Modeling energy landscapes of proton motion in nonaqueous, tethered proton wires

We have modeled structures and energetics of anhydrous proton-conducting wires: tethered hydrogen-bonded chains of the form ···HX···HX···HX···, with functional groups HX = imidazole, triazole, and formamidine; formic, sulfonic, and phosphonic acids. We have applied density functional theory (DFT) to model proton wires up to 19 units long, where each proton carrier is linked to an effective backbone to mimic polymer tethering. This approach allows the direct calculation of hydrogen bond strengths. The proton wires were found to be stabilized by strong hydrogen bonds (up to 50 kJ/mol) whose strength correlates with the proton affinity of HX [related to pK(b)(HX)] and not to pK(a)(HX) as is often assumed. Geometry optimizations and ab initio molecular dynamics near 400 K on imidazole-based proton wires both predict that adding a proton to the end of such wires causes the excess charge to embed into the interior segments of these wires. Proton translocation energy landscapes for imidazole-based wires are sensitive to the imidazole attachment point (head or feet) and to wire architecture (linear or interdigitated). Linear imidazole wires with head-attachment exhibit low barriers for intrawire proton motion, rivaling proton diffusion in liquid imidazole. Excess charge relaxation from the edge of wires is found to be dominated by long-range Grotthuss shuttling for distances as long as 42 ?, especially for interdigitated wires. For imidazole, we predict that proton translocation is controlled by the energetics of desorption from the proton wire, even for relatively long wires (600 imidazole units). Proton desorption energies show no correlation with functional group properties, suggesting that proton desorption is a collective process in proton wires.     

Mimicking helical antibacterial peptides with nonpeptidic folding oligomers

Unnatural oligomeric scaffolds designed to adopt defined secondary structures (e.g., helices), while retaining the chemical diversity of amino acid side chains, are of practical value to elaborate functional mimetics of bioactive alpha-polypeptides. Enantiopure N,N'-linked oligoureas as short as seven residues long have been previously shown to fold into a stable helical structure, stabilized by 12- and 14-membered H-bonded rings. We now report that eight-residue oligoureas designed to mimic globally amphiphilic alpha-helical host-defense peptides are effective against both gram-negative and gram-positive bacteria (including methicillin-resistant Staphylococcus aureus [MRSA]) and exhibit selectivity for bacterial versus mammalian cells. Circular dichroism (CD) spectroscopy studies suggest enhanced helical propensity of oligoureas in the presence of phospholipid vesicles. The utility of this new class of nonpeptidic foldamers for biological applications is highlighted by high resistance to proteolytic degradation.     

The mobile proton in polyalanine peptides

Ion mobility measurements have been performed for protonated polyalanine peptides (A10 + H+, A15 + H+, A20 + H+, A25 + H+, and A15NH2 + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A10 + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A15 + H+ and A15NH2 + H+ spend most of their time as globules when heated, while A20 + H+ and A25 + H+ spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intramolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate freely along the backbone) at around 450 K. The peptides dissociate as the temperature is increased further to give predominantly the bn(+), b(n-1)(+), b(n-2)(+), ... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the An + H+ peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.     

The influence of dipole moments on the mechanism of electron transfer through helical peptides

The life time of aromatic radical cations is limited by reactions like β-elimination, dimerization, and addition to the solvent. Here we show that the attachment of such a radical cation to the C-terminal end of an α-/3(10)-helical peptide further reduces its life time by two orders of magnitude. For PPII-helical peptides, such an effect is only observed if the peptide contains an adjacent electron donor like tyrosine, which enables electron transfer (ET) through the peptide. In order to explain the special role of α-/3(10)-helical peptides, it is assumed that the aromatic radical cation injects a positive charge into an adjacent amide group. This is in accord with quantum chemical calculations and electrochemical experiments in the literature showing a decrease in the amide redox potentials caused by the dipole moments of long α-/3(10)-helical peptides. Rate measurements are in accord with a mechanism for a multi-step ET through α-/3(10)-helical peptides that uses the amide groups or H-bonds as stepping stones.     

NMR detection of pH-dependent histidine-water proton exchange reveals the conduction mechanism of a transmembrane proton channel

The acid-activated proton channel formed by the influenza M2 protein is important for the life cycle of the virus. A single histidine, His37, in the M2 transmembrane domain (M2TM) is responsible for pH activation and proton selectivity of the channel. Recent studies suggested three models for how His37 mediates proton transport: a shuttle mechanism involving His37 protonation and deprotonation, a H-bonded imidazole-imidazolium dimer model, and a transporter model involving large protein conformational changes in synchrony with proton conduction. Using magic-angle-spinning (MAS) solid-state NMR spectroscopy, we examined the proton exchange and backbone conformational dynamics of M2TM in a virus-envelope-mimetic membrane. At physiological temperature and pH, (15)N NMR spectra show fast exchange of the imidazole (15)N between protonated and unprotonated states. To quantify the proton exchange rates, we measured the (15)N T(2) relaxation times and simulated them for chemical-shift exchange and fluctuating N-H dipolar fields under (1)H decoupling and MAS. The exchange rate is 4.5 × 10(5) s(-1) for Nδ1 and 1.0 × 10(5) s(-1) for Nε2, which are approximately synchronized with the recently reported imidazole reorientation. Binding of the antiviral drug amantadine suppressed both proton exchange and ring motion, thus interfering with the proton transfer mechanism. By measuring the relative concentrations of neutral and cationic His as a function of pH, we determined the four pK(a) values of the His37 tetrad in the viral membrane. Fitting the proton current curve using the charge-state populations from these pK(a)'s, we obtained the relative conductance of the five charge states, which showed that the +3 channel has the highest time-averaged unitary conductance. At physiologically relevant pH, 2D correlation spectra indicated that the neutral and cationic histidines do not have close contacts, ruling out the H-bonded dimer model. Moreover, a narrowly distributed nonideal helical structure coexists with a broadly distributed ideal helical conformation without interchange on the sub-10 ms time scale, thus excluding the transporter model in the viral membrane. These data support the shuttle mechanism of proton conduction, whose essential steps involve His-water proton exchange facilitated by imidazole ring reorientations.     

Effects of confinement on small water clusters structure and proton transport

Analyses of the structure of two to four water molecule clusters confined between two benzene and between two naphthalene molecules have been performed using ab initio methods. The water clusters tend to maximize the number of hydrogen bonds via formation of a cyclic network. The oxygen atoms locate approximately in the middle of the confined geometry, and the dipole vectors arrange either parallel or pointing to the surfaces. Energy barriers for proton transfer calculated for H3O+-(H2O) complexes in the same confined geometries suggest that there is a specific range of confinement that helps to lower the energy barriers of the proton transfer. When the walls are too close to each other, at a separation of 4 A, the energy barriers are extremely high. Confinement does not lower the barrier energies of proton transfer when the H3O+-(H2O) complexes are located further from each of the surfaces by more than approximately 8 A.     

2'-hydroxyl proton positions in helical RNA from simultaneously measured heteronuclear scalar couplings and NOEs

The 2'-hydroxyl group in RNA plays an important structural role; it defines hydration in the minor groove, impacts thermodynamic stability of RNA, and often participates in RNA catalysis. To better study this important functional group in RNA, we describe a constant-time HMQC-IPAP-NOESY 3D NMR experiment. It simultaneously yields highly resolved 13C-separated NOEs from ribose protons to the 2'OH proton, as well as E.COSY-type measurement of JC-OH couplings, thereby permitting a quantitative study of the orientation of the 2'OH proton in RNA. The observed NOE patterns indicate that the 2'OH bonds in A-form helical RNA are primarily oriented toward the base domain, as further supported by small (1.3 +/- 0.7 Hz) 3JC1'-2'OH and relatively large (4.2 +/- 0.7 Hz) 3JC3'-2'OH couplings. The constant-time HMQC-IPAP-NOESY is suitable for measurement of interactions of rapidly exchanging protons in proteins and nucleic acids.     

New Helical Folds in α‐Peptides with Alternating Chirality

In α‐peptides, the 8/10 helix is theoretically predicted to be energetically unstable and has not been experimentally observed so far. Based on our earlier studies on ‘helical induction’ and ‘hybrid helices’, we have adopted the ‘end‐capping’ strategy to induce the 8/10 helix in α‐peptides by using short α/β‐peptides. Thus, α‐peptides containing a regular string of α‐amino acids with alternating chirality were end capped by α/β‐peptides with 11/9‐helical motifs at the termini. Extensive NMR spectroscopy studies of these peptides revealed the presence of a hitherto unknown 8/10‐helical pattern; the H‐bonds in the shorter pseudorings were rather weak. The approach of using short helical motifs to induce new mixed helices in α‐peptides could provide avenues for more versatile design strategies.     

A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation

The gas-phase fragmentation mechanisms of small models for peptides containing intermolecular disulfide links have been studied using a combination of tandem mass spectrometry experiments, isotopic labeling, structural labeling, accurate mass measurements of product ions, and theoretical calculations (at the MP2/6-311 + G(2d,p)//B3LYP/3-21G(d) level of theory). Cystine and its C-terminal derivatives were observed to fragment via a range of pathways, including loss of neutral molecules, amide bond cleavage, and S-S and C-S bond cleavages. Various mechanisms were considered to rationalize S-S and C-S bond cleavage processes, including charge directed neighboring group processes and nonmobile proton salt bridge mechanism. Three low-energy fragmentation pathways were identified from theoretical calculations on cystine N-methyl amide: (1) S-S bond cleavage dominated by a neighboring group process involving the C-terminal amide N to form either a protonated cysteine derivative or protonated sulfenyl amide product ion (44.3 kcal mol(-1)); (2) C-S bond cleavage via a salt bridge mechanism, involving abstraction of the alpha-hydrogen by the N-terminal amino group to form a protonated thiocysteine derivative (35.0 kcal mol(-1)); and (3) C-S bond cleavage via a Grob-like fragmentation process in which the nucleophilic N-terminal amino group forms a protonated dithiazolidine (57.9 kcal mol(-1)). Interestingly, C-S bond cleavage by neighboring group processes have high activation barriers (63.1 kcal mol(-1)) and are thus not expected to be accessible during low-energy CID experiments. In comparison to the energetics of simple amide bond cleavage, these S-S and C-S bond cleavage reactions are higher in energy, which helps rationalize why bond cleavage processes involving the disulfide bond are rarely observed for low-energy CID of peptides with mobile proton(s) containing intermolecular disulfide bonds. On the other hand, the absence of a mobile proton appears to "switch on" disulfide bond cleavage reactions, which can be rationalized by the salt bridge mechanism. This potentially has important ramifications in explaining the prevalence of disulfide bond cleavage in singly protonated peptides under MALDI conditions.     

Theoretical models of directional proton molecular transport

The important topic of proton transport through molecular wires is usually associated with the Grotthuss mechanism. In this paper we propose an alternative conductor based on chains of lone pairs. B3LYP/6-31+G** and PW91 DFT calculations on model compounds (1,2,3,4-tetrasubstituted benzenes) show that these compounds could play the role of proton conductors.     

Temperature selectivity effects in reversed-phase liquid chromatography due to conformation differences between helical and non-helical peptides

In order to characterize the effect of temperature on the retention behaviour and selectivity of separation of polypeptides and proteins in reversed-phase high-performance liquid chromatography (RP-HPLC), the chromatographic properties of four series of peptides, with different peptide conformations, have been studied as a function of temperature (5-80 degrees C). The secondary structure of model peptides was based on either the amphipathic alpha-helical peptide sequence Ac-EAEKAAKEX(D/L)EKAAKEAEK-amide, (position X being in the centre of the hydrophobic face of the alpha-helix), or the random coil peptide sequence Ac-X(D/L)LGAKGAGVG-amide, where position X is substituted by the 19 L- or D-amino acids and glycine. We have shown that the helical peptide analogues exhibited a greater effect of varying temperature on elution behaviour compared to the random coil peptide analogues, due to the unfolding of alpha-helical structure with the increase of temperature during RP-HPLC. In addition, temperature generally produced different effects on the separations of peptides with different L- or D-amino acid substitutions within the groups of helical or non-helical peptides. The results demonstrate that variations in temperature can be used to effect significant changes in selectivity among the peptide analogues despite their very high degree of sequence homology. Our results also suggest that a temperature-based approach to RP-HPLC can be used to distinguish varying amino acid substitutions at the same site of the peptide sequence. We believe that the peptide mixtures presented here provide a good model for studying temperature effects on selectivity due to conformational differences of peptides, both for the rational development of peptide separation optimization protocols and a probe to distinguish between peptide conformations.     

Grotthus-type and diffusive proton transfer in 7-hydroxyquinoline.(NH(3))(n) clusters.

Proton translocation along ammonia wires is investigated in 7-hydroxyquinoline.(NH(3))(n) clusters, both experimentally by laser spectroscopy and theoretically by Hartree-Fock and density functional (DFT) calculations. These clusters serve as realistic finite-size models for proton transfer along a chain of hydrogen-bonded solvent molecules. In the enol tautomer of 7-hydroxyquinoline (7-HQ), the OH group acts as a proton injection site into the (NH(3))(n)cluster. Proton translocation along a chain of three NH(3) molecules within the cluster can take place, followed by reprotonation of 7-HQ at the quinolinic N atom, forming the 7-ketoquinoline tautomer. Exoergic proton transfer from the OH group of 7-HQ to the closest NH(3) molecule within the cluster giving a zwitterion 7-HQ-.(NH(3))(6)H+ (denoted PT-A) occurs at a threshold cluster size of n = 6 in the DFT calculations and at n = 5 or 6 experimentally. Three further locally stable zwitterion clusters denoted PT-B, PT-B', and PT-C, the keto tautomer, and several transition structures along the proton translocation path were characterized theoretically. Grotthus-type proton-hopping mechanisms occur for three of the proton transfer steps, which have low barriers and are exoergic or weakly endoergic. The step with the highest barrier involves a complex proton transfer mechanism, involving structural reorganization and large-scale diffusive motions of the cluster.     

Fabrication of Ni-decorated helical ribbon composite microstructure from self-assembled lipid tubule by electroless metallization

Molecular self-assembly is a powerful approach for preparing new supermolecular architectures such as nanofibers and nanotubes[1]. Lipid molecules, due to their amphiphilic nature, can self-assemble to form a variety of microstructures, such as spherical liposome, tubules and helical ribbons[2]. Many lipid molecules can self-organize into the helical ribbon structures[3,4], for example, helical ribbons were self-assembled in a variety of multicomponent enantiomerically pure sys- tems that cont…     

Hydroxystilbene isomer-specific photoisomerization versus proton transfer

The ground- and excited-state acidities of 3- and 4-hydroxystilbene have been investigated in aqueous solution. Approximate pKa* values determined from the F?rster equation are similar for the two isomers; however, 3-hydroxystilbene behaves as a photoacid in water, whereas 4-hydroxystilbene does not. Singular value decomposition with self-modeling is used to obtain more accurate pKa* values for 3-hydroxystilbene. The different behavior of the isomeric hydroxystilbenes is attributed to differences in their excited-state C=C torsional barriers. 3-Hydroxystilbene has a high barrier and a long singlet lifetime, permitting proton transfer to compete with other singlet decay pathways, whereas 4-hydroxystilbene has a low barrier, and thus proton transfer cannot compete with C=C torsion.     

Folding kinetics of a naturally occurring helical peptide: implication of the folding speed limit of helical proteins

The folding mechanism and dynamics of a helical protein may strongly depend on how quickly its constituent alpha-helices can fold independently. Thus, our understanding of the protein folding problem may be greatly enhanced by a systematic survey of the folding rates of individual alpha-helical segments derived from their parent proteins. As a first step, we have studied the relaxation kinetics of the central helix (L9:41-74) of the ribosomal protein L9 from the bacterium Bacillus stearothermophilus , in response to a temperature-jump ( T-jump) using infrared spectroscopy. L9:41-74 has been shown to exhibit unusually high helicity in aqueous solution due to a series of side chain-side chain interactions, most of which are electrostatic in nature, while still remaining monomeric over a wide concentration range. Thus, this peptide represents an excellent model system not only for examining how the folding rate of naturally occurring helices differs from that of the widely studied alanine-based peptides, but also for estimating the folding speed limit of (small) helical proteins. Our results show that the T-jump induced relaxation rate of L9:41-74 is significantly slower than that of alanine-based peptides. For example, at 11 degrees C its relaxation time constant is about 2 micros, roughly seven times slower than that of SPE(5), an alanine-rich peptide of similar chain length. In addition, our results show that the folding rate of a truncated version of L9:41-74 is even slower. Taken together, these results suggest that individual alpha-helical segments in proteins may fold on a time scale that is significantly slower than the folding time of alanine-based peptides. Furthermore, we argue that the relaxation rate of L9:41-74 measured between 8 and 45 degrees C provides a realistic estimate of the ultimate folding rate of (small) helical proteins over this temperature range.     

Charge mapping in 3(10)-helical peptide chains by oxidation of the terminal ferrocenyl group

Two series of 3(10)-helical peptides of different lengths and rigidity, based on the strongly foldameric α-aminoisobutyric acid and containing a terminal ferrocenyl unit, have been synthesized. Oxidation-state sensitive spectroscopic tags of helical peptides, the N-H groups, allowed mapping of the charge delocalization triggered by oxidation of the terminal ferrocenyl moiety and were monitored by IR spectroelectrochemistry.     

Helical water chain mediated proton conductivity in homochiral metal-organic frameworks with unprecedented zeolitic unh-topology

Four new homochiral metal-organic framework (MOF) isomers, [Zn(l-L(Cl))(Cl)](H(2)O)(2) (1), [Zn(l-L(Br))(Br)](H(2)O)(2) (2), [Zn(d-L(Cl))(Cl)](H(2)O)(2) (3), and [Zn(d-L(Br))(Br)](H(2)O)(2) (4) [L = 3-methyl-2-(pyridin-4-ylmethylamino)butanoic acid], have been synthesized by using a derivative of L-/D-valine and Zn(CH(3)COO)(2)·2H(2)O. A three-periodic lattice with a parallel 1D helical channel was formed along the crystallographic c-axis. Molecular rearrangement results in an unprecedented zeolitic unh-topology in 1-4. In each case, two lattice water molecules (one H-bonded to halogen atoms) form a secondary helical continuous water chain inside the molecular helix. MOFs 1 and 2 shows different water adsorption properties and hence different water affinity. The arrangement of water molecules inside the channel was monitored by variable-temperature single-crystal X-ray diffraction, which indicated that MOF 1 has a higher water holding capacity than MOF 2. In MOF 1, water escapes at 80 °C, while in 2 the same happens at a much lower temperature (～40 °C). All the MOFs reported here shows reversible crystallization by readily reabsorbing moisture. In MOFs 1 and 2, the frameworks are stable after solvent removal, which is confirmed by a single-crystal to single-crystal transformation. MOFs 1 and 3 show high proton conductivity of 4.45 × 10(-5) and 4.42 × 10(-5) S cm(-1), respectively, while 2 and 4 shows zero proton conductivity. The above result is attributed to the fact that MOF 1 has a higher water holding capacity than MOF 2.     

Rational design of a nanoscale helical scaffold derived from self-assembly of a dimeric coiled coil motif

We describe a model for the design of synthetic α-helical peptides that are competent for self-assembly into structurally defined supramolecular fibrils on the basis of architectural features that have been programmed into the peptide sequence. In order to test the validity of this experimental model, we have synthesized an oligopeptide YZ1 that was designed to conform to this model and to self-assemble into an α-helical fibril in which the structural sub-units that comprise the fibril corresponded to coiled coil dimers. Peptide YZ1 was prepared via conventional solid-phase peptide synthesis and was composed of 42 amino acid residues such that the sequence defined six distinct heptad repeats of a coiled coil structure. The sequence of YZ1 was designed to adopt an α-helical conformation in which the helical protomers self-associate in a parallel orientation with a staggered orientation between adjacent peptides that corresponded to an axial displacement of three heptads. The self-assembly of peptide YZ1 was examined at varying levels of structural hierarchy for compliance of the observed structures with the experimental model. Circular dichroism spectroscopy provided evidence for an α-helical coiled coil structure for YZ1 in aqueous solution, which could be reversibly denatured through thermal methods. TEM measurements indicated the formation of long aspect-ratio fibers of uniform diameter from aqueous solutions of YZ1, however the dimensions of the fibers suggested that lateral association occurred between the fibrils corresponding to the 2-stranded helical bundles. The α-helical coiled coil structure was confirmed in the solid-state for fibers derived from self-assembly of YZ1 by a combination of wide-angle X-ray diffraction and ¹³C CP/MAS NMR spectroscopy. SANS and synchrotron SAXS measurements on dilute aqueous solutions of YZ1 provided a fibril diameter that corresponded to the lateral dimensions estimated for a dimeric coiled coil assembly on the basis of structural determinations of model peptides.     

The effect of octahedral tilting on proton binding sites and transition states in pseudo-cubic perovskite oxides

Proton conducting oxide ceramics have shown potential for use in fuel cell technologies. Understanding the energy pathways for proton conduction could help us design more efficient fuel cell materials. This paper describes how octahedral tilting affects the relative energies of proton binding sites, transition states, and conduction pathways in cubic and pseudo-cubic perovskites. First, the structure for cubic and pseudo-cubic forms of BaTiO(3), BaZrO(3), CaTiO(3), and CaZrO(3), is found. Even when cubic symmetry is enforced, CaTiO(3), and CaZrO(3) exhibit octahedral tilting distortions characteristic of orthorhombic phases while BaTiO(3) and BaZrO(3) remain undistorted. Octahedral tilting gives rise to proton binding sites facilitating inter- and intra-octahedral proton transfer while the proton binding sites of undistorted perovskites facilitate only intra-octahedral proton transfer. The nudged elastic band method is used to find minimum energy paths between the proton binding sites. As distortions increase, inter-octahedral proton transfer barriers decrease while intra-octahedral proton transfer barriers increase. Concurrently, rotational barriers from oxygens facilitating inter-octahedral proton transfer increase while rotational barriers from oxygens facilitating intra-octahedral proton transfer decrease. Intra-octahedral transfer is the rate-limiting step to the lowest energy extended proton conduction pathway in all the perovskites considered.     

A computational study of intramolecular proton transfer in gaseous protonated glycine

The minimum energy paths for intramolecular proton transfer between the amino nitrogen and carbonyl oxygen atoms in gaseous protonated glycine were estimated at the Hartree-Fock (HF) and second-order M?ller-Plesset Perturbation (MP2) levels of theory. Potential energy profiles and their associated reactant, transition state, and product species calculated at the MP2/6-31G* level were shown to differ significantly from those obtained at the HF/6-31G* level. Effects of electron correlation and basis functions on the calculated geometries and energies of relevant species were examined at the HF, MP2, MP4, CCSD, and B3LYP levels using the 6-31G*, 6-31G**, 6-31+G**, 6-311+G**, 6-31+G(2d,2p), 6-311+G(3df,2p), cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. The HF and MP2 optimized levels with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** bases were used to calculate the thermodynamic and kinetic properties of the proton transfer reaction at 298.15 K and 1 atm, which include enthalpy, entropy, Gibbs free energy, equilibrium constant, potential energy barriers, tunneling transmission coefficients, and rate constants. Results indicate that the proton in a carbonyl O-protonated glycine undergoes a rapid migration to the amino nitrogen atom, while the reverse process is extremely unfavorable. The objective of this work is to develop practical theoretical procedures for studying proton transfer reactions in amino acids and peptides and to assemble physical data from these model calculations for future references.