The intrinsic helix-forming tendency of L-alanine

Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide

A new force field has been created for simulating hydrated alanine polypeptides using the adaptive force matching (AFM) method. Only density functional theory calculations using the Perdew-Burke-Ernzerhof exchange-correlation functional and the D3 dispersion correction were used to fit the force field. The new force field, AFM2020, predicts NMR scalar coupling constants for hydrated homopolymeric alanine in better agreements with experimental data than several other models including those fitted directly to such data. For Ala₇, the new force field shows about 15% helical conformations, 20% conformation in the β basin, and 65% polyproline II. The predicted helical population of short hydrated alanine is higher than previous estimates based on the same experimental data. Gas-phase simulations indicate that the force field developed by AFM solution-phase data is likely to produce a reasonable conformation distribution when hydration water is no longer present, such as the interior of a protein.

Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance

The ion-pumping NADH: ubiquinone dehydrogenase (NQR) is a vital component of the respiratory chain of numerous species of marine and pathogenic bacteria, including Vibrio cholerae. This respiratory enzyme couples the transfer of electrons from NADH to ubiquinone (UQ) to the pumping of ions across the plasma membrane, producing a gradient that sustains multiple homeostatic processes. The binding site of UQ within the enzyme is an important functional and structural motif that could be used to design drugs against pathogenic bacteria. Our group recently located the UQ site in the interface between subunits B and D and identified the residues within subunit B that are important for UQ binding. In this study, we carried out alanine scanning mutagenesis of amino acid residues located in subunit D of V. cholerae NQR to understand their role in UQ binding and enzymatic catalysis. Moreover, molecular docking calculations were performed to characterize the structure of the site at the atomic level. The results show that mutations in these positions, in particular, in residues P185, L190, and F193, decrease the turnover rate and increase the Km for UQ. These mutants also showed an increase in the resistance against the inhibitor HQNO. The data indicate that residues in subunit D fulfill important structural roles, restricting and orienting UQ in a catalytically favorable position. In addition, mutations of these residues open the site and allow the simultaneous binding of substrate and inhibitors, producing partial inhibition, which appears to be a strategy used by Pseudomonas aeruginosa to avoid autopoisoning.

Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides

Reliability of force fields is an essential aspect of protein-folding simulation. In this work, we introduced a newly developed on-the-fly charge-updating scheme called the polarized structure-specific backbone charge (PSBC) model. The PSBC model was designed with the purpose of building the polarizability of backbone hydrogen bonds into the force field by updating the partial charges of backbone hydrogen-bond donor and acceptor atoms during folding simulation. This implementation was intended to mimic the heterogeneity of the protein surrounding during folding. Multiple single-trajectory molecular dynamics simulations were performed to fold a polyalanine peptide, namely ER (Ac-A(EAAAR)₃A-NH₂), using both polarizable (PSBC) and nonpolarizable (Amber03) force fields. Through the PSBC model, ER was folded into a helical peptide with helix content that agrees well with experiments. Comparison between simulations performed using the aforementioned force fields demonstrably showed the importance of electrostatic polarization effect in the folding of the short α-helical peptide. The PSBC model was further validated by folding two other short peptides with different helicities.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Ab initio folding of extended α-helix: a theoretical study about the role of electrostatic polarization in the folding of helical structures

In this work, we report the ab initio folding of three different extended helical peptides namely 2khk, N36, and C34 through conventional molecular dynamics simulation at room temperature using implicit solvation model. Employing adaptive hydrogen bond specific charge (AHBC) scheme to account for the polarization effect of hydrogen bonds established during the simulation, the effective folding of the three extended helices were observed with best backbone RMSDs in comparison to the experimental structures over the helical region determined to be 1.30 Å for 2khk, 0.73 Å for N36 and 0.72 Å for C34. In this study, 2khk will be used as a benchmark case serving as a means to compare the ability of polarized (AHBC) and nonpolarized force field in the folding of an extended helix. Analyses conducted revealed the ability of the AHBC scheme in effectively folding the extended helix by promoting helix growth through the stabilization of backbone hydrogen bonds upon formation during the folding process. Similar observations were also noted when AHBC scheme was employed during the folding of C34 and N36. However, under Amber03 force field, helical structures formed during the folding of 2khk was not accompanied by stabilization thus highlighting the importance of electrostatic polarization in the folding of helical structures.

Water-mediated ionic interactions in protein structures

It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.

Polypeptides in alpha-helix conformation perform as diodes

Molecules that resemble a semiconductor diode depletion zone are those with an intrinsic electric dipole, which were suggested as potential electronic devices. However, so far, no single molecule has met such a goal because any electron donor-acceptor linker strongly diminishes any possibility of diode behavior. We find an intrinsic diode behavior in polypeptides such as poly(L-alanine) and polyglycine in alpha-helix conformation, explained in terms of molecular orbital theory using ab initio methods. The application of an antiparallel electric field with respect to the molecular dipole yields a gradual increase in current through the junction because the valence and conduction orbitals approach each other reducing their gap as the bias increases. However, a parallel field makes the gap energy increase, avoiding the pass of the electrons.

Context-independent, temperature-dependent helical propensities for amino acid residues

Assigned from data sets measured in water at 2, 25, and 60 degrees C containing (13)C=O NMR chemical shifts and [theta](222) ellipticities, helical propensities are reported for the 20 genetically coded amino acids, as well as for norvaline and norleucine. These have been introduced by chemical synthesis at central sites within length-optimized, spaced, solubilized Ala(19) hosts. The resulting polyalanine-derived, quantitative propensity sets express for each residue its temperature-dependent but context-independent tendency to forego a coil state and join a preexisting helical conformation. At 2 degrees C their rank ordering is: P << G < H < C, T, N < S < Y, F, W < V, D < K < Q < I < R, M < L < E < A; at 60 degrees C the rank becomes: H, P < G < C < R, K < T, Y, F < N, V < S < Q < W, D < I, M < E < A < L. The DeltaDeltaG values, kcal/mol, relative to alanine, for the cluster T, N, S, Y, F, W, V, D, Q, imply that at 2 degrees C all are strong breakers: DeltaDeltaG(mean) = +0.63 +/- 0.11, but at 60 degrees C their breaking tendencies are dramatically attenuated and converge toward the mean: DeltaDeltaG(mean) = +0.25 +/- 0.07. Accurate modeling of helix-rich proteins found in thermophiles, mesophiles, and organisms that flourish near 0 degrees C thus requires appropriately matched propensity sets. Comparisons are offered between the temperature-dependent propensity assignments of this study and those previously assigned by the Scheraga group; the special problems that attend propensity assignments for charged residues are illustrated by lysine guest data; and comparisons of errors in helicity assignments from shifts and ellipticity data show that the former provide superior precision and accuracy.

Statistical mechanical model for helix-sheet-coil transitions in homopolypeptides

In this paper, we propose a simple statistical mechanical model to study the conformation transition between the alpha helix, beta sheet, and random coil in homopolypeptides. In our model, five parameters are introduced to obtain the partition function. There are two factors for helical propagation and initiation, which are the same as those used in the Zimm-Bragg model, and three newly introduced parameters for beta structures: the strand propagation factor for residues in beta strands and two correction factors for the initiation effect of the beta strand and beta sheet. Our model shows that the variation of these parameters may induce conformation transition from alpha helix or random coil to beta sheet. The sharpness of the transition depends on the initiation factors.

Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices

The helix-disfavoring, versus alanine, propagation values of lysine (0.8) and arginine (1.0) residues placed centrally in an (Ala)(9) unit have been measured by (13)C NMR.

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

Thermal Denaturation of Polyalanine Peptide in Water by Molecular Dynamics Simulations and Theoretical Prediction of Infrared Spectra: Helix−Coil Transition Kinetics

Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)(21)-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K approximately 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 3(10)-helix and type I beta-turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining T(m) by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.

Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution

We test molecular level hypotheses for the high thermal stability of alpha-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to alpha-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of "i, i + 3" glutamic acid(-) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of alpha-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples alpha-helical configurations with 80% fractional helicity at 300 K. The helix melts over a broad range of temperatures with melting temperature, T(m), equal to 350 K, that is significantly higher than the T(m) of a 21-residue polyalanine peptide, A(21). Salt-bridges between oppositely charged Glu(-) and Lys(+) side chains can, in principle, provide thermal stability to alpha-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with approximately 10-20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific "i, i + 4" backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing alpha-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably.

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH

The structure of the 36 residue villin headpiece subdomain is investigated with the electrostatically driven Monte Carlo method. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) force field, plus two different continuum solvation models, were used to describe the conformational energy of the chain with both blocked and unblocked N and C termini. A statistical analysis of an ensemble of ab initio generated conformations was carried out, based on a comparison with a set of ten native-like structures derived from published experimental data, by using rigid geometry and NMR-derived constraints obtained at pH 3.7. The ten native-like structures satisfy the NMR-derived constraints. The whole ensemble of conformations of the terminally unblocked villin headpiece sub-domain, generated by using ECEPP/3 with a continuum solvation model, were subsequently evaluated at pH 3.7 with a potential function that includes ECEPP/3 combined with a fast multigrid boundary element method. At pH 3.7, the lowest-energy conformation found during the conformational search satisfies approximately 70% of both the distance and the dihedral-angle constraints, and possesses the characteristic packing of three phenylalanine residues that constitute the main part of the hydrophobic core of the molecule. On the other hand, computations at pH 3.7 and pH 7.0 for the ten native-like structures satisfying the NMR-derived constraints indicate a substantial change in the charge distribution for each type of amino acid residue with the change in pH. The results of this study provide a basis to understand the effect of the interactions, such as hydrophobicity, charge-charge interaction and solvent polarization, on the stability of this small alpha-helical protein.

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements

Extensive conformational sampling and calculations of vibrational coupling provide a quantitative basis for the structurally inhomogeneous spectra of the amide unit in aqueous solutions containing folded and unfolded state distributions of helices. Replica exchange molecular dynamics simulations of the capped helical peptide, AA(AAKAA)(3)AAY, is carried out over a range of temperatures, where the system populates the folded and unfolded states. This sampling defines a set of ensembles that characterizes the conformational variability for configurations identified by their fraction of helical content. The effects of hydrogen bonding, both internal and external (with water), and the coupling between amide-I modes are computed as a function of temperature and helical content. End-to-end distance and coupling distributions are also computed. The solvent H-bonding, which is present at all temperatures, shifts the amide-I band toward lower frequency compared with the unsolvated band. Upon thermal denaturation of the peptide, the amide-I band shifts to higher frequency because the increase in solvent H-bonding fails to compensate for the loss in internal (helical) H-bonds. The loss of uniformity of the mode coupling along the helix at higher temperatures accounts for the well-known thermal broadening of the amide IR spectrum. The calculated inhomogeneities of segments of the peptide predict experimental properties of isotope-edited helices.

The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy

The present article reports the conformation of cationic tetraalanine in aqueous solution. The determination of the dihedral angles of the two central amino acid residues was achieved by analyzing the amide I' band profile in the respective polarized visible Raman, Fourier transform-IR, and vibrational circular dichroism (VCD) spectra by means of a novel algorithm which utilizes the excitonic coupling between the amide I modes of nearest neighbor and second nearest peptide groups. It is an extension of a recently developed theory (Schweitzer-Stenner, R. Biophys. J., 2002, 83, 523-532). UV electronic circular dichroism (ECD) spectra of the peptides were used to validate the results of the structure analysis. The analyses yielded the dihedral angles (phi(12), psi(12)) = (-70 degrees, 155 degrees ) and (phi(23), psi(23)) = (-80 degrees, 145 degrees ). The obtained values are very close to the Ramachandran coordinates of the polyproline II helix (PPII). The data suggest that this is the conformation predominantly adopted by the peptide at room temperature. This notion was corroborated by the corresponding electronic circular dichroism spectrum. Tetraalanine exhibits a higher propensity for PPII than trialanine for which a 50:50 mixture of polyproline II and an extended beta-strand-like conformation was obtained from recent spectroscopic studies (Eker et al., J. Am. Chem. Soc. 2002, 124, 14330-14341). The temperature dependence of the CD spectra rule out that any cooperativity is involved in the strand if PPII transition. This led to the conclusion that solvent-peptide interactions give rise to the observed PPII stability. Our result can be utilized to understand why the denaturation of helix-forming peptides generally yields a PPII rather than a heterogeneous random conformation.

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

The conformational space of the 10-55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 A and 4.54 A were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information.

Structural changes and facilitated association of tropoelastin

Circular dichroism studies of tropoelastin secondary structure show 4+/-1% alpha-helix in aqueous solutions. This is in contrast to the substantially higher amounts (up to 23+/-7%) of alpha-helix predicted by computer algorithms, which propose that regions of alpha-helix are limited to the alanine-rich cross-linking domains. Through the addition of trifluoroethanol, the amount of alpha-helix increased to 17+/-1%, equivalent to that expected on the basis of primary structure. The physiological ability of the protein to coacervate and the critical concentration of monomer required for coacervation were unaffected by levels of alpha-helix. However, the temperature required for coacervation decreased linearly with increasing alpha-helical structure, which correlates with the participation of alpha-helices in association. We propose that the alanine-rich cross-linking domains exist as nascent helices in tropoelastin in aqueous solution. We further suggest a novel mechanism for coacervation whereby formation of alpha-helices and subsequent helical side chain interactions limit the conformational flexibility of the polypeptide, to facilitate associations between hydrophobic domains during elastogenesis.

Helix-coil transitions re-visited

The thermally-induced helix-coil transition in polyamino acids is a good model for determining the helix-forming propensities of amino acids but not for the two-state folding/unfolding transition in globular proteins. The equilibrium and kinetic treatments of the helix-coil transition are summarized here together with a description of applications to various types of homopolymers and copolymers. Attention is then focused on the helix-coil transition in poly-L-alanine as an example of a non-polar polyamino acid. To render such a non-polar polymer water soluble, it is necessary to introduce polar amino acids such as lysines, but care must be taken as to the location of such polar residues. If they are attached as end groups, as in a triblock copolymer, they do not perturb the helix-forming tendency of the central poly-L-alanine block significantly, but if they are introduced within the sequence of alanine residues, then the hydration properties of the lysines dominate the behavior of the resulting copolymer, thereby leading to erroneous values of the parameters characterizing the helix-forming tendency of the alanines. Neutral but polar residues, such as glutamines, also exhibit hydration-dominating properties but less so than charged lysines. Some details of the calculations for an alanine/glutamine copolymer are presented here. It is concluded that random copolymers based on a neutral water-soluble host provide reliable information about the helix-forming tendencies of amino acid residues that are introduced as guests among such neutral host residues.

Solubilized, spaced polyalanines: a context-free system for determining amino acid alpha-helix propensities

The logical design principles behind a system of properly water-solubilized, spaced polyalanines are presented. Peptides conforming to these design principles are shown to be unaggregated, and their helical properties as measured by the circular dichroism (CD) residue ellipticity at 222 nm, [theta](222), are shown to be dependent upon the lengths of their alanine regions. It is further demonstrated that CD contributions of the alanine cores are independent of the CD contributions attributable to other features of the peptides. The CD response of these polyalanines to variations in temperature and salt or denaturant concentration is described. CD data for a series of peptides with Ala(n) cores varying in length from 12 to 45 residues are presented that allow calculation of the helical propensity, w(Ala), in a purely alanine context. Mathematical modeling of these unprecedented data reveals the insufficiency of currently accepted literature helicity modeling parameters. A modification to the standard Lifson-Roig algorithm is introduced based on hydrogen-bonding cooperativity.

Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.

Influence of lysine content and pH on the stability of alanine-based copolypeptides

To account for the relative contributions of lysine and alanine residues to the stability of alpha-helices of copolymers of these two residues, conformational energy calculations were carried out for several hexadecapeptides at several pHs. All the calculations considered explicitly the coupling between the conformation of the molecule and the ionization equilibria as a function of pH. The total free energy function used in these calculations included terms that account for the solvation free energy and free energy of ionization. These terms were evaluated by means of a fast multigrid boundary element method. Reasonable agreement with experimental values was obtained for the helix contents and vicinal coupling constants ((3)J(HNalpha)). The helix contents were found to depend strongly on the lysine content, in agreement with recent experimental results of Williams et al. (Journal of the American Chemical Society, 1998, Vol. 120, pp. 11033-11043) In the lowest energy conformation computed for a hexadecapeptide containing 3 lysine residues at pH 6, the lysine side chains are preferentially hydrated; this decreases the hydration of the backbone CO and NH groups, thereby forcing the latter to form hydrogen bonds with each other in the helical conformation. The lowest energy conformation computed for a hexadecapeptide containing 6 lysine residues at pH 6 shows a close proximity between the NH3(+) groups of the lysine side chains, a feature that was previously observed in calculations of short alanine-based oligopeptides. The calculation on a blocked 16-mer of alanine shows a 7% helix content based on the Boltzmann averaged vicinal coupling constants computed from the dihedral angles phi, consistent with previous experimental evidence on triblock copolymers containing a central block of alanines, and with earlier theoretical calculations.

Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides

We have carried out conformational energy calculations on alanine-based copolymers with the sequence Ac-AAAAAXAAAA-NH(2) in water, where X stands for lysine or glutamine, to identify the underlying source of stability of alanine-based polypeptides containing charged or highly soluble polar residues in the absence of charge-charge interactions. The results indicate that ionizable or neutral polar residues introduced into the sequence to make them soluble sequester the water away from the CO and NH groups of the backbone, thereby enabling them to form internal hydrogen bonds. This solvation effect dictates the conformational preference and, hence, modifies the conformational propensity of alanine residues. Even though we carried out simulations for specific amino acid sequences, our results provide an understanding of some of the basic principles that govern the process of folding of these short sequences independently of the kind of residues introduced to make them soluble. In addition, we have investigated through simulations the effect of the bulk dielectric constant on the conformational preferences of these peptides. Extensive conformational Monte Carlo searches on terminally blocked 10-mer and 16-mer homopolymers of alanine in the absence of salt were carried out assuming values for the dielectric constant of the solvent epsilon of 80, 40, and 2. Our simulations show a clear tendency of these oligopeptides to augment the alpha-helix content as the bulk dielectric constant of the solvent is lowered. This behavior is due mainly to a loss of exposure of the CO and NH groups to the aqueous solvent. Experimental evidence indicates that the helical propensity of the amino acids in water shows a dramatic increase on addition of certain alcohols, such us trifluoroethanol. Our results provide a possible explanation of the mechanism by which alcohol/water mixtures affect the free energy of helical alanine oligopeptides relative to nonhelical ones.

Guidelines for membrane protein engineering derived from de novo designed model peptides

Notwithstanding great advances in the engineering and structural analysis of globular proteins, relatively limited success has been achieved with membrane proteins--due largely to their intrinsic high insolubility and the concomitant difficulty in obtaining crystals. Progress with de novo synthesis of model membrane-interactive peptides presents an opportunity to construct simpler peptides with definable structures, and permits one to approach an understanding of the properties of the membrane proteins themselves. In the present article, we review how our laboratory and others have used peptide approaches to assess the detailed interactions of peptides with membranes, and primary folding at membrane surfaces and in membranes. Structural studies of model peptides identified the existence of a "threshold hydrophobicity," which controls spontaneous peptide insertion into membranes. Related studies of the relative helicity of peptides in organic media such as n-butanol indicate that the helical propensity of individual residues--not simply their hydrophobicity--may dictate the conformations of peptides in membranes. The overall experimental results provide fundamental guidelines for membrane protein engineering.

Structure-based conformational preferences of amino acids

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for alpha-helices and beta-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.

Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices

A theoretical study to identify the conformational preferences of lysine-based oligopeptides has been carried out. The solvation free energy and free energy of ionization of the oligopeptides have been calculated by using a fast multigrid boundary element method that considers the coupling between the conformation of the molecule and the ionization equilibria explicitly, at a given pH value. It has been found experimentally that isolated alanine and lysine residues have somewhat small intrinsic helix-forming tendencies; however, results from these simulations indicate that conformations containing right-handed alpha-helical turns are energetically favorable at low values of pH for lysine-based oligopeptides. Also, unusual patterns of interactions among lysine side chains with large hydrophobic contacts and close proximity (5-6 A) between charged NH3+ groups are observed. Similar arrangements of charged groups have been seen for lysine and arginine residues in experimentally determined structures of proteins available from the Protein Data Bank. The lowest-free-energy conformation of the sequence Ac-(LYS)6-NMe from these simulations showed large pKalpha shifts for some of the NH3+ groups of the lysine residues. Such large effects are not observed in the lowest-energy conformations of oligopeptide sequences with two, three, or four lysine residues. Calculations on the sequence Ac-LYS-(ALA)4-LYS-NMe also reveal low-energy alpha-helical conformations with interactions of one of the LYS side chains with the helix backbone in an arrangement quite similar to the one described recently by (Proc. Natl. Acad. Sci. U.S.A. 93:4025-4029). The results of this study provide a sound basis with which to discuss the nature of the interactions, such as hydrophobicity, charge-charge interaction, and solvent polarization effects, that stabilize right-handed alpha-helical conformations.

Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins

The physiochemical bases of amino acid preferences for alpha-helical, beta-strand, and other main-chain conformational states in proteins is controversial. Hydrophobic effect, side-chain conformational entropy, steric factors, and main-chain electrostatic interactions have all been advanced as the dominant physical factors which determine these preferences. Many attempts to resolve the controversy have focused on small model systems. The disadvantage of such systems is that the amino acids in small molecules are largely exposed to the solvent. In proteins, however, the amino acids are in contact with the solvent to a different degree, causing a large variability of strengths of all interactions. The estimates of mean strengths of interactions in the actual protein environment are therefore essential to resolve the controversy. In this work the experimental protein structures are used to estimate the mean strengths of various interactions in proteins. The free energy contributions of the interactions are implemented into the Lifson-Roig theory to calculate the helix and strand free energy profiles. From the profiles the secondary structures of proteins and peptides are predicted using simple rules. The role of hydrophobic effect, side-chain conformational entropy, and main-chain electrostatic interactions in determining the secondary structure of proteins is assessed from the abilities of different models, describing stability of secondary structures, to correctly predict alpha-helices, beta-strands and coil in 130 proteins. The three-state accuracy of the model, which contains only the free energy terms due to the main-chain electrostatics with 40 coefficients, is 68.7%. This accuracy is approaching to the accuracy of currently the best secondary structure prediction algorithm based on neural networks (72%); however, many thousands of parameters have to be optimized during the training of the neural networks to reach this level of accuracy. The correlation coefficient between the calculated and the experimental helix contents of 37 alanine based peptides is 0.91. If the hydrophobic and the side-chain conformational entropy terms are included into the helix-coil transition parameters, the accuracy of the algorithm does not improve significantly. However, if the main-chain electrostatic interactions are excluded from the helix-coil and strand-coil transition parameters, the accuracy of the algorithm reaches only 59.5%. These results support the dominant role of the short-range main-chain electrostatics in determining the secondary structure of proteins and peptides. The role of the hydrophobic effect and the side-chain conformational entropy is small.

The role of context on alpha-helix stabilization: host-guest analysis in a mixed background peptide model

The helix content of a series of peptides containing single substitutions of the 20 natural amino acids in a new designed host sequence, succinyl-YSEEEEKAKKAXAEEAEKKKK-NH2, has been determined using CD spectroscopy. This host is related to one previously studied, in which triple amino acid substitutions were introduced into a background of Glu-Lys blocks completely lacking alanine. The resulting free energies show that only Ala and Glu- prove to be helix stabilizing, while all other side chains are neutral or destabilizing. This agrees with results from studies of alanine-rich peptide modela, but not the previous Glu-Lys block oligomers in which Leu and Met also stabilize helix. The helix propensity scale derived from the previous block oligomers correlated well with the frequencies of occurrence of different side chains in helical sequences of proteins, whereas the values from the present series do not. The role of context in determining scales of helix propensity values is discussed, and the ability of algorithms designed to predict helix structure from sequence is compared.

Curious structure in "canonical" alanine-based peptides

We have performed all atom simulations of blocked peptides of the form (AAXAA)3, where X = Gln, Asn, Glu, Asp, Arg, and Lys with explicit water molecules to examine the interactions between side chains spaced i,i-5 in the sequence. Although side chains in this i,i-5 arrangement are commonly believed to be noninteracting, we have observed the formation of unusual i,i-5 main chain hydrogen bonding in such sequences with positively charged residues (Lys) as well as polar uncharged groups (Gln). Our results are consistent with the unusual percentage of hydrogen bonding curves produced by amide exchange measurements on the well-studied sequence acetyl-(AAQAA)3-amide in water (Shalongo, W., Dugad, L., Stellwagen, E. J. Am. Chem. Soc. 116:8288-8293, 1994). Analysis of our simulations indicated that the glutamine side chain showed the greatest propensity to support pi helix formation and that the i,i-5 intramolecular hydrogen bonds were stabilized by water-bridging side chain interactions. This intermittent formation of the unusual pi helix structure was observed for up to 23% of the total simulation time in some residues in (AAQAA)3. Control studies on peptides with glutamine side chains spaced i,i-3, i,i-4 and i,i-6 did not reveal similar unique structures, providing stronger evidence for the unique role side chain interactions with i,i-5 spacing.

Template-nucleated alanine-lysine helices are stabilized by position-dependent interactions between the lysine side chain and the helix barrel

The helicity in water has been determined for several series of alanine-rich peptides that contain single lysine residues and that are N-terminally linked to a helix-inducing and reporting template termed Ac-Hel1. The helix-propagating constant for alanine (sAla value) that best fits the properties of these peptides lies in the range of 1.01-1.02, close to the value reported by Scheraga and coworkers [Wojcik, J., Altmann, K.-H. & Scheraga, H.A. (1990) Biopolymers 30, 121-134], but significantly lower than the value assigned by Baldwin and coworkers [Chakrabartty, A., Kortemme, T. & Baldwin, R.L. (1994) Protein Sci. 3,843-852]. From a study of conjugates Ac-Hel1-Ala(n)-Lys-Ala(m)-NH2 and analogs in which the methylene portion of the lysine side chain is truncated, we find that the unusual helical stability of Ala(n)Lys peptides is controlled primarily by interactions of the lysine side chain with the helix barrel, and only passively by the alanine matrix. Using 1H NMR spectroscopy, we observe nuclear Overhauser effect crosspeaks consistent with proton-proton contacts expected for these interactions.