Peptide Hydration Research Articles

Deciphering Spectroscopic Signatures of Competing Ca2+ - Peptide Interactions.

Calcium-protein interactions are of paramount importance in biochemistry. They are a key element in a number of biological processes, such as neuronal signaling. Therefore, an understanding of the interaction at the molecular level is highly desirable. Here, we study the zwitterionic model peptide l-alanyl-l-alanine (2Ala), which has two distinct and competing binding sites for Ca2+: The carbonyl of the peptide bond and the C-terminus, the carboxylate group. We perform linear and two-dimensional IR spectroscopy experiments and find that the spectroscopic signatures of both moieties in the IR spectra change in amplitude and peak position upon the addition of CaCl2: A blueshift of the asymmetric carboxylate band and a redshift for the amide I mode. Ab initio molecular dynamics simulations confirm the direct interaction of the Ca2+ ion at both the carboxylate and the amide CO site leading to different spectral responses. The blueshift of the asymmetric carboxylate band is caused by a localization of the charge, leading to a decoupling of the CO stretching modes of the carboxylate group. The slight redshift of the amide I mode of 2Ala upon the addition of CaCl2 contrasts the blueshift that has been observed for isolated amide motifs, such as N-methylacetamide (NMA). This difference is caused by the smaller number of water molecules being replaced by the Ca2+ ion for 2Ala's amide compared to less sterically hindered, isolated amide carbonyls, in conjunction with vibrational Stark effects. Our results highlight the importance of considering potential competing binding sites, such as the amide CO backbone, the termini and residues, as well as the nature of the hydration of both peptide and ion, when exploring ions' interacting with small peptides and larger proteins.

Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I’ bands in FTIR, VCD, and Raman spectra

The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I’ band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.

Effect of ectoine on hydration spheres of peptides–spectroscopic studies

In this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides–diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte influences the hydration shells of both peptides and does so in a different way for both peptides: (1) the interfacial interaction of the NAGMA peptide and ectoine hydration spheres strengthened the hydration shell of this peptide; (2) the inclusion of water molecules from the ectoine hydration sphere into the diglycine hydration sphere had only a marginally enhancing effect. Since ectoine is being used in more and more biopharmaceutical products and cosmetics, knowledge of the properties of its hydration shell and its effect on the hydration shell of other molecules is extremely relevant to understanding its protective mechanism.

Exploring the Barriers in the Aggregation of a Hexadecameric Human Prion Peptide through the Markov State Model.

The prefibrillar aggregation kinetics of prion peptides are still an enigma. In this perspective, we employ atomistic molecular dynamics (MD) simulations of the shortest human prion peptide (HPP) (127GYMLGS132) at various temperatures and peptide concentrations and apply the Markov state model to determine the various intermediates and lag phases. Our results reveal that the natural mechanism of prion peptide self-assembly in the aqueous phase is impeded by two significant kinetic barriers with oligomer sizes of 6-9 and 12-13 peptides, respectively. The first one is the aggregation of unstructured lower-order oligomers, and the second is fibril nucleation, which impedes the further growth of prion aggregates. Among these two activation barriers, the second one is found to be dominant irrespective of the increase in temperature and peptide concentration. These lag phases are captured in all three different force-field parameters, namely, GROMOS-54a7, AMBER-99SB-ILDN, and CHARMMS 36m, at different concentrations. The GROMOS-54a7 and AMBER-99SB-ILDN force fields showed a comparatively higher percentage of β-sheet formation in the metastable aggregate that evolved during the aggregation process. In contrast, the CHARMM-36m force field showed mostly coil or turn conformations. The addition of a novel catecholamine derivative (naphthoquinone dopamine (NQDA)) arrests the aggregation process between the lag phases by increasing the activation barrier for the Lag1 and Lag2 phases in all of the force fields, which further validates the existence of these lag phases. The preferential binding of NQDA with the peptides increases the hydration of peptides and eventually disrupts the organized morphology of prefibrillar aggregates. It reduces the dimer dissociation energy by -24.34 kJ/mol.

Why do polyarginines adsorb at neutral phospholipid bilayers and polylysines do not? An insight from density functional theory calculations and molecular dynamics simulations.

Adsorption of cell-penetrating peptides (CPPs) at cellular membranes is the first and necessary step for their subsequent translocation across cellular membranes into the cytosol. It has been experimentally shown that CPPs rich in arginine (Arg) amino acid penetrate across phospholipid bilayers more effectively than their lysine (Lys) rich counterparts. In this work, we aim to understand the differences in the first translocation step, adsorption of Arg9 and Lys9 peptides at fully hydrated neutral phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers and evaluate in detail the energetics of the process using molecular dynamics (MD) simulations and free energy calculations of adsorption of the single peptide. We show that the adsorption of Arg9 is energetically feasible, with the free energy of adsorption being ∼-5.0 kcal mol-1 at PC and ∼-5.5 kcal mol-1 at PE bilayers. In contrast, adsorption of Lys9 is not observed at PC bilayers, and their adsorption at PE bilayers is very weak, being ∼-0.5 kcal mol-1. We show by energy decomposition and analysis of peptide hydration along the membrane that significantly stronger electrostatic interactions of Arg9 with lipid phosphate groups, together with the greater loss of peptide hydration (and in turn stronger hydrophobic interactions) along the membrane translocation path, are the main driving factors governing the adsorption of Arg-rich peptides at neutral lipid bilayers in contrast to Lys-rich peptides. Finally, we also compare the energetics in lipid/bilayer systems with the density functional theory (DFT) calculations of the corresponding model systems in the continuum water model and reveal the energetic differences in different environments.

A Molecular Dynamics Study of Antimicrobial Peptide Interactions with the Lipopolysaccharides of theOuterBacterial Membrane.

With rising bacterial resistance, antimicrobial peptides (AMPs) have been widely investigated as potential antibacterial molecules to replace conventional antibiotics. Our understanding of the molecular mechanisms for membrane disruption are largely based on AMP interactions with the inner phospholipid bilayers of both Gram-negative and Gram-positive bacteria. Mechanisms for AMP translocation across the outer membrane of Gram-negative bacteria composed of lipopolysaccharides and the asymmetric lipid bilayer are complicated by the secondary structure adopted by the peptide in the different membrane environments. We have employed atomistic molecular dynamics and umbrella-sampling simulations with an aggregate duration of [Formula: see text] 6 microseconds to obtain the free energy landscape of CM15 peptide translocating through the lipopolysaccharide region of Gram-negative bacteria, E. coli. The peptide has a favorable binding-free energy (-130 kJ mol[Formula: see text]) in the O-antigen region with a large barrier (150 kJ mol[Formula: see text]) at the interface between the anionic core saccharides and upper bilayer leaflet made up of lipid-A molecules. Restraint-free molecular dynamics simulations show that the random coil structure is favored over the helix in both the extracellular aqueous region and the cation-rich core-saccharide regions of the outer membrane. The peptide and membrane properties are analyzed at each of the 100 ns duration of the umbrella-sampling windows toillustrate changes in peptide length, orientation, and hydration. Our study provides insights into the free energy landscape for the insertion of the AMP CM15 in the outer membrane of Gram-negative bacteria, and we discuss the implications of our findings with the broader question of how AMPs overcome this barrier during antimicrobial activity.

Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations.

The stimuli-responsive character of elastin-like polypeptides (ELP) has led to their use in a wide range of applications. The temperature-triggered aggregation, or LCST behavior, of ELPs is a complex and multistep phenomenon, which proposed to include the structural transitions, loss of hydrophobic hydration, expulsion of water molecules and physical association of chains. Thus, the origin and detailed mechanism of LCST in ELPs is difficult to elucidate. Here, to gain insights into structure and dynamics of coacervates, we performed all-atom molecular dynamics simulations of 27 90-mer ELPs in explicit water at 350 K. Two sequences, poly(VGPVG)18 and poly(VPGVG)18, were examined due to their experimentally observed differences in thermal hysteresis albeit identical overall composition but different arrangement of amino acids. The simulation results indicate that surface hydrophobicity of poly(VGPVG) aggregate is less than that of the poly(VPGVG) aggregate, and there are marked changes in torsion angles and the propensities of secondary structural motifs during the aggregation process. Moreover, there are significant differences between structure of a single polypeptide in water and structure within the aggregate. Overall, the aggregation process is driven by the formation of peptide-peptide interactions whereas the average hydration of peptides remains almost the same between dissolved and aggregated states. Even though the aggregation is driven by the hydrophobic interactions, ELP coacervate has no hydrophobic core and contains many water molecules. Overall, our findings provide an insight into the sequence-dependent structure of coacervates and molecular behavior of individual peptides during aggregation.

Mutual structural effects of unmodified and pyroglutamylated amyloid β peptides during aggregation.

Amyloid β (Aβ) peptide aggregates are linked to Alzheimer's disease (AD). Posttranslationally pyroglutamylated Aβ (pEAβ) occurs in AD brains in significant quantities and is hypertoxic, but the underlying structural and aggregation properties remain poorly understood. Here, the structure and aggregation of Aβ1-40 and pEAβ3-40 are analyzed separately and in equimolar combination. Circular dichroism data show that Aβ1-40 , pEAβ3-40 , and their combination assume α-helical structure in dry state and transition to unordered structure in aqueous buffer. Aβ1-40 and the 1:1 combination gradually acquire β-sheet structure while pEAβ3-40 adopts an α-helix/β-sheet conformation. Thioflavin-T fluorescence studies suggest that the two peptides mutually inhibit fibrillogenesis. Fourier transform infrared (FTIR) spectroscopy identifies the presence of β-turn and α-helical structures in addition to β-sheet structure in peptides in aqueous buffer. The kinetics of transitions from the initial α-helical structure to β-sheet structure were resolved by slow hydration of dry peptides by D2 O vapor, coupled with isotope-edited FTIR. These data confirmed the mutual suppression of β-sheet formation by the two peptides. Remarkably, pEAβ3-40 maintained a significant fraction of α-helical structure in the combined sample, implying a reduced β-sheet propensity of pEAβ3-40 . Altogether, the data imply that the combination of unmodified and pyroglutamylated Aβ peptides resists fibrillogenesis and favors the prefibrillar state, which may underlie hypertoxicity of pEAβ.

Circular Dichroism Study of Late Embryogenesis Abundant Peptides in Reverse Micelles

Late Embryogenesis Abundant (LEA) proteins are a class of characteristically unstructured proteins found within plants at their later stages of seed development. While LEA proteins lack distinct structural characteristics under standard conditions, certain extreme conditions of temperature or drought may allow the formation of functional structure. Through the use of Circular Dichroism (CD) spectroscopy, the structural characteristics of two different 11-mer repeat units of Group 3 LEA proteins has been studied. Here, solutions of the peptides in AOT reverse micelles have been used to simulate conditions of low peptide hydration, with a variety of w0 values investigated. In comparison to aqueous CD results which confirm the characteristic disordered structure of LEA proteins, CD results in reverse micelles suggest a preference for α-helical character under low hydration conditions. Furthermore, temperature-dependent CD scans show interesting non-monotonic behavior. These results enhance our understanding of how LEA proteins may be structured biologically and allow further speculation regarding their role in seed development.

Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics.

Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.

Tuning the structure of monomeric amyloid beta peptide by the curvature of carbon nanotubes

Carbon nanotubes can affect the self-assembly of amyloid beta peptides (Aβ) related to neurodegenerative diseases. We use molecular dynamics (MD) to investigate the effects of carbon nanotubes (CNT) on the conformational evolution of monomeric Aβ1-42 peptide. The chirality of CNT varies from (10, 10), (15, 15), (20, 20) and (25, 25) that corresponds to declining curvatures. We show that the adhesion of peptide on CNT surface leads to internal structures predisposes to collapse, which might be reasonable methods to impede the initial nucleation and self-assembly. Adsorption induce the loss of the peptides' native structures. Adsorption and subsequent denaturation accompanies by a loss of surface hydration of peptide. When the curvature of CNT decreases, peptide spread almost completely over the CNT surface. Conversely, peptide will wrap around the CNT when the curvature of CNT is high. Peptide adsorption onto CNT also reduces their α-helical content and β-sheet ratio, indicating that the CNT significantly affect the formation of α-helical structures while inducing random coil conformations. The arrangement of peptides on CNT surface relates to the affinity of various amino acids onto CNT. These insights provide useful information for understanding the binding and winding tendency of peptides on carbon nanostructures’ surface.

Real-Time, Semi-Automated Fluorescent Measurement of the Airway Surface Liquid pH of Primary Human Airway Epithelial Cells.

In recent years, the importance of mucosal surface pH in the airways has been highlighted by its ability to regulate airway surface liquid (ASL) hydration, mucus viscosity and activity of antimicrobial peptides, key parameters involved in innate defense of the lungs. This is of primary relevance in the field of chronic respiratory diseases such as cystic fibrosis (CF) where these parameters are dysregulated. While different groups have studied ASL pH both in vivo and in vitro, their methods report a relatively wide range of ASL pH values and even contradictory findings regarding any pH differences between non-CF and CF cells. Furthermore, their protocols do not always provide enough details in order to ensure reproducibility, most are low throughput and require expensive equipment or specialized knowledge to implement, making them difficult to establish in most labs. Here we describe a semi-automated fluorescent plate reader assay that enables the real-time measurement of ASL pH under thin film conditions that more closely resemble the in vivo situation. This technique allows for stable measurements for many hours from multiple airway cultures simultaneously and, importantly, dynamic changes in ASL pH in response to agonists and inhibitors can be monitored. To achieve this, the ASL of fully differentiated primary human airway epithelial cells (hAECs) are stained overnight with a pH-sensitive dye in order to allow for the reabsorption of the excess fluid to ensure thin film conditions. After fluorescence is monitored in the presence or absence of agonists, pH calibration is performed in situ to correct for volume and dye concentration. The method described provides the required controls to make stable and reproducible ASL pH measurements, which ultimately could be used as a drug discovery platform for personalized medicine, as well as adapted to other epithelial tissues and experimental conditions, such as inflammatory and/or host-pathogen models.

Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures

Interactions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions.In this paper, the influence of NMA and N,N-dimethylacetamide (DMA) on surrounding water molecules in a range of temperature (25–75 °C) is studied by means of the FTIR spectroscopy. The results of the difference HDO spectra method are compared with the results of theoretical DFT calculations of NMA and DMA aqueous complexes.Both NMA and DMA can be regarded as “structure-makers”, yet their hydration spheres are different. These molecules exhibit a mixed and mutually dependent types of hydration: hydrophilic and hydrophobic. In the case of a NMA molecule that has one methyl group less than DMA, the type of hydrophobic hydration is more important. The DMA hydration sphere is less stable: the interactions between water molecules around the methyl groups are strained. Moreover, the hydration of NMA is much more temperature dependant than in the case of DMA. The source of the differences may be hidden in the NH⋯H2O interaction.The delicate nature of water interactions with the peptide block models may be cautiously translated into the much more complicated interactions of proteins with their hydration shells.

Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15

Simulations and experiments show oligo-glycines, polypeptides lacking any side chains, can collapse in water. We assess the hydration thermodynamics of this collapse by calculating the hydration free energy at each of the end points of the reaction coordinate, here taken as the end-to-end distance (r) in the chain. To examine the role of the various conformations for a given r, we study the conditional distribution, P(Rg|r), of the radius of gyration for a given value of r. The free energy change versus Rg, -kBT ln P(Rg|r), is found to vary more gently compared to the corresponding variation in the excess hydration free energy. Using this observation within a multistate generalization of the potential distribution theorem, we calculate a tight upper bound for the hydration free energy of the peptide for a given r. On this basis, we find that peptide hydration greatly favors the expanded state of the chain, despite primitive hydrophobic effects favoring chain collapse. The net free energy of collapse is seen to be a delicate balance between opposing intrapeptide and hydration effects, with intrapeptide contributions favoring collapse.

Hydration properties of glycylglycine in aqueous ionic liquid solutions at different temperatures: Volumetric and acoustic approach

The apparent molar volume and isentropic compression of glycylglycine in aqueous 1-methylimidazolium chloride, [mim][Cl], 1-ethyl-3-methylimidazolium chloride [C2mim][Cl], and 1-methyl-3-octylimidazolium chloride [C8mim][Cl] solutions have been calculated from the measured experimental data on density and speed of sound at temperature, T=288.15, 298.15 and 308.15K. The apparent molar volumes at infinite dilution, Vϕ0 and the apparent isentropic molar compression at infinite dilution Kϕ,S0, were also calculated. Furthermore, apparent specific volumes, apparent molar expansivity, Eϕ0, Hepler's constant values, ∂Eϕ0∂TP and hydration numbers, nH, have been evaluated to support the conclusions obtained from the volumetric and acoustic studies. The Hepler's constant values were found negative which indicating the peptide under study is predominantly a structure breaker due to hydrophobic hydration of small peptide in aqueous ionic liquid.

Exploring the Effects on the Conformational Propensity of Alanine in the Unblocked Tripeptide Glycyl-Analyl-Glycine in Water/Ethanol Mixtures

Short peptides have been shown to be model systems for obtaining the conformational propensities of individual amino acids. Recent studies on cationic GxG (x: different guest amino acid residues) peptides in water revealed the Ramachandran plots for 16 amino acid residues. Out of the natural amino acids, alanine in GAG has been shown to stand out owing to its unusually high propensity for polyproline II (pPII) conformations (0.72). Thus, its conformational distribution differs substantially from the classical ones of Ramachandran and Flory. Peptide-water interactions have been proposed as the major determinant of alanine's preference for pPII. To elucidate how peptide hydration affects conformational preferences of alanine we used FTIR, vibrational circular dichroism, polarized Raman and NMR spectroscopy to determine Ramachandran plots of GAG in aqueous solutions with 3, 12, and 42mol% ethanol. We observed a modest decrease of the pPII fraction from 0.72 to 0.65 and an increase in β-strand population from 0.15 to 0.20 from pure water to 12 mol% ethanol. Interestingly, the corresponding changes of the enthalpic and entropic differences between pPII and β -strand by far exceed changes in Gibbs energy at room temperature owing to enthalpy-entropy compensation effects. Our thermodynamic data reveal that the cosolvent stabilizes pPII enthalpically (−10 kJ/mol in water to −18 kJ/mol in 12 mol% ethanol) but destabilizes it even more entropically (−23 to −50 J/mol∗K). Comparisons of IR and NMR spectra of GAG and N- methylacetamide in the same ethanol/water mixtures reveal changes of peptide hydration which causes the observed destabilization of pPII of alanine and the concomitant increase of its conformational entropy.

Peptide Hydration Phenomena through a Combined Quantum Chemical and Bottom-Up Approach

Abstract The M06-2X, TPSS, and B3PW91 density functionals and the classical ab initio MP2 method were used to study microsolvation around the protonated trialanine, Ala3H+. All adopted electronic structure approaches show the formation of wires or compact ring clusters of water molecules strongly bonded to peptidic polar groups through hydrogen bonds with hydration energy ranging from − 93 to –66 kcal mol –1. Independently from the adopted electronic structure methods, explicit water molecules favor peptidic chain with the polyproline II (PPII) conformation, thus the electronic energy stability order of the four unfolded conformers follows the sequence: PPII-PPII > β-PPII ∼ PPII-β > β-β, while entropy favors the reversed order. The delicate balance of electronic energy (or enthalpy) and entropy modulated by the temperature accounts for the change in abundance of the PPII and β conformations experimentally observed. The proposed bottom-up approach has been developed following the energetically dominant polar groups of peptide and water dipoles interactions. The intrapeptide dipole decoupling, caused by the β → PPII transformation, and the consequent greater dipole coupling with water molecules provide a rational base to explain the energy gain due to the explicit water coordination to PPII residues.

Stepwise microhydration of aromatic amide cations: formation of water solvation network revealed by infrared spectra of formanilide(+)-(H2O)(n) clusters (n ≤ 5).

Hydration of peptides and proteins has a strong impact on their structure and function. Infrared photodissociation spectra (IRPD) of size-selected clusters of the formanilide cation, FA(+)-(H2O)n (n = 1-5), are analyzed by density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the sequential microhydration of this prototypical aromatic amide cation. IRPD spectra are recorded in the hydride stretch and fingerprint ranges to probe the preferred interaction motifs and the cluster growth. IRPD spectra of cold Ar-tagged clusters, FA(+)-(H2O)n-Ar, reveal the important effects of temperature and entropy on the observed hydration motifs. At low temperature, the energetically most stable isomers are prominent, while at higher temperature less stable but more flexible isomers become increasingly populated because of entropy. In the most stable structures, the H2O ligands form a hydrogen-bonded solvent network attached to the acidic NH proton of the amide, which is stabilized by large cooperative effects arising from the excess positive charge. In larger clusters, hydration bridges the gap between the NH and CO groups (n ≥ 4) solvating the amide group rather than the more positively charged phenyl ring. Comparison with neutral FA-(H2O)n clusters reveals the strong impact of ionization on the acidity of the NH proton, the strength and topology of the interaction potential, and the structure of the hydration shell.

The Role of Lipid Environment on Peptide Structure and Folding

Membrane proteins are an important class of proteins that are difficult to characterize structurally and functionally. In order to gain a better understanding of the forces that govern membrane protein folding and structure, a series of simple leucine-alanine peptides ranging from 12 to 18 residues were designed. The peptides were anchored by two lysine residues at each end and spontaneously inserted into negatively charged lipid bilayers. The effects of peptide length, lipid length, bilayer/micelle composition and the presence of structure breaking residues glycine and proline on the uniformity of helical structure were evaluated. An increase in the intensities of the amide III and S bands in deep-UV resonance Raman spectra indicated loss of helical structure. Differences in peptide hydration were monitored using tryptophan fluorescence. Loss of helical structure was observed in cases of negative hydrophobic mismatch, increased peptide hydration and upon introduction helix breaking residues. No loss of helical structure was observed in cases of positive hydrophobic mismatch while the shortest peptide adopted beta-sheet structure in instances of negative hydrophobic mismatch. Greater hydration of the peptide, which occurred in surfactant/lipid micelles, magnified the helix breaking- effects of glycine and proline. These studies highlight the potential importance of the lipid environment itself on membrane protein structure.

Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles.

The propensity of peptides to form α-helices has been intensely studied using theory, computation, and experiment. Important model peptides for the study of the coil-to-helix transition have been alanine–lysine (AKA) peptides in which the lysine residues are placed on opposite sides of the helix avoiding charge repulsion while enhancing solubility. In this study, the effects of capped versus zwitterionic peptide termini on the secondary structure of alanine-rich peptides in reverse micelles are explored. The reverse micelles are found to undergo substantial shape fluctuations, a property observed in previous studies of AOT reverse micelles in the absence of solvated peptide. The peptides are observed to interact with water, as well as the AOT surfactant, including interactions between the nonpolar residues and the aliphatic surfactant tails. Computation of IR spectra for the amide I band of the peptide allows for direct comparison with experimental spectra. The results demonstrate that capped AKA2 peptides form more stable α helices than zwitterionic AKA2 peptides in reverse micelles. The rotational anisotropy decay of water is found to be distinctly different in the presence or absence of peptide within the reverse micelle, suggesting that the introduction of peptide significantly alters the number of free waters within the reverse micelle nanopool. However, neither the nature of the peptide termini (capped or charged) nor the degree of peptide helicity is found to significantly alter the balance of interactions between the peptides and the environment. Observed changes in the degree of helicity in AKA2 peptides in bulk solution and in reverse micelle environments result from changes in peptide confinement and hydration as well as direct nonpolar and polar interactions with the water–surfactant interface.