Electrical behavior of molecular junctions incorporating alpha-helical peptide

We synthesized an alpha-helical peptide containing two terminal thiol groups and demonstrated the method of preparation of a self-assembled monolayer (SAM) on gold with uniform orientation of the molecules on the surface. The monolayers were employed as model systems for the investigations of mediated electron transfer. The measurements of electron transfer efficiency through the peptide were performed using scanning tunneling spectroscopy (STS). The molecules were trapped between the gold tip and the substrate using a Au-S linkage. The electron transfer behavior of the peptide was examined as a function of the tip-substrate distance at fixed bias voltage and as a function of bias voltage at a fixed distance between the tip and the substrate. The data obtained from these experiments indicated that the electron transfer through alpha-helical peptide is very efficient, and its conductivity is comparable to those observed for dodecanedithiol. There is also a directional dependence of electron transmission through the peptide, which is connected with the electric field generated by the molecular dipole of the helix.     

Aromatic-backbone interactions in model alpha-helical peptides

The effects on helical stability of weak polar interactions between aromatic side-chains and the peptide backbone were examined. alpha-Helical model peptides, hexa-Ala, with sequential Tyr replacement, were investigated computationally to obtain the geometries and energetics of the interactions. Geometries were obtained with the B3LYP/6-31G* level of theory. Interaction energies were calculated using BHandHLYP/cc-pVTZ and an improved method to correct for basis set superposition error when fragmentation caused steric clashes. Both i, i + 1 and i, i - 4 interactions were observed when Tyr was in position i = 5. The position of the aromatic residue in the amino acid sequence was crucial in facilitating aromatic-backbone interactions. The distance between the center of the aromatic ring of Tyr and the individual interacting backbone atoms ranged from 3.65 to 5.50 A. The interactions have energies of the same order as hydrogen bonds and, thus, could have a significant impact on the stability of the helix.     

Cation-pi interaction in model alpha-helical peptides

Cation-pi interactions are increasingly recognized as important in chemistry and biology. Here we investigate the cation-pi interaction by determining its effect on the helicity of model peptides using a combination of CD and NMR spectroscopy. The data show that a single Trp/Arg interaction on the surface of a peptide can make a significant net favorable free energy contribution to helix stability if the two residues are positioned with appropriate spacing and orientation. The solvent-exposed Trp-->Arg (i, i + 4) interaction in helices can contribute -0.4 kcal/mol to the helix stability, while no free energy gain is detected if the two residues have the reversed orientation, Arg-->Trp (i, i + 4). The derived free energy is consistent with other experimental results studied in proteins or model peptides on cation-pi interactions. However in the same system the postulated Phe/Arg (i, i + 4) cation-pi interaction provides no net free energy to helix stability. Thus the Trp-->Arg interaction is stronger than Phe-->Arg. The cation-pi interactions are not sensitive to the screening effect by adding neutral salt as indicated by salt titration. Our results are in qualitative agreement with theoretical calculations emphasizing that cation-pi interactions can contribute significantly to protein stability with the order Trp > Phe. However, our and other experimental values are significantly smaller than estimates from theoretical calculations.     

Conductance of single cobalt chalcogenide cluster junctions

Understanding the electrical properties of semiconducting quantum dot devices have been limited due to the variability of their size/composition and the chemistry of ligand/electrode binding. Furthermore, to probe their electrical conduction properties and its dependence on ligand/electrode binding, measurements must be carried out at the single dot/cluster level. Herein we report scanning tunneling microscope based break junction measurements of cobalt chalcogenide clusters with Te, Se and S to probe the conductance properties. Our measured conductance trends show that the Co-Te based clusters have the highest conductance while the Co-S clusters the lowest. These trends are in very good agreement with cyclic voltammetry measurements of the first oxidation potentials and with density functional theory calculations of their HOMO-LUMO gaps.     

Site-selective metal binding by designed alpha-helical peptides

It is known that the designed alpha-helical peptide family TRI [(Ac-G(LKALEEK)4G-CONH2)], containing single site substitution of a cysteine for a leucine, is capable of binding Cd(II) within a three-stranded coiled coil. The binding affinity of cadmium is dependent upon the site of substitution, with cysteine incorporated at the a site leading to cadmium complexes of higher affinity than when a d site was modified. In this work we have examined whether this differential binding affinity can be expressed in a di-cysteine-substituted peptide in order to develop site specificity within a designed system. The peptide TRI L9CL19C was used to determine whether significant differences in binding affinities at nearly proximal sites could be achieved in a short designed peptide. On the basis of 113Cd, 1H NMR, and circular dichroic spectroscopies, we have shown that 1 equiv of Cd(II) binds exclusively at the a site. Only after that position is filled does the second site become populated. Thus, the TRI system represents the first example where stoichiometrically equivalent peptides with different sequences form the framework for designing molecular assemblies that show site-specific ion recognition. We propose that the distinct metal affinities are due to the cysteine conformers at different substitution points along the peptide. Furthermore, we have shown that site selectivity in biomolecules can be encoded into relatively short peptides with helical sequences and, therefore, do not necessarily require the extensive protein scaffolds found in natural systems.     

Conductance of nano-tube junctions and its scaling law

The conductance is calculated by Landauer’s formula with a simple tight binding model for junctions connecting two different metallic carbon nanotubes. These junctions are formed by a pair of disclinations, a 5-membered ring and a 7-membered ring, without dangling bonds. Conductances of about eight hundred kinds of junctions are obtained. The conductance is determined only by the ratio i/R where i is the distance between the two disclinations and R is the circumference of the thinner tube. When i/R ? 1, the conductance is found to be almost proportional to (i/R)^-3. Even when the Fermi energy is shifted by doping, an extended scaling law holds, so far as the channel number is kept two.     

Design and synthesis of alpha-helical peptides and mimetics

The alpha-helix is the most abundant secondary structural element in proteins and is an important structural domain for mediating protein-protein and protein-nucleic acid interactions. Strategies for the rational design and synthesis of alpha-helix mimetics have not matured as well as other secondary structure mimetics such as strands and turns. This perspective will focus on developments in the design, synthesis and applications of alpha-helices and mimetics, particularly in the last 5 years. Examples where synthetic compounds have delivered promising biological results will be highlighted as well as opportunities for the design of mimetics of the type I alpha-helical antifreeze proteins.     

Spectroscopy of molecular junctions

In this tutorial review we present in detail recent studies in which molecular junctions were simultaneously probed by conductance measurements and optical spectroscopy methods such as electroluminescence (EL) and Raman scattering. The advantages of combining these experimental approaches to improve our understanding of charge transport through molecular junctions are discussed and routes for future developments are suggested.     

Mechanisms of the interaction of alpha-helical transmembrane peptides with phospholipid bilayers

The synthetic peptide acetyl-K(2)-G-L(24)-K(2)-A-amide (P(24)) and its analogs have been successfully utilized as models of the hydrophobic transmembrane alpha-helical segments of integral membrane proteins. The central polyleucine region of these peptides was designed to form a maximally stable, very hydrophobic alpha-helix which will partition strongly into the hydrophobic environment of the lipid bilayer core, while the dilysine caps were designed to anchor the ends of these peptides to the polar surface of the lipid bilayer and to inhibit the lateral aggregation of these peptides. Moreover, the normally positively charged N-terminus and the negatively charged C-terminus have both been blocked in order to provide a symmetrical tetracationic peptide, which will more faithfully mimic the transbilayer region of natural membrane proteins and preclude favorable electrostatic interactions. In fact, P(24) adopts a very stable alpha-helical conformation and transbilayer orientation in lipid model membranes. The results of our recent studies of the interaction of this family of alpha-helical transmembrane peptides with phospholipid bilayers are summarized here.     

D/H amide isotope effect in model alpha-helical peptides

The contribution of amide related hydrogen bonds to protein stability has recently been evaluated using the "Cm experiment", which measures the D/H amide isotope effect in proteins. We show here using isolated alpha-helical peptides that there is a significant effect of denaturant concentration on the measured D/H isotope effect, and that valid comparison of different proteins requires correcting for differences in denaturant (GdmHCl) concentration. Finally our results suggest that H-bonds in an isolated alpha-helix may contribute more to helix stability because of less strain compared to those in helical proteins and that the buried helical H-bonds in helical proteins are not necessarily energetically more favorable than solvent exposed H-bonds in isolated helices.     

All-carbon molecular tunnel junctions

This Article explores the idea of using nonmetallic contacts for molecular electronics. Metal-free, all-carbon molecular electronic junctions were fabricated by orienting a layer of organic molecules between two carbon conductors with high yield (>90%) and good reproducibility (rsd of current density at 0.5 V <30%). These all-carbon devices exhibit current density-voltage (J-V) behavior similar to those with metallic Cu top contacts. However, the all-carbon devices display enhanced stability to bias extremes and greatly improved thermal stability. Completed carbon/nitroazobenzene(NAB)/carbon junctions can sustain temperatures up to 300 °C in vacuum for 30 min and can be scanned at ±1 V for at least 1.2 × 10(9) cycles in air at 100 °C without a significant change in J-V characteristics. Furthermore, these all-carbon devices can withstand much higher voltages and current densities than can Cu-containing junctions, which fail upon oxidation and/or electromigration of the copper. The advantages of carbon contacts stem mainly from the strong covalent bonding in the disordered carbon materials, which resists electromigration or penetration into the molecular layer, and provides enhanced stability. These results highlight the significance of nonmetallic contacts for molecular electronics and the potential for integration of all-carbon molecular junctions with conventional microelectronics.     

Coherently controlled molecular junctions

Within a generic model, we discuss the possibility of coherent control of charge fluxes in unbiased molecular junctions. The control is induced by resonances between the Rabi frequency due to a pumping laser field and internal characteristic frequencies of pre-designed molecular donor-bridge-acceptor complexes. Two models are considered: a coherently controlled molecular charge pump and a molecular switch. The study generalizes previous consideration of light induced current [M. Galperin and A. Nitzan, Phys. Rev. Lett. 95, 206802 (2005)] and of a molecular electron pump [R. Volkovich and U. Peskin, Phys. Rev. B 83, 033403 (2011)] and accounts for the coherently driven charge transport in an unbiased molecular junction with symmetric coupling to leads. Numerical examples demonstrate the feasibility of the control mechanism for realistic junctions parameters.     

Heat rectification in molecular junctions

Heat conduction through molecular chains connecting two reservoirs at different temperatures can be asymmetric for forward and reversed temperature biases. Based on analytically solvable models and on numerical simulations we show that molecules rectify heat when two conditions are satisfied simultaneously: the interactions governing the heat conduction are nonlinear, and the junction has some structural asymmetry. We consider several simplified models where a two-level system (TLS) simulates a highly anharmonic vibrational mode, and asymmetry is introduced either through different coupling of the molecule to the contacts, or by considering internal molecular asymmetry. In the first case, we present analytical results for the asymmetric heat current flowing through a single anharmonic mode using different forms for the TLS-reservoirs coupling. We also demonstrate numerically, studying a realistic molecular model, that a uniform anharmonic molecular chain connecting asymmetrically two thermal reservoirs rectifies heat. This effect is stronger for longer chains, where nonlinear interactions dominate the transfer process. When asymmetry is related to the internal level structure of the molecule, numerical simulations reveal a nontrivial rectification behavior. We could still explain this behavior in terms of an effective system-bath coupling. Our study suggests that heat rectification is a fundamental characteristic of asymmetric nonlinear thermal conductors. This phenomenon is important for heat control in nanodevices and for understanding of energy flow in biomolecules.     

Variability of conductance in molecular junctions

The conductance of molecular junctions, formed by breaking gold point contacts dressed with various thiol functionalized organic molecules, is measured at 293 K and at 30 K. In the presence of molecules, individual conductance traces measured as a function of increasing gold electrode displacement show clear steps below the quantum conductance steps of the gold contact. These steps are distributed over a wide range of molecule-dependent conductance values. Histograms constructed from all conductance traces therefore do not show clear peaks either at room or low temperatures. Filtering of the data sets by an objective automated procedure only marginally improves the visibility of such features. We conclude that the geometrical junction to junction variations dominate the conductance measurements.     

UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations

We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations of these peptides are dominantly PPII. Thus, AP, which is highly alpha-helical at room temperature, melts to a PPII conformation. There is no indication of any population of intermediate disordered conformations. We continued our development of methods to relate the Ramachandran Psi-angle to the amide III band frequency. We describe a new method to estimate the Ramachandran Psi-angular distributions from amide III band line shapes measured in 204-nm UV Raman spectra. We used this method to compare the Psi-distributions in XAO, ala(5), the non-alpha-helical state of AP, and acid-denatured apomyoglobin. In addition, we estimated the Psi-angle distributions of peptide bonds which occur in non-alpha-helix and non-beta-sheet conformations in a small library of proteins.     

De novo design of fibrils made of short alpha-helical coiled coil peptides.

BACKGROUND: The alpha-helical coiled coil structures formed by 25-50 residues long peptides are recognized as one of Nature's favorite ways of creating an oligomerization motif. Known de novo designed and natural coiled coils use the lateral dimension for oligomerization but not the axial one. Previous attempts to design alpha-helical peptides with a potential for axial growth led to fibrous aggregates which have an unexpectedly big and irregular thickness. These facts encouraged us to design a coiled coil peptide which self-assembles into soluble oligomers with a fixed lateral dimension and whose alpha-helices associate in a staggered manner and trigger axial growth of the coiled coil. Designing the coiled coil with a large number of subunits, we also pursue the practical goal of obtaining a valuable scaffold for the construction of multivalent fusion proteins. RESULTS: The designed 34-residue peptide self-assembles into long fibrils at slightly acid pH and into spherical aggregates at neutral pH. The fibrillogenesis is completely reversible upon pH change. The fibrils were characterized using circular dichroism spectroscopy, sedimentation diffusion, electron microscopy, differential scanning calorimetry and X-ray fiber diffraction. The peptide was deliberately engineered to adopt the structure of a five-stranded coiled coil rope with adjacent alpha-helices, staggered along the fibril axis. As shown experimentally, the most likely structure matches the predicted five-stranded arrangement. CONCLUSIONS: The fact that the peptide assembles in an expected fibril arrangement demonstrates the credibility of our conception of design. The discovery of a short peptide with fibril-forming ability and stimulus-sensitive behavior opens new opportunities for a number of applications.     

Two-dimensional infrared spectral signatures of 3(10)- and alpha-helical peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.     

Uncoupled peptide bond vibrations in alpha-helical and polyproline II conformations of polyalanine peptides

We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.     

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.