Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study

The conformational equilibria of the acetyl and methyl amide terminally blocked L-alanine, L-leucine and L-glutamine amino acids are examined in vacuum, in bulk water, and at the water-hexane interface, using multi-nanosecond molecular dynamics simulations. The two-dimensional probability distribution functions of finding the peptides at different dihedral angles of the backbone, phi and psi, are calculated, and free energy differences between different conformational states are determined. All three peptides are interfacially active, i.e. tend to accumulate at the interface even though they are not amphiphilic. Conformational states stable in both gas phase and water are also stable in the interfacial environment. Their populations, however, cannot be simply predicted from the knowledge of conformational equilibria in the bulk phases, indicating that the interface exerts a unique effect on the peptides. Conformational preferences in the interfacial environment arise from the interplay between electrostatic and hydrophobic effects. As in an aqueous solution, electrostatic solute-solvent interactions lead to the stabilization of more polar peptide conformations. The hydrophobic effect is manifested at the interface by a tendency to segregate polar and nonpolar moieties of the solute into the aqueous and the hexane phases, respectively. For the terminally blocked glutamine, this favors conformations for which such a segregation is compatible with the formation of strong, backbone-side chain intramolecular hydrogen bonds on the hexane side of the interface. The influence of the hydrophobic effect can be also noted in the orientational preferences of the peptides at the interface. The terminally blocked leucine is oriented such that its nonpolar side chain is buried in hexane, whereas the polar side chain of glutamine is immersed in water. The free energies of rotating the peptides along the axis parallel to the interface by more than 90 degrees are substantial. This indicates that peptide folding at interfaces is strong by driven by the tendency to adopt amphiphilic structures.     

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.     

Structure, assembly, and topology of the G185R mutant of the fourth transmembrane domain of divalent metal transporter

The mammalian iron transporter, divalent metal transporter (DMT1), is a 12-transmembrane domain integral protein, responsible for dietary iron uptake in the duodenum and iron acquisition from transferrin in peripheral tissues. Two disease-causing mutants in animals have been found and attributed to the same missense mutation (G185R), which occurs within the putative transmembrane domain 4 (TM4) of DMT1. We have characterized a synthetic 24-mer peptide, corresponding to the sequence of the TM4 of DMT1 with G185R mutation using circular dichroism (CD) and NMR spectroscopy and show that the G185R peptide assumes mainly alpha-helical conformations in various membrane-mimetic environments. Solution structures derived from NMR and molecular dynamics/simulated annealing calculations demonstrate that the peptide exhibits a highly defined alpha-helix in its middle portion, flanked by a highly flexible N-terminus and a relatively ordered C-terminus. Both the folding and location of the C-terminus in SDS micelles are regulated by pH values. Paramagnetic broadening on peptide NMR signals by spin-labeled 5- and 16-doxylstearic acids and Mn(2+) ion suggests that both the N-terminus and the helical region of the peptide are embedded in SDS micelles. Surprisingly, self-association of the peptides for both the wild type and the G185R mutant studied by CD, electrospray ionization mass spectrometry, and NMR diffusion-ordered spectroscopy demonstrated that mutation of the Gly185 to a bulky and positively charged arginine causes a different self-assembly of the peptide, e.g., from a trimer to a hexamer, which implies that the quaternary structure of integral DMT1 may be crucial for its function in vivo.     

Molecular dynamics of phenol at the liquid-vapor interface of water

Molecular dynamics results are presented for phenol at the water liquid-vapor interface at 300 K. The calculated excess free energy of phenol at the interface is -2.8 +/- 0.4 kcal/mol, in good agreement with the recent experimental results of Eisenthal and co-workers. The most probable orientation of the phenol molecule at the surface is such that the aromatic ring is perpendicular to the interface and the OH group is fully immersed in water. The hydroxyl substituent has a preferred orientation which is similar to the orientation of OH bonds of water at the pure water liquid-vapor interface. The transition between interfacial and bulk-like behavior of phenol is abrupt and occurs when the center of mass of the solute is located about 6 angstroms from the Gibbs surface of water. In this region the para carbon atom of the hydrophobic benzene ring can reach the interface and become partially dehydrated. This result suggests that the width of the interfacial region in which the behavior of a simple amphiphilic solute in water is influenced by the presence of the surface depends primarily on the size of its hydrophobic part. The role of the OH substituent was investigated by comparing phenol at the interface with two model systems: benzene with and without partial charges on carbon and hydrogen atoms. It is shown that in the absence of the hydrophilic substituent the solute is located further away from the liquid phase and is more likely to be oriented parallel to the interface. However, when the center of mass of the solute is moved into the interfacial region where the density of water approaches that of the bulk solvent, all three molecules become oriented perpendicularly to the surface. In this orientation the work of cavity formation needed to accommodate the hydrophobic ring in aqueous solvent is minimized.     

Probing the formation of stable tertiary structure in a model miniprotein at atomic resolution: determinants of stability of a helical hairpin

The minimal model system to study the basic principles of protein folding is the hairpin. The formation of beta-hairpins, which are the basic components of antiparallel beta-sheets, has been studied extensively in the past decade, but much less is known about helical hairpins. Here, we probe hairpin formation between a polyproline type-II helix and an alpha-helix as present in the natural miniprotein peptide YY (PYY). Both turn sequence and interactions of aromatic side chains from the C-terminal alpha-helix with the pockets formed by N-terminal Pro residues are shown by site-directed mutagenesis and solution NMR spectroscopy in different solvent systems to be important determinants of backbone dynamics and hairpin stability, suggesting a close analogy with some beta-hairpin structures. It is shown that multiple relatively weak contacts between the helices are necessary for the formation of the helical hairpin studied here, whereas the type-I beta-turn acts like a hinge, which through certain single amino acid substitutions is destabilized such that hairpin formation is completely abolished. Denaturation and renaturation of tertiary structure by temperature or cosolvents were probed by measuring changes of chemical shifts. Folding of PYY is both reversible and cooperative as inferred from the sigmoidal denaturation curves displayed by residues at the interface of the helical hairpin. Such miniproteins thus feature an important hallmark of globular proteins and should provide a convenient system to study basic aspects of helical hairpin folding that are complementary to those derived from studies of beta-hairpins.     

Membrane Structure of Substance P. I. Prediction of Preferred Conformation,Orientation, and Accumulation of Substance P on Lipid Membranes

Preferred conformation, orientation, and accumulation of substance P on a neutral hydrophilic-hydrophobic interface was estimated and extrapolated to interactions with neutral and anionic lipid bilayer membranes according to our general procedure. Nine residues at the C-terminus were predicted to be transferred to the hydrophobic phase as an α-helical domain, oriented quite perpendicularly on the membrane surface. The N-terminal residues remained in the aqueous phase with their charges exposed to H₂O. The molecular amphiphilic moment vector was strong (338 arbitrary units) and pointed its hydrophilic end towards the N-terminus, only 15° away from the helix axis. The molecular electric dipole moment vector was also strong (124 debye) and pointed its positive end towards the N-terminus, only 9° away from the helix axis. Thus, it reinforced the effect of the amphiphilic moment of a peptide intruding into the membrane dipole layer. The estimated dissociation constant for the equilibrium between membrane-bound and free substance P was K_d ≈? 46 mM for neutral membranes, and K_d ≈?0.43 mM for anionic membranes with a Gouy-Chapman surface potential of ?40 mV. Thus, substance P behaved similarly to dynorphin A and adrenocorticotropin peptides which insert their N-terminal message segments as perpendicularly oriented helical domains into membranes, whereas their C-terminal address segments remain in the aqueous phase as random coils. Substance P is the first instance of a neuropeptide which is expected to insert a C-terminal message into lipid membranes.     

'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR

Solid state (19)F NMR revealed the conformation and alignment of the fusogenic peptide sequence B18 from the sea urchin fertilization protein bindin embedded in flat phospholipid bilayers. Single (19)F labels were introduced into nine distinct positions along the wild-type sequence by substituting each hydrophobic amino acid, one by one, with L-4-fluorophenylglycine. Their anisotropic chemical shifts were measured in uniaxially oriented membrane samples and used as orientational constraints to model the peptide structure in the membrane-bound state. Previous (1)H NMR studies of B18 in 30% TFE and in detergent micelles had shown that the peptide structure consists of two alpha-helical segments that are connected by a flexible hinge. This helix-break-helix motif was confirmed here by the solid-state (19)F NMR data, while no other secondary structure (beta-sheet, 3(10)-helix) was compatible with the set of orientational constraints. For both alpha-helical segments we found that the helical conformation extends all the way to the respective N- and C-termini of the peptide. Analysis of the corresponding tilt and azimuthal rotation angles showed that the N-terminal helix of B18 is immersed obliquely into the bilayer (at a tilt angle tau approximately 54 degrees), whereas the C-terminus is peripherally aligned (tau approximately 91 degrees). The azimuthal orientation of the two segments is consistent with the amphiphilic distribution of side-chains. The observed 'boomerang'-like mode of insertion into the membrane may thus explain how peptide binding leads to lipid dehydration and acyl chain perturbation as a prerequisite for bilayer fusion to occur.     

UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting

We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.     

Molecular dynamics simulation of folding of a short helical peptide with many charged residues

A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.     

A molecular dynamics study on the conformational stability of PrP 180–193 helix II prion fragment

Molecular dynamics of PrP 180–193 has allowed us to investigate the stability of the -helical conformation of the zwitterionic peptide (L₁) and the neutralized (L₂). In water, the helical structure of L₁ is unstable; in L₂, the -helix breaks up in the middle at Gln186, and the two resulting connected helices are stable. The hydrophobic enviroment decreases the stability of the helical structure of L₁, this effect is more evident for L₂ for which the unfolding of the C-terminus is followed by the formation of an intramolecular hydrogen bond connecting His¹⁸⁷ with Thr¹⁹¹.     

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

We have carried out a 40-ns all-atom molecular dynamics simulation of the helical antimicrobial peptide ovispirin-1 (OVIS) in a zwitterionic diphosphocholine (DPC) micelle. The DPC micelle serves as an economical and effective model for a cellular membrane owing to the presence of a choline headgroup, which resembles those of membrane phospholipids. OVIS, which was initially placed along a micelle diameter, diffuses out to the water-DPC interface, and the simulation stabilizes to an interface-bound steady state in 40 ns. The helical content of the peptide marginally increases in the process. The final conformation, orientation, and the structure of OVIS are in excellent agreement with the experimentally observed properties of the peptide in the presence of lipid bilayers composed of 75% zwitterionic lipids. The amphipathic peptide binds to the micelle with its hydrophobic face buried in the micellar core and the polar side chains protruding into the aqueous phase. There is overwhelming evidence that points to the significant and indispensable participation of hydrophobic residues in binding to the zwitterionic interface. The simulation starts with a conformation that is unbiased toward the final experimentally known binding state of the peptide. The ability of the model to reproduce experimental binding states despite this starting conformation is encouraging.     

Mixed films of poly(n-hexyl isocyanate) and poly(vinyl acetate) at the air-water interface

We study interfacial properties of rigid-rod-like poly(n-hexyl isocyanate) (PHIC), flexible poly(vinyl acetate) (PVAc), and mixed films of PHIC and PVAc spread at the air-water interface as a function of the molar fraction of PHIC by surface pressure measurements and fluorescence microscopy. From the plots of the experimental mean area of the mixed polymer films at a constant surface pressure as a function of the molar fraction of PHIC in the mixed films, the binary mixtures of PHIC/PVAc were concluded to be compatible at the air-water interface. This means that the hydrophobic hexyl group of PHIC takes a horizontal orientation to the air-water interface rather than a perpendicular one, leading to PHIC and PVAc having the same interfacial orientation. Compatibility of the binary mixtures of PHIC/PVAc at the air-water interface is also confirmed by their fluorescence microscopic images, since PHIC proves to be inhomogeneous and PVAc is homogeneous with the aid of a fluorescence probe, respectively.     

Oligomeric cholates: amphiphilic foldamers with nanometer-sized hydrophilic cavities

The hydroxyl at the C-3 of cholic acid was converted to an amino group, and the resulting amino-functionalized cholic acid was used as a monomer to prepare amide-linked oligomeric cholates. These cholate oligomers fold into helical structures with nanometer-sized hydrophilic internal cavities in solvent mixtures consisting of mostly nonpolar solvents such as carbon tetrachloride or ethyl acetate/hexane and 2-5% of a polar solvent such as methanol or DMSO. The conformations of the foldamers were studied by UV, fluorescence, fluorescence quenching, and fluorescence resonance energy transfer. The nature of the polar/nonpolar solvents and their miscibility strongly influenced the folding reaction. Folding was cooperative, as evidenced by the sigmoidal curves in solvent denaturation experiments. The folded conformers became more stable with an increase in the chain length. The folding/unfolding equilibrium was highly sensitive toward the amount of polar solvent. One percent variation in the solvent composition could change the folding free energies by 0.5-1.4 kcal/mol.     

Effect of electron-donating and electron-withdrawing groups on peptide/single-walled carbon nanotube interactions

Nano-1, a designed peptide, has been demonstrated to efficiently disperse individual single-walled carbon nanotubes (SWNTs) by folding into an amphiphilic alpha-helix wherein the phenylalanine (Phe) residues on the hydrophobic face of the helix interact via pi-stacking with the aromatic surface of the SWNT. In this study, the ability of electron-donating (hydroxyl) and electron-withdrawing (nitro) groups on the phenyl ring of Phe to affect the interactions between the peptide and SWNTs is examined by substituting the Phe residues in the nano-1 sequence with tyrosine and p-nitro-phenylalanine, respectively. Atomic force microscopy measurements and optical absorption spectroscopy revealed that the ability to disperse individual SWNTs increases with increasing electron density of the aromatic residue on the hydrophobic face of the amphiphilic helical peptides. Scanning tunneling spectroscopy (STS) and Raman analyses were used to examine the effect of noncovalent protein functionalization on the electronic properties of SWNTs. Small shifts in the Raman G band peak for the peptide/SWNT composites, as well as weak features that appear near the Fermi energy (Ef) in the STS dI/dV spectra of the peptide-coated SWNTs, are suggestive of a weak charge-transfer interaction between the peptides and the SWNTs.     

Monolayer formation of short helical turn forming peptide derivatives at the air–water and air–solid interfaces

Two tetrapeptide derivatives [peptide A (Boc–Ala–Ile–Ile–Gly–OMe) and peptide B (Boc–Ala–Ile–Leu–Ser–OMe)], that take helical turn conformation in solution, were shown to form monolayer at the air/water interface. Circular dichroism (CD) measurements indicate that peptide A has more helical turn propensity than peptide B in sodium dodecyl sulphate (SDS) micelles. Langmuir–Blodgget film study of peptides A and B suggest that both the peptides form stable monolayer at the air/water interface. Spectroscopic investigations reveal that peptide A forms helical turn assemblage on transferring the film into hydrophilic quartz and hydrophobic ZnSe surfaces. Whereas, peptide B adopts β-sheet structure on hydrophilic surface and a mixture of β-sheet and helical turn conformation on hydrophobic surface.     

Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location

The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at the N- and C-termini of peptides while varying the functional end-groups at the termini. We substituted all 20 naturally occurring amino acids at the N- and C-termini of a model peptide sequence, where the functional end-groups were N(alpha)-acetyl-X- and N(alpha)-amino-X- at the N-terminus and -X-C(alpha)-carboxyl and -X-C(alpha)-amide at the C-terminus. Amino acid coefficients were subsequently derived from the RP-HPLC retention behaviour of these peptides and compared to each other as well as to coefficients determined in the centre of the peptide chain (internal coefficients). Coefficients generated from residues substituted at the C-terminus differed most (between the -X-C(alpha)-carboxyl and -X-C(alpha)-amide peptide series) for hydrophobic side-chains. A similar result was seen for the N(alpha)-acetyl-X- and N(alpha)-amino-X- peptide series, where the largest differences in coefficient values were observed for hydrophobic side-chains. Coefficients derived from substitutions at the C-terminus for hydrophobic amino acids were dramatically different compared to internal coefficients for hydrophobic side-chains, ranging from 17.1 min for Trp to 4.8 min for Cys. In contrast, coefficients derived from substitutions at the N-terminus showed relatively small differences from the internal coefficients. Subsequent prediction of peptide retention time, within an error of just 0.4 min, was achieved by a predictive algorithm using a combination of internal coefficients and coefficients for the C-terminal residues. For prediction of peptide retention time, the sum of the coefficients must include internal and terminal coefficients.     

Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins

Aromatic residues are frequently found in helical and beta-barrel integral membrane proteins enriched at the membrane-water interface. Although the importance of these residues in membrane protein folding has been rationalized by thermodynamic partition measurements using peptide model systems, their contribution to the stability of bona fide membrane proteins has never been demonstrated. Here, we have investigated the contribution of interfacial aromatic residues to the thermodynamic stability of the beta-barrel outer membrane protein OmpA from Escherichia coli in lipid bilayers by performing extensive mutagenesis and equilibrium folding experiments. Isolated interfacial tryptophanes contribute -2.0 kcal/mol, isolated interfacial tyrosines contribute -2.6 kcal/mol, and isolated interfacial phenylalanines contribute -1.0 kcal/mol to the stability of this protein. These values agree well with the prediction from the Wimley-White interfacial hydrophobicity scale, except for tyrosine residues, which contribute more than has been expected from the peptide models. Double mutant cycle analysis reveals that interactions between aromatic side chains become significant when their centroids are separated by less than 6 A but are nearly insignificant above 7 A. Aromatic-aromatic side chain interactions are on the order of -1.0 to -1.4 kcal/mol and do not appear to depend on the type of aromatic residue. These results suggest that the clustering of aromatic side chains at membrane interfaces provides an additional heretofore not yet recognized driving force for the folding and stability of integral membrane proteins.     

Facile assignment of sequence ions of a peptide labelled with 18O at the carboxyl terminus.

The combination of collision-induced dissociation (CID) and linked-scan analysis was used for analysing the sequence ions from the precursor ion of a peptide, which had been labelled with 18O at its carboxyl terminus (C-terminus) using 40 atom % H2 18O. The CID and linked-scan mass spectrum of the labelled peptide gave two series of sequence-ion signals: the one, originating from the C-terminus of the labelled peptide, showed a doublet signal due to the part-incorporation of 18O into the carboxyl group at the C-terminus, while the other, originating from the amino terminus (N-terminus), has the natural isotopic ion distribution. From the distribution of the isotopic ions in a single CID spectrum, the sequence ions containing the C-terminus could be readily differentiated from those containing the N-terminus, allowing the facile assignment of sequence ions to the amino-acid sequence of a peptide by CID and linked-scan analysis. This method was successfully applied to determination of the amino-acid sequence of the light-chain of mouse anti-porphyrin monoclonal antibody.     

Preferential solvation within hydrophilic nanocavities and its effect on the folding of cholate foldamers

The conformations of three cholate foldamers and one molecular basket were studied by fluorescence and NMR spectroscopy. In nonpolar solvents (e.g., hexane/ethyl acetate or ethyl acetate) mixed with a small amount of a polar solvent (e.g., alcohol or DMSO), the cholate oligomer folded into a helix with the hydrophilic faces of the cholates turned inward. Folding created a hydrophilic nanocavity preferentially solvated by the entrapped polar solvent concentrated from the bulk. This microphase separation of the polar solvent was critical to the folding process. Folding was favored by larger-sized polar solvent molecules, as fewer such molecules could occupy and solvate the nanocavity, thus requiring a smaller extent of phase separation during folding. Folding was also favored by smaller/acyclic nonpolar solvent molecules, probably because they could avoid contact with the OH/NH groups within the nanocavity better than larger/cyclic nonpolar solvent molecules.     

Examination of the folding of a short alanine-based helical peptide with salt bridges using molecular dynamics simulation

A molecular dynamics simulation of the folding of a short alanine-based helical peptide of 17 residues with three Glu...Lys (i, i + 4) salt bridge pairs, referred to as the AEK17 peptide, was carried out. The simulation gave an estimated simulation folding time of 2.5 ns, shorter than 12 ns for an alanine-based peptide of 16 residues with three Lys residues only, referred to as the AK16 peptide, simulated previously. After folded, the AEK17 peptide had a helical content of 77%, in excellent agreement with the experimentally determined value of 80%. An examination of the folding pathways of AEK17 indicated that the peptide proceeded via three-turn helix conformations more than the helix-turn-helix conformation in the folding pathways. An analysis of interactions indicated that the formation of hydrogen bonds between Lys residue side chains and backbone carbonyls is a major factor in the abundant conformation of the three-turn helix intermediate. The substitution of three Ala with Glu residues reduces the extent of hydrophobic interaction in alanine-based AK peptides with the result that the breaking of the interactions of Lys epsilon-NH3+(side chain)...C=O(backbone) is a major activation action for the AEK17 to achieve a complete fold, in contrast to the AK16 peptide, in which breaking non-native hydrophobic interaction is the rate-determining step.