Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation.

The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of holo-pMMO from Methylococcus capsulatus (Bath) at 2.5 Å, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear CuI at the A site, resolve two CuIs at the B site, and uncover additional CuI clusters at the PmoA/PmoC interface within the membrane (D site) and in the water-exposed C-terminal subdomain of the PmoB (E clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier.

High-resolution proton magnetic resonance spectra of a rabbit sciatic nerve.

Proton magnetic resonance spectra (220-megahertz field) of an isolated rabbit sciatic nerve in its native state have been observed and assigned to the extracellular water, intracellular water, and phospholipids of the nerve. This study indicates that the nerve fibers contain fluid-like hydrophobic regions, in agreement with the results of recent electron spin resonance spin-labeled studies of excitable membranes of nerve and muscle.

Magnetic resonance studies of lunar samples.

Electron spin resonance searches at 9.5 gigahertz on several fines samples and portions of several rocks have yielded signals whose lineshapes and temperature dependences show that the samples are principally ferromagnetic in nature. Proton magnetic resonance searches at 60 megahertz of these samples have not revealed any signals ascribable to water or any other types of hydrogen in concentrations greater than 0.0001 percent by weight contained in narrow lines (5 oersteds wide or less) and 0.01 percent by weight in wide lines (as wide as 100 oersteds).

Excited-state backbone twisting of polyfluorene as detected from photothermal after-effects.

By means of time-resolved photoluminescence and photothermal techniques, after-effects from excited-state dynamics, energy migration, and conformational rearrangement of poly(9,9-di-n-octyl-2,7-fluorene) (PFO) and its homologues has been examined and interpreted with rotational potential maps from quantum mechanical calculations. Steady-state photoluminescence spectral changes and time-resolved photoluminescence measurements of oligofluorenes and PFO diluted in toluene suggest excited state ring torsion occurring within 30 ps of photoexitation. With all effects from internal conversion/intersystem crossing processes properly accounted for, we show that the conformational changes associated with this twisting motion can be quantitatively probed by means of photothermal methods. Results suggest mean torsion between neighboring fluorene units by ca. 40 degrees upon excitation, in agreement with the shift of rotational potential minimum from +/-40 degrees (and +/-140 degrees) in the ground state to +/-20 degrees (and +/-160 degrees) in the first excited singlet state according to results of quantum mechanical calculations.

The effect of surface curvature on the head-group structure and phase transition properties of phospholipid bilayer vesicles.

Proton nuclear magnetic resonance spectra at 360 MHz of small sonicated distearoyl phosphatidylcholine vesicles show easily distinguishable resonances due to choline N-methyl head-group protons located in the inner and outer bilayer halves. A study of the chemical shift of these resonances as a function of temperature reveals that the splitting between them increases below the phase transition. This occurs as a result of an upfield shift of the inner layer resonance at the phase transition. Consideration of the possible causes of this effect results in the conclusion that, at the phase transition, there is a change in the organization of the inner layer head-groups which does not occur for the outer layer head-groups.

The effects of the thermal prephase transition and salts on the coagulation and flocculation of phosphatidylcholine bilayer vesicles.

Absorbance measurements of sonicated dipalmitoyl phosphatidylcholine vesicles reveal two aggregation processes: flocculation and coagulation. Flocculation is only observed for samples in monovalent cationic salt solutions or in salt-free suspensions. This process is abolished in the presence of di- or trivalent cations. It is also found to be strongly temperature dependent, occurring only below the thermal prephase transition of the lipid. Dispersal of the flocculates is rapid but they re-form at a rate dictated by the hysteresis in the prephase transition. In contrast, coagulation is slow. The extent of coagulation does not seem to be strongly dependent on the temperature, the nature of the electrolyte or its concentration. The relation of the coagulated state to vesicle-vesicle fusion is briefly discussed.

Organization of chlorophyll a in bilayer membranes. The chlorophyll a/dimyristoylphosphatidylcholine system.

In order to investigate the relative importance of the hydrophobic and headgroup interactions of chlorophyll a in phospholipid bilayers, we have carried out differential scanning calorimetry (DSC) and deuterium (2H) and phosphorus (31P) nuclear magnetic resonance (NMR) experiments on the multilamellar system of chlorophyll a in dimyristoylphosphatidylcholine (DMPC). Compared to the phytol chain of chlorophyll and the previously reported distearoylphosphatidylcholine (DSPC), the acyl chains of DMPC are shorter in length by three and four carbons, respectively. A lowering in the phase-transition temperature was observed for the DMPC multilayers in the presence of chlorophyll a in the DSC thermograms and in the 31P chemical shift anisotropy measurements. These results, together with data on hydrophobic interactions as measured by 2H-NMR and on headgroup interactions as evidenced from 31P-NMR, suggest a phase diagram for the chlorophyll a/DMPC system in which phase separation readily occurs between a chlorophyll-rich compound phase and a chlorophyll-poor phospholipid phase. Compound formation appears to be important in the stabilization of chlorophyll a in bilayers with shorter chains.

Physicochemical characterization of 1,2-diphytanoyl-sn-glycero-3-phosphocholine in model membrane systems.

We report here on a series of studies aimed at characterization of the structural and dynamical properties of the synthetic lipid diphytanoyl phosphatidylcholine, in multilamellar dispersions and vesicle suspensions. The lipid exhibits no detectable gel to liquid crystalline phase transition over a large temperature range (-120 degrees C to +120 degrees C). Examination of proton nuclear magnetic resonance (NMR) free induction decays obtained from multilayer dispersions of diphytanoyl phosphatidylcholine provided an estimate of the methylene proton order parameter. The estimated magnitude of 0.21 is comparable to those determined for other phospholipids. Sonication of aqueous dispersions of diphytanoyl phosphatidylcholine led to formation of bilayer vesicles as determined by the measurement of the outer/inner choline methyl proton resonances, vesicle sizes in electron micrographs, and comparison of proton NMR linewidths between multilayer and sonicated dispersions. Ultracentrifugation studies of diphytanoyl phosphatidylcholine vesicles in H2O and 2H2O media yielded a value of 1.013 +/- 0.026 ml/g for the partial specific volume of this lipid. We have measured spin lattice relaxation rates for the methyl and methylenemethyne protons of the hydrocarbon chains of diphytanoyl phosphatidylcholine in bilayer vesicles over a range of temperatures and at two NMR frequencies (100 and 220 MHz). The observed relaxation rates for the methylene protons in this system were approximately twice those previously reported for dipalmitoyl phosphatidylcholine at comparable temperatures and resonance frequencies, whereas the relaxation rates measured for the methyl protons were greater than those of the straight chain lipid by an order of magnitude. Measurement of the spin lattice relaxation rates of the hydrocarbon protons of the diphytanoyl phosphatidylcholine in a 10 mol% mixture of the branched-chain lipid in a deuterated host lipid, diperdeuteropalmitoyl phosphatidylcholine, showed a discontinuity in the temperature dependence of the proton NMR longitudinal relaxation rates of the branched-chain lipid in the region of the gel to liquid crystalline phase transition temperature of the deuterated dipalmitoyl phosphatidylcholine host lipid. This result may be taken as evidence of lateral phase separation of a liquid cyrstalline phase enriched in diphytanoyl phosphatidylcholine from a gel phase enriched in diperdeuteropalmitoyl phosphatidylcholine at temperatures below the phase transition temperature of deuterated host lipid. This conclusion is supported by the observation of an abrupt change in the hydrocarbon methylene linewidth (at 100 MHz) of 10 mol% diphytanoyl phosphatidylcholine in diperdeuteropalmitoyl phosphatidylcholine over the temperature range where lateral phase separation is taking place according to differential thermograms.

The proton-pumping site of cytochrome c oxidase: a model of its structure and mechanism.

Cytochrome c oxidase is an electron-transfer driven proton pump. In this paper, we propose a complete chemical mechanism for the enzyme's proton-pumping site. The mechanism achieves pumping with chemical reaction steps localized at a redox center within the enzyme; no indirect coupling through protein conformational changes is required. The proposed mechanism is based on a novel redox-linked transition metal ligand substitution reaction. The use of this reaction leads in a straightforward manner to explicit mechanisms for achieving all of the processes previously determined (Blair, D.F., Gelles, J. and Chan, S.I. (1986) Biophys. J. 50, 713-733) to be needed to accomplish redox-linked proton pumping. These processes include: (1) modulation of the energetics of protonation/deprotonation reactions and modulation of the energetics of redox reactions by the structural state of the pumping site; (2) control of the rates of the pump's redox reactions with its electron-transfer partners during the turnover cycle (gating of electrons); and (3) regulation of the rates of the protonation/deprotonation reactions between the pumping site and the aqueous phases on the two sides of the membrane during the reaction cycle (gating of protons). The model is the first proposed for the cytochrome oxidase proton pump which is mechanistically complete and sufficiently specific that a realistic assessment can be made of how well the model pump would function as a redox-linked free-energy transducer. This assessment is accomplished via analyses of the thermodynamic properties and steady-state kinetics expected of the model. These analyses demonstrate that the model would function as an efficient pump and that its behavior would be very similar to that observed of cytochrome oxidase both in the mitochondrion and in purified preparations. The analysis presented here leads to the following important general conclusions regarding the mechanistic features of the oxidase proton pump. (1) A workable proton-pump mechanism does not require large protein conformational changes. (2) A redox-linked proton pump need not display a pH-dependent midpoint potential, as has frequently been assumed. (3) Mechanisms for redox-linked proton pumps that involve transition metal ligand exchange reactions are quite attractive because such reactions readily lend themselves to the linked gating processes necessary for proton pumping.

The formation and annealing of structural defects in lipid bilayer vesicles.

It is shown that sonication of phospholipid-water dispersions below the crystalline leads to liquid crystalline phase transition temperature (Tc) produces bilayer vesicles with structural defects within the bilayer membrane, which permit rapid permeation of ions and catalyze vesicle-vesicle fusion. These structural defects are annihilated simply by annealing the vesicle suspension above Tc. The rate of annealing was found to be slow, of the order of an hour for T = 3 degrees C above Tc, but annealing is complete within 10 min for T = 10 degrees C above Tc. It is proposed that these structural defects are fault-dislocations in the bilayer structure, which arise from a population defect in the distribution of the lipid molecules between the outer and inner monolayers, when small bilayer fragments reassemble to form the small bilayer vesicles during the sonication procedure. Such a population defect can only be remedied by lipid transport via the inside in equilibrium outside flip-flop mechanism, which would account for the slow kinetics of annealing observed even at 3 degrees C above the phase transition.

Effect of chlorophyll a on the phase behavior of hydrated monogalactosyldiacylglycerols.

We have studied the effect of chlorophyll a (chl a) on the X-ray diffraction patterns and the appearance of freeze-fracture electron micrographs of aqueous dispersions of monogalactosyldiacylglycerols (MGDG), the most abundant lipid in the thylakoid membrane. In MGDG systems containing 0-18 mol% of chl a, the diffraction patterns indicate the presence of a well-ordered reverse hexagonal phase. When 30 mol% of chl a was incorporated into the MGDG, the low-angle X-ray diffraction lines of the hexagonal lattice were slightly broadened and were accompanied by additional weak lines. With higher mol percents of chl a, the low-angle lines could no longer be indexed on a hexagonal or lamellar lattice. The freeze-fracture electron micrographs of similar samples showed that the patterns characteristic of the reverse hexagonal phase of an aqueous dispersion of pure MGDG were replaced by large liposomes, the fracture pattern of which is circular. We conclude that chl a in excess of 20 mol% destabilized the orderly reverse hexagonal phase of aqueous MGDG dispersions and disturbed the long-range order of the lipid array. These results are summarized in a temperature-composition isobaric phase diagram over a temperature range of -60 degrees C to 60 degrees C.

The phospholipid packing arrangement in small bilayer vesicles as revealed by proton magnetic resonance studies at 500 MHz.

Proton magnetic resonance spectra of saturated phospholipids in small unilamellar vesicles has been recorded at 500 MHz on a Bruker WM500 spectrometer. The additional spectral dispersion reveals new structure in the acyl chain resonances. At temperatures near the thermal phase transition, the chain methylene and methyl peaks are split, both showing a broad and a relatively sharp component. Magnetization transfer experiments together with studies in the presence of manganese ions inside or outside the vesicles indicate that the sharp component is to be assigned to the protons from the acyl chains in the inner half of the bilayer and the broad component to chains in the outer monolayer. These experiments demonstrate unambiguously that the extreme surface curvature intrinsic to small unilamellar vesicles induces a profound asymmetry in the packing arrangement of the hydrocarbon chains in the two leaflets of the bilayer and causes the two monolayers to exist in markedly different motional states.

Reaction of Escherichia coli cytochrome bo(3) and mitochondrial cytochrome bc(1) with a photoreleasable decylubiquinol.

In order to probe the reaction chemistry of respiratory quinol-oxidizing enzymes on a rapid time scale, a photoreleasable quinol substrate was synthesized by coupling decylubiquinol with the water-soluble protecting group 3',5'-bis(carboxymethoxy)benzoin (BCMB) through a carbonate linkage. The resulting compound, DQ-BCMB, was highly soluble in aqueous detergent solution, and showed no reactivity with quinol-oxidizing enzymes prior to photolysis. Upon photolysis in acetonitrile, 5, 7-bis(carboxymethoxy)-2-phenylbenzofuran, carbon dioxide, and decylubiquinol were formed. In aqueous media, free 3', 5'-bis(carboxymethoxy)benzoin was also produced. Photolysis of DQ-BCMB with a 308 nm excimer laser led to the release of the BCMB group in less than 10(-6) s. Decylubiquinol was released in the form of a carbonate monoester, which decarboxylated with an observed first-order rate constant of 195-990 s(-1), depending on the reaction medium. Yields of decylubiquinol as high as 35 microM per laser pulse were attained readily. In the presence of Escherichia coli cytochrome bo(3), photolysis of DQ-BCMB led to the oxidation of quinol by the enzyme with a rate that was limited by the rate of the decylubiquinol release. Mitochondrial cytochrome bc(1) reacted with photoreleased decylubiquinol with distinct kinetic phases corresponding to rapid b heme reduction and somewhat slower c heme reduction. Oxidation of photoreleased ubiquinol by this enzyme showed saturation kinetics with a K(m) of 3.6 microM and a k(cat) of 210 s(-1). The saturation behavior was a result of decylubiquinol being released as a carbonate monoester during the photolysis of DQ-BCMB and interacting with cytochrome bc(1) before decarboxylation of this intermediate yielded free decylubiquinol. The reaction of cytochrome bc(1) and photoreleased decylubiquinol in the presence of antimycin A led to monophasic b heme reduction, but also yielded slower quinol oxidation kinetics. The discrimination of kinetic phases in the reaction of cytochrome bc(1) with ubiquinol substrates has provided a means of exploring the bifurcation of electron transfer that is central to the operation of the Q-cycle in this enzyme.

Evidence for the absence of photoreduction of the metal centers of cytochrome C oxidase by X-irradiation.

Samples of X-irradiated cytochrome c oxidase were examined by electron paramagnetic resonance and optical spectroscopy. Both radiation from the Stanford Synchrotron Radiation Laboratory and a conventional X-ray source (W target) were utilized. The X-ray flux from these sources ranges from 10(9) to 10(13) photons/s. No evidence was found for photoreduction of the metal centers in the enzyme by X-ray photons. These results demonstrate that the integrity of cytochrome c oxidase is maintained using the conditions under which X-ray absorption measurements are presently being made.

The interpretation of proton magnetic resonance linewidths for lecithin dispersions. Effect of particle size and chain packing.

Two previously reported theoretical treatments of the effect of sonication on the PMR spectrum of phospholipid bilayer membranes have led to divergent conclusions regarding the effects of sonication on the structure of the bilayer membrane. In this report these two theoretical treatments will be critically reviewed, and it will be shown that only the theory of Seiter and Chan (Seiter, C.H.A. and Chan, S.I. (1973) J. Am. Chem. Soc. 95, 7541-7553) yields predictions which are in agreement with experiment. Analysis of available and newly acquired NMR results for sonicated bilayer vesicles of different sizes, both above and below the thermal phase transition, indicates that sonication does disrupt the regular molecular packing of the phospholipid molecules in these systems.

Interactions between a helical residue and tertiary structures: helix propensities in small peptides and in native proteins.

We compare three complete sets of helix propensities for the 20 naturally occurring amino acids. These propensities are derived from three different experimental systems: small synthetic peptides, coiled-coil dimers, and real proteins. Thermodynamic analyses show that propensities from the different sets should be perfectly correlated if (1) the helix in a protein is formed when and only when the protein is folded (tight-coupling); and (2) the amino acid side-chains are not involved in tertiary interactions. A simple thermodynamic model is proposed in order to understand those systems that fail (1). The model incorporates fluctuations in both native and unfolded states of the protein. Measurements on hydrogen-exchange rate from proteins also question the validity of (2). A complementary model that assumes a cooperation between helix formation and tertiary structures through side-chain interactions can explain the correlation between data from the peptides and proteins. One possible source of this side-chain tertiary interaction is the amphiphilicity of helices in proteins. Our model is consistent with the ideas of "minimal frustration" and "protein malleability"; it exhibits entropy-enthalpy compensation, and suggests that local unfolding and solvent penetration are correlated in a fluctuating protein. It also suggests experiments to quantitatively verify and differentiate between the models. The electrostatic nature of hydrogen bonding and its manifestations in protein helix stability is also discussed.

Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process model.

The recent progress in measurements on the amide hydrogen exchange (HX) in proteins under varying denaturing conditions, both at equilibrium and in transient relaxation, necessitates the development of a unifying theory which quantitatively relates the HX rates to the conformational energetics of the proteins. We present here a comprehensive kinetic model for the site-specific HX of proteins under varying solvent denaturing conditions based on the two-state protein folding model. The generalized two-process model considers both conformational fluctuations and residual protections, respectively, within the folded and unfolded states of a protein, as well as a global kinetic folding-unfolding transition between the two states. The global transition can be either rapid or slow, depending on the solvent condition for the protein. This novel model is applicable to the traditional equilibrium HX measurements in both EX2 and EX1 regimes, and also the recently introduced transient pulse-labeling HX experiments. A set of simple analytical equations is provided for quantitative interpretation of experimental data. The model emphasizes the use of full time-course of bi-exponential HX kinetics, rather than fitting time-course data to single rate constants, to obtain quantitative information about fluctuating conformers within the folded and unfolded states of proteins. This HX kinetic model naturally unfolds into a simple two-state and two-stage kinetic interpretation for protein folding. It suggests that the various observed intermediates of a protein can be interpreted as dominant isomers of either the folded or the unfolded state under different solvent conditions. This simple, minimalist's view of protein folding is consistent with various recent experimental observations on folding kinetics by HX.

Structure of Alamethicin in solution. One- and two-dimensional 1H nuclear magnetic resonance studies at 500 MHz.

We report here the 500 MHz 1H nuclear magnetic resonance spectra of Alamethicin, an icosapeptide antibiotic isolated from Trichoderma viride, in methanol, water and methanol/water mixtures. At this frequency, resonances from all the protons are well-resolved in methanol and may be assigned unambiguously. Spectral assignments were made using two-dimensional spin-echo correlated spectroscopy and by spin-decoupling experiments. The amide coupling constants (JNH-alpha CH) facilitated conformational predictions, which were confirmed in part by two-dimensional nuclear Overhauser experiments. On the basis of these data, we propose a secondary structure for Alamethicin that is alpha-helical toward the N terminus and extended beta-sheet at the C-terminal end. This structure is consistent with earlier circular dichroism measurements (McMullen et al., 1971), infrared attenuated total reflection spectroscopy studies (Fringeli & Fringeli, 1979) and proton exchange data (Davis & Gisin, 1981). The proposed structure is a tightly bound dimer, wherein the beta-sheet is stabilized by intermolecular hydrogen-bonds between opposing molecules. An interesting feature of this structure is that it exhibits both a hydrophobic and a hydrophilic surface. This highly amphiphilic nature of the dimer structure may account for the extensive further aggregation of Alamethicin in water. The 1H n.m.r. spectrum of Alamethicin in water is broad, suggesting extensive association. However, spectral assignments and amide coupling constant measurements in water, which were accomplished by titration of methanolic solution of Alamethicin by water, revealed no gross changes in the basic secondary structure of the molecule.

Purification and characterization of a cobalt-activated carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus.

A novel metallocarboxypeptidase (PfuCP) has been purified to homogeneity from the hyperthermophilic archaeon, Pyrococcus furiosus, with its intended use in C-terminal ladder sequencing of proteins and peptides at elevated temperatures. PfuCP was purified in its inactive state by the addition of ethylenediaminetetraacetic acid (EDTA) and dithiothreitol (DTT) to purification buffers, and the activity was restored by the addition of divalent cobalt (K, = 24 +/- 4 microM at 80 degrees C). The serine protease inhibitor phenylmethylsulfonyl fluoride (PMSF) had no effect on the activity. The molecular mass of monomeric PfuCP is 59 kDa as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 58 kDa by SDS-PAGE analysis. In solution, PfuCP exists as a homodimer of approximately 128 kDa as determined by gel filtration chromatography. The activity of PfuCP exhibits a temperature optimum exceeding 90 degrees C under ambient pressure, and a narrow pH optimum of 6.2-6.6. Addition of Co2+ to the apoPfuCP at room temperature does not alter its far-UV circular dichroism (CD) or its intrinsic fluorescence spectrum. Even when the CoPfuCP is heated to 80 degrees C, its far-UV CD shows a minimal change in the global conformation and the intrinsic fluorescence of aromatic residues shows only a partial quenching. Changes in the intrinsic fluorescence appear essentially reversible with temperature. Finally, the far-UV CD and intrinsic fluorescence data suggest that the overall structure of the holoenzyme is extremely thermostable. However, the activities of both the apo and holo enzyme exhibit a similar second-order decay over time, with 50% activity remaining after approximately 40 min at 80 degrees C. The N-blocked synthetic dipeptide, N-carbobenzoxy-Ala-Arg (ZAR), was used in the purification assay. The kinetic parameters at 80 degrees C with 0.4 mM CoCl2 were: Km, 0.9 +/- 0.1 mM; Vmax, 2,300 +/- 70 U mg(-1); and turn over number, 600 +/- 20 s(-1). Activity against other ZAX substrates (X = V, L, I, M, W, Y, F, N, A, S, H, K) revealed a broad specificity for neutral, aromatic, polar, and basic C-terminal residues. This broad specificity was confirmed by the C-terminal ladder sequencing of several synthetic and natural peptides, including porcine N-acetyl-renin substrate, for which we have observed (by MALDI-TOF MS) stepwise hydrolysis by PfuCP of up to seven residues from the C-terminus: Ac-Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu-Leu-Val-Tyr-Ser.

Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.

Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm to a series of N- and C-capped polyelectrolyte peptides, (Glu)20, (Asp)20, (PSer)20, and (PSer-Asp)10, that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na+ for COO-; two Na for CO(PO3)-2) plus a distance-dependent (shielded) dielectric constant, epsilon = epsilon 0 R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG-MC conformational search with epsilon 0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole-Langevin dipole method of Warshel. These calculations predict a correlation between amino acid sequence and global folded conformational minima: 1. Poly-L-Glu20, our structural benchmark, exhibited a preference for right-handed alpha-helix (47% helicity), which approximates experimental observations of 55-60% helicity in solution. 2. For Asp- and PSer-containing sequences, all conformers exhibited a low preference for right-handed alpha-helix formation (< or = 10%), but a significant percentage (approximately 20% or greater) of beta-strand and beta-turn dihedrals were found in all three sequence cases: (1) Aspn forms supercoil conformers, with a 2:1:1 ratio of beta-turn:beta-strand:alpha-helix dihedral angles; (2) PSer20 features a nearly 1:1 ratio of beta-turn:beta-sheet dihedral preferences, with very little preference for alpha-helical structure, and possesses short regions of strand and turn combinations that give rise to a collapsed bend or hairpin structure; (3) (PSer-Asp)10 features a 3:2:1 ratio of beta-sheet:beta-turn:alpha-helix and gives rise to a superturn or C-shaped structure.