEKE-PPPPC-Am forms a secondary structure while EKEKEKE-C-Am has a random structure. Surface plasmon resonance sensor results showed that protein adsorption on EKEKEKE-PPPPC-Am/gold is very low with small variation while protein adsorption on EKEKEKE-C-Am/gold is high with large variation. X-ray photoelectron spectroscopy results showed that both peptides have strong gold-thiol binding with the gold surface, indicating that their difference in protein adsorption is due to their assembled structures. Further experimental and simulation studies were performed to show that -PPPPC is a better linker than -PC, -PPC, and -PPPC. Finally, we extended EKEKEKE-PPPPC-Am with the cell-binding sequence RGD and demonstrated control over specific versus nonspecific cell adhesion without using poly(ethylene glycol). Adding a functional peptide to the nonfouling EK sequence avoids complex chemistries that are used for its connection to synthetic materials.     

Mapping the nanoparticle-coating monolayer with NMR pseudocontact shifts

Lanthanide ions Yb(3+) and Tb(3+), once bound to the monolayer of organic molecules coating the surface of gold nanoparticles, induce pseudo-contact shifts on the signals of nearby nuclear spins. This not only allows the investigation of the average structure of the ligands in the monolayer but also the mapping of the position of organic molecules bound to it.     

Stimuli induced structural changes of gold nanoparticle assemblies having sequential alternating amphiphilic peptides at the surface

Gold nanoparticles having sequential alternating amphiphilic peptide chains, Phe-(Leu-Glu)8, on the surface have been prepared. We describe structural control of the amphiphilic peptide coated gold nanoparticle assembly by a conformational transition of the surface peptides. Under the acidic condition, the conformation of the surface amphiphilic peptide was converted to a beta-sheet structure from an aggregated alpha-helix by incubation. Under this condition, the amphiphilic peptide coated gold nanoparticles formed a nanosheet assembly. The plasmon absorption maximum of the gold nanoparticles shifted to a shorter wavelength with the formation of the beta-sheet assembly of the surface peptide. This suggests that the structure of the peptide coated gold nanoparticle assembly could be controlled by the conformational transition of the surface peptide. Furthermore, the core gold nanoparticle could be fixed in the beta-sheet assembly in the state that stood alone. This system may be useful for novel molecular devices that exhibit quantized properties.     

Frequency-selective homonuclear dipolar recoupling in solid state NMR

We introduce a new approach to frequency-selective homonuclear dipolar recoupling in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS). This approach, to which we give the acronym SEASHORE, employs alternating periods of double-quantum recoupling and chemical shift evolution to produce phase modulations of the recoupled dipole-dipole interactions that average out undesired couplings, leaving only dipole-dipole couplings between nuclear spins with a selected pair of NMR frequencies. In principle, SEASHORE is applicable to systems with arbitrary coupling strengths and arbitrary sets of NMR frequencies. Arbitrary MAS frequencies are also possible, subject only to restrictions imposed by the pulse sequence chosen for double-quantum recoupling. We demonstrate the efficacy of SEASHORE in experimental (13)C NMR measurements of frequency-selective polarization transfer in uniformly (15)N, (13)C-labeled L-valine powder and frequency-selective intermolecular polarization transfer in amyloid fibrils formed by a synthetic decapeptide containing uniformly (15)N, (13)C-labeled residues.     

IR study of cross-strand coupling in a beta-hairpin peptide using isotopic labels

Model beta-hairpin peptides can be used to develop understanding of fundamental elements of beta-sheet secondary structure formation and stability. We have studied two 13C-labeled variants of a beta-hairpin peptide modified from a design originally proposed by Gellman: Arg-Tyr-Val-Glu-Val-Aib-Gly-Lys-Lys-Ile-Leu-Gln. (In this peptide, the two italicized residues form a beta-turn, while 13C-labels are on the amide C=O of Val3, Lys8 in HBG-L and Val3, Ile10 in HBG-S.) Both these peptides are labeled on opposite strands of the hairpin, but differ in the labeling pattern. One (HBG-L) forms a large (14-atom) H-bonded ring of labeled C=Os, while the other (HBG-S) forms a small (10-atom) H-bonded ring. These impact the amide I infrared spectra, with HBG-L having a 13C frequency and intensity higher than that of HBG-S, in good agreement with our spectral simulations based on quantum mechanically derived force fields. The thermal behavior of both peptides yields a broad thermal transition and lacks an isosbestic point. The 13C band for HBG-L has the largest intensity change with temperature, distinct from the 12C change and the HBG-S 13C change.     

Membrane binding and structure of de novo designed alpha-helical cationic coiled-coil-forming peptides.

We introduce a de novo designed peptide model system that enables the systematic study of 1) the role of a membrane environment in coiled-coil peptide folding, 2) the impact of different domains of an alpha-helical coiled-coil heptad repeat on the interaction with membranes, and 3) the dynamics of coiled-coil peptide-membrane interactions depending on environmental conditions. Starting from an ideal alpha-helical coiled-coil peptide sequence, several positively charged analogues were designed that exhibit a high propensity toward negatively charged lipid membranes. Furthermore, these peptides differ in their ability to form a stable alpha-helical coiled-coil structure. The influence of a membrane environment on peptide folding is studied. All positively charged peptides show strong interactions with negatively charged membranes. This interaction induces an alpha-helical structure of the former random-coil peptides, as revealed by circular dichroism measurements. Furthermore, vesicle aggregation is induced by a coiled-coil interaction of vesicle-bound peptides. Dynamic light scattering experiments show that the strength of vesicle aggregation increases with the peptide's intrinsic ability to form a stable alpha-helical coiled coil. Thus, the peptide variant equipped with the strongest inter- and intra-helical coiled-coil interactions shows the strongest effect on vesicle aggregation. The secondary structure of this peptide in the membrane-bound state was studied as well as its effect on the phospholipids. Peptide conformation within the peptide-lipid aggregates was analyzed by (13)C cross-polarization magic-angle spinning NMR experiments. A uniformly (13)C- and (15)N-labeled Leu residue was introduced at position 12 of the peptide chain. The (13)C chemical shift and torsion angle measurements support the finding of an alpha-helical structure of the peptide in its membrane-bound state. Neither membrane leakage nor fusion was observed upon peptide binding, which is unusual for amphiphatic peptide structures. Our results lay the foundation for a systematic study of the influence of the alpha-helical coiled-coil folding motif in membrane-active events on a molecular level.     

Ultrasmall gold nanoparticles for highly specific isolation/enrichment of N-linked glycosylated peptides

In recent years, gold nanoparticles have been increasingly utilized as a promising material for biomedical analysis. We report here for the first time the synthesis of ultrasmall gold nanoparticles with core diameter of 1.2 nm functionalized with hydrazide groups and their use in isolation/enrichment of N-glycosylated peptides. Hydrazide-functionalized gold nanoparticles showed excellent stability in biological samples and exhibited a large capacity for peptide capturing. The captured peptides from tested standard glycoproteins were found to be highly specific as determined by Agilent HPLC chip and quadrupole time-of-flight (Q-TOF) mass spectrometer. The hydrazide-functionalized gold nanoparticles were successfully utilized in the isolation of a real proteome complex, which showed that more than 90% of captured product was glycopeptide. These results demonstrate that the ultrasmall gold nanoparticles can be used for a high-throughput analysis platform of glycoproteins.     

Short peptides enhance single cell adhesion and viability on microarrays

Single cell patterning holds important implications for biology, biochemistry, biotechnology, medicine, and bioinformatics. The challenge for single cell patterning is to produce small islands hosting only single cells and retaining their viability for a prolonged period of time. This study demonstrated a surface engineering approach that uses a covalently bound short peptide as a mediator to pattern cells with improved single cell adhesion and prolonged cellular viability on gold patterned SiO2 substrates. The underlying hypothesis is that cell adhesion is regulated by the type, availability, and stability of effective cell adhesion peptides, and thus covalently bound short peptides would promote cell spreading and, thus, single cell adhesion and viability. The effectiveness of this approach and the underlying mechanism for the increased probability of single cell adhesion and prolonged cell viability by short peptides were studied by comparing cellular behavior of human umbilical cord vein endothelial cells on three model surfaces whose gold electrodes were immobilized with fibronectin, physically adsorbed Arg-Glu-Asp-Val-Tyr, and covalently bound Lys-Arg-Glu-Asp-Val-Tyr, respectively. The surface chemistry and binding properties were characterized by reflectance Fourier transform infrared spectroscopy. Both short peptides were superior to fibronectin in producing adhesion of only single cells, whereas the covalently bound peptide also reduced apoptosis and necrosis of adhered cells. Controlling cell spreading by peptide binding domains to regulate apoptosis and viability represents a fundamental mechanism in cell-materials interaction and provides an effective strategy in engineering arrays of single cells.     

Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling

Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.     

Playing with peptides: how to build a supramolecular peptide nanostructure by exploiting helix···helix macrodipole interactions

A novel method to build bicomponent peptide self-assembled monolayers (SAMs) has been developed, by exploiting helix···helix macrodipole interactions. In this work, a peptide-based self-assembled monolayer composed of two helical peptides was immobilized on a gold surface. Specifically, a pyrene-containing octapeptide, devoid of any sulfur atom (A8Pyr), and a hexapeptide, functionalized at the N-terminus with (S,R) lipoic acid, for binding to gold substrates (SSA4WA) via a Au-S linkage, have been employed. Both peptides investigated attain a helical structure, because they are almost exclusively formed by strongly folding inducer C(α)-tetrasubstituted α-amino acids. We demonstrate that the two peptides generate a stable supramolecular nanostructure (a densely packed bicomponent peptide monolayer), where A8Pyr is incorporated into the SSA4WA palisade by exploiting helix···helix macrodipole interactions. The presence of both peptides on the gold surface was investigated by spectroscopic and electrochemical techniques, while the morphology of the monolayer was analyzed by ultra high-vacuum scanning tunnelling microscopy. The composition of the bicomponent SAM on the surface was studied by a combination of electrochemical and spectroscopic techniques. In particular, the amount of Au-S linkages from the sulfur-containing peptides was quantified from reductive desorption of the peptide-based SAM, while the amount of A8Pyr was estimated by fluorescence spectroscopy. The antiparallel orientation of the A8Pyr and SSA4WA peptide chains minimizes the interaction energy between the helix dipoles, suggesting that this kind of electrostatic phenomenon is the driving force that stabilizes the bicomponent SAM.     

Circular dichroism analysis of penicillin G acylase covalently immobilized on silica nanoparticles

Circular dichroism (CD) was used to characterize the secondary structure of penicillin G acylase upon covalent immobilization on silica nanoparticles. Covalent immobilization was achieved by functionalizing the silica nanoparticles with glutardialdehyde and coupling to the free NH(2) groups of the enzyme (lysine and arginine side chains). The loading of the covalently bound enzyme was increased up to saturation, which was reached at 54.6 mg immobilized enzyme per g silica nanobeads. For structural characterization of the commercially available enzyme its exact molecular mass was determined by mass spectrometry in order to enable precise evaluation of the CD data. The fraction of secondary structure elements of the free and immobilized enzyme were estimated from the respective CD spectra using standard algorithms (CONTINLL, CDSSTR, SELCON3). The fractions obtained by the different algorithms for the free enzyme agreed well with one another and also with data from X-ray diffraction described in the literature. Interestingly, the secondary structure fractions found for the immobilized enzyme were very similar to the free enzyme and nearly constant over all experiments. These results indicate that even a loading of up to 55.8 mg/g (enzyme per silica nanoparticles) causes only slight structural changes. However, the specific activity determined by a kinetic assay decreased by around 60%, when increasing the loading from 14.9 to 55.8 mg/g. Because of the fact that we found no major changes in the secondary structure, diffusion limitation seems to be the main reason for the decline of the specific activity.