Folding of polypeptide chains induced by the amino acid side-chains

Protected homo-oligopeptide structure: Model for preferred conformation of a linear methionine heptapeptide in chloroform

The (1)H nuclear magnetic resonance spectra for a protected linear heptapeptide of methionine, Boc-Met(7)-OMe, were measured in dimethyl-d(6) sulfoxide and C(2)HCl(3) solutions. In the former, the peptide is disordered. In C(2)HCl(3), preferred (short-range) interactions exist that dominate the overall secondary structure of the peptide. A model is proposed in which seven-membered ring structures are initiated at the NH(2)-terminus and propagate toward the carboxyl terminus. The first seven-membered ring contains a strong hydrogen bond between the amide NH of residue 2 and the carbonyl oxygen atom of the urethane blocking group. As one proceeds toward the carboxyl terminus the hydrogen bond strength of succeeding rings decreases, and at residue 5 the peptide chain assumes an extended structure that is stabilized by intermolecular hydrogen bonds. The model accounts for most of the results from (1)H NMR and infrared studies on the heptapeptide and is consistent with conformational energy calculations on homo-oligopeptides. It suggests that the COOH-terminal residues may serve as the nucleus for intermolecular peptide-peptide associations.

Conformational analysis of a chain reversal in alpha-chymotrypsin

A complete conformational analysis of the fold (Asp-Lys-Thr-Gly) (residues 35-38), and additional adjacent residues of alpha-chymotrypsin has been performed. A comparison of these findings with those of Lewis et al. (1) is made, and a discussion of the implications of protein-fold models is discussed. This particular residue sequence prefers to bend over maintaining a helical conformation. However, the bend conformation of the tetramer is different from that of the native bend. The native bend conformation is nearly realized when an additional residue of the native primary structure is added to each side of the tetramer. Early and late folding-sequence studies suggests that while the native fold is of low energy, there are fold-points along the primary structure which are more stable. The structural implications of this finding are discussed.

Affinity labeling of cysteine-mutants evidences contact residues in modeled receptor binding sites

To investigate the topology of binding sites in two ionotropic receptors, we have initiated a strategy combining affinity labeling with cysteine-scanning mutagenesis. For the GABAA receptor we have used reactive derivatives of non-competitive blockers (NCBs) to explore interacting positions in its channel. The polypeptide positions of the M2 segment of the alpha1 subunit which we mutated into cysteine were selected for their established accessibility, as determined by the substituted-cysteine accessibility method (SCAM). Using the Xenopus oocyte expression system, we show that receptors containing mutations V257C and S272C are inactivated by several reactive NCBs. These position-selective inactivations lead to an analysis of NCB binding in the channel. For the NMDA receptor glycine-binding site, the prototype antagonist L-701,324 was derivatized at different positions with different reactive groups. The receptor positions to mutate into cysteine were selected after a 3-D homology model. The observed receptor inactivations are mutant- and probe-selective, leading to an unambiguous chemical docking of the antagonist pharmacophore and supporting the model. The site-specificity of the inactivating reactions is assessed by protection experiments and by mutant to wild-type (WT) comparisons. The scope and limitations of the method are briefly discussed.

Modulation of intrinsic phi,psi propensities of amino acids by neighbouring residues in the coil regions of protein structures: NMR analysis and dissection of a beta-hairpin peptide

Analysis of residues in coil regions of protein structures presents a novel approach to deconvoluting the various competing factors which determine the intrinsic phi,psi propensities of amino acids free from the regular interactions associated with beta-strands and alpha-helices. We have considered the role of context on phi,psi preferences by examining the effects of neighbouring residues in modulating coil propensities within a data base of 512 high-resolution, low-homology structures. In the general case, when flanking residues are beta-branched or aromatic (Val, Ile, Tyr and Phe) the beta-propensity (Pbeta) increases significantly, largely due to steric effects between flanking residues. More subtle residue-specific effects are apparant when Pbeta values are examined in detail, showing "random coil" conformations to be highly sequence-dependent. The effects of flanking residues on phi distributions have been used to calculate context-dependent average 3JNH-Halpha coupling constants. We have examined these findings in the context of the folding of a model 16-residue beta-hairpin peptide, "mutant" hairpin (VSI-->KSK sequence change) and the isolated C-terminal beta-strand fragments of both hairpins. We find a better correlation between 3JNH-Halpha values derived from the data base model and those determined experimentally when context-dependent phi distributions are considered. The individual C-terminal beta-strand sequences (GKKITVSI versus GKKITKSK) of the two hairpins are predisposed to different extents to formation of an extended beta-like conformation. Conformational "predisposition" in this context may contribute significantly to beta-hairpin stability.

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures

Many different factors contribute to secondary structure propensities, including phi, psi preferences, side-chain interactions, steric effects and hydrophobic tertiary contacts. To deconvolute these competing factors, we have adopted a novel approach which quantifies the intrinsic phi, psi propensities for residues in coil regions (that is, residues not in alpha-helix and not in beta-strand). Comparisons of intrinsic phi, psi propensities with their equivalent secondary structure propensities show that while correlations for helix are relatively weak, those for strand are much stronger. This paper describes our new phi, psi propensities and provides an explanation for the variations observed.

Computational molecular modeling in peptide drug design

The review concentrates on practical applications of computer molecular modeling in peptide drug design. The examples of the predictions (successful or not) made by computational modeling before synthesis of peptide analogs, not the explanations provided after synthesis and biological testing of peptides, are discussed. The review spans over 20 years of predictions made by computer molecular modeling for bradykinin, angiotensin, thyrotropin-releasing factor, tuftsin, substance P, CCK-related peptides, luliberin, alpha-melanotropin and opioid peptides. The described examples are discussed in terms of finding the optimal way to use computer modeling for peptide design. The step-by-step 'technology' of peptide design is outlined in detail.

Theoretical conformational analysis and synthesis of analogues of the heptapeptide antibiotic K-582 A

A detailed theoretical conformational analysis of the linear heptapeptide antibiotic [Arg2]K-582 A (Arg-Arg-D-Orn-Thr-D-Orn-Lys-D-Tyr) was carried out. The results of the computer simulation suggest that the linear peptide has a high propensity to fold in solution into a quasi-cyclic conformation in equilibrium with pi(L-D) helices. The synthesis of two inactive analogues with an L-Lys in place of D-Orn3 or D-Orn5 confirms the importance of the proposed folding pattern for the occurrence of the antimicrobial activity of K-582 A.

Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc-Gly-Val-Gly-Gly-Leu-OMe

The conformational behavior of the synthetic peptide, Boc-Gly-Val-Gly-Gly-Leu-OMe, containing the X-Gly-Gly and Gly-Gly-X (X = Val or Leu) repeating sequences and constituting a fragment of elastin was investigated by molecular mechanics and molecular dynamics (MD) simulation. The results suggest that, irrespective of the approximations used, the molecule shows a manifold of low energy conformations characterized by gamma-turns and type II beta-turns. Furthermore, MD simulations point out a conformational floppiness due to very low barriers between different conformations. Experimental CD measurements in a virtually apolar medium (dioxane--epsilon = 2.209), which better mimics the vacuum conditions of the simulation, support the theoretical results. The general emerging picture, indicating the molecule as characterized by a combination of flexibility with conformational preferences, is in agreement with previous experimental findings and enriches of new aspects the description of the microscopic behavior of this molecule suggesting more detailed interpretation of previous data.

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions

A method is developed to compute backbone tertiary folds from the amino acid sequence. In this method, the number of degrees of freedom is drastically reduced by neglecting side-chain flexibility, and by describing backbone conformations as combinations of only seven structural states. These are characterized by single values of the dihedral angles phi, psi and omega, representing allowed conformations of the isolated dipeptide. We show that this restrictive model is none the less capable of describing native backbones to within acceptable deviations. Using our backbone description, potentials of mean force are derived from a database of known protein structures, based on statistical influences of single residues and residue pairs on the conformational states in their vicinity along the chain. This yields the force-field component due to local interactions, which is then used to predict lowest-energy conformations from any given amino acid sequence. The prediction algorithm does not require searching conformational space and is therefore extremely fast. Another important asset of our method is that it is able to compute not only the minimum energy conformation, but any number of lowest energy structures, whose relative preferences can be determined from the corresponding computed energy values. The performance of our procedure is tested on short peptides that are likely to be stabilized by local interactions. These include several helical structures and a hexapeptide with a beta-bend conformation, corresponding to peptides shown to have relatively well-defined conformations in aqueous solution, and to protein segments believed to adopt their native conformation early during folding. In addition, several flexible peptides are analysed. Except for the problems encountered in predicting observed disulphide bridges in two of the flexible peptides, and in a somewhat larger fragment comprising residues 30 to 51 of bovine trypsin inhibitor, prediction results compare very favourably with experimental data. Potential applications of our procedure to protein modelling and its extension to protein folding are discussed.

The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements

The 8-fold parallel alpha/beta-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the beta-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-stranded beta-barrel. To facilitate the de novo design of such structures, a collection of modeling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the phi, psi requirements to design symmetric eight stranded beta barrels with optimal hydrogen bonding between adjacent beta-strands. It is observed that: (a) the beta-sheet structure can be closed without introducing irregular stagger between beta-strands and (b) the region of phi, psi dihedral angle space compatible with the formation of regular symmetric eight stranded beta-barrels coincides with the phi, psi region corresponding to average beta-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on beta-strand geometry.

Physico-chemical properties of prostaglandins and related pharmacological compounds. A theoretical study on conformational related activity

Thromboxane A2, prostaglandin H2, a series of chemically stable cyclic endoperoxide analogues (U 46619, U 44069, ONO 11113, 9, 11, diazo PGH2 and SQ 26655) and different isomers of SQ 26655 were analysed for their spatial configuration by conformational analysis in a simulated membrane-water interface environment with a "structure tree" procedure already described for prostaglandins, leukotrienes and lipoxins. The conformers derived from the structure tree and with a high probability of existence are presented. A new method allows one to visualize the surface charge density of the calculated molecules. The spatial configuration and the surface charge density of each molecule are compared to their known order of competition binding to the putative TXA2/PGH2 receptor of platelets. The conformational and charge density analysis merely shows that the different stereochemistry of these molecules lead to spatial conformation, that mimics (agonists), or that are far from (antagonists) the TXA2/PGH2 conformation.

Computed conformational analysis of lipoxins and their ionic complexes

The possible molecular conformations of four structurally and biologically different lipoxins derivatives were predicted by a systematic structure tree theoretical analysis. This method takes into account the London-Van der Waals energy of interaction, the electrostatic interaction, the rotation energy of the torsional angles and the energy of transfer through a possible lipid-water interface. Finally, the conformers derived from the structure tree and with a high probability of existence were submitted to the energy minimization procedure. The most probable conformers of lipoxin A: 5S,6R,15S-trihydroxy-7,9,13 trans-11 cis-eicosatetraenoic acid (LXA); 11 trans lipoxin A: 5S,6R,15S-trihydroxy-7,9,11,13 trans-eicosatetraenoic acid (11t-LXA); lipoxin B: 5S,14R 15S-trihydroxy-6,10,12 trans-8 cis-eicosatetraenoic acid (LXB) and 8 trans lipoxin B: 5S,14R,15S-trihydroxy- 6,8,10,12 trans-eicosatetraenoic acid (8t-LXB) in their isolated form or when forming complexes with one calcium ion are presented. The four isolated compounds lead to vastly different conformations. Lipoxin A can form the most globular conformer while lipoxin B seems to be slightly more extended. The all trans isomer of lipoxin B forms an extended conformer and 11 trans lipoxin A gives a fully extended molecule. Complexes of a pair of these compounds with one calcium ion were shown to lead to vastly different conformations. Both (LXA) 2Ca and (LXB)2Ca form crumpled or extended structure, the LXA molecules being more wrapped around Ca2+ than LXB molecules. The (11t-LXA)2Ca and (8t-LXB)2Ca complexes present a high probability of extended conformations. Our description merely shows that the peculiar stereochemistry of these molecules lead to equilibria between conformers or to very static conformers, the flexibility and rigidity of which being probably relevant in view of their different biological activities.

Semi-empirical conformational analysis of propranolol interacting with dipalmitoylphosphatidylcholine

A semi-empirical conformational analysis is used to compute the conformation of (+)-propranolol inserted in dipalmitoylphosphatidylcholine. In a first step, the minimal conformational energy of the isolated molecule at the hydrocarbon-water interface is calculated as the sum of the contributions resulting from the Van der Waals, the torsional, the electrostatic and the transfer energies. Five pairs of conformers of minimal energy are determined. They are compared to data available from other experimental approaches. In a second step, they are assembled with dipalmitoylphosphatidylcholine at the interface. Although propranolol is considered in its protonated form, the electrostatic interaction with dipalmitoylphosphatidylcholine is negligible as compared to the Van der Waals interaction. The area occupied per propranolol molecule is between 0.53 and 0.64 nm2/molecule. In the most probable modes of insertion of propranolol into the lipid layer, the naphthyl moiety of the compound interacts with the lipid acyl chains. The protonated amino group is located in the vicinity of the phosphate residue possibly causing an electrostatic interaction.

Interaction of streptomycin and streptomycylamine derivatives with negatively charged lipid layers. Correlation between binding, conformation of complexes and inhibition of lysosomal phospholipase activities

Aminoglycoside antibiotics induce a lysosomal phospholipidosis in kidney proximal tubules after conventional therapy in animals and man. We have previously demonstrated that these drugs bind to negatively charged phospholipid bilayers at acid pH and inhibit the activity of lysosomal acid phospholipases in vitro and in vivo. A combined biochemical and conformational study [Brasseur et al., Biochem. Pharmac. 33, 629 (1984)] showed major and consistent differences between 6 aminoglycosides in current clinical use with respect to the stability of the complexes they form with phosphatidylinositol, their inhibitory potency towards the activity of lysosomal phospholipases and their current toxicity ranking (e.g. gentamicin greater than amikacin greater than streptomycin). In the present study we have extended this approach to experimental derivatives of streptomycin. The derivatives examined were: dihydrostreptomycin, dideguanyldihydrostreptomycin, streptomycylamine, dideguanylstreptomycylamine, N-butyl- and N-benzyl-dideguanylstreptomycylamine. These compounds were examined for (i) their binding to negatively charged liposomes, measured by gel permeation on Sepharose 4B; (ii) their interactions with phosphatidylinositol assessed by semi-empirical conformational analysis and (iii) their inhibitory effect on the activities of lysosomal phospholipases towards phosphatidylcholine present in negatively charged liposomes. Streptomycin and gentamicin were also used as reference compounds with low and high affinity (and inhibitory potency), respectively. Our observations can be summarized as follows: (i) the replacement of the aldehyde in the streptose ring by a methylamino group strikingly changes the conformation of the molecule, allowing a better interaction with phosphatidylinositol. Thus, streptomycylamine binds much more tightly to phospholipid bilayers and shows a higher inhibitory potency towards phospholipase activity, as compared to streptomycin. The conformational analysis shows, however, that this effect is only partially due to the additional cationic charge carried by streptomycylamine. Other modifications of the streptomycin molecule, such as the replacement of the guanidinium groups by aminogroups or the addition of hydrophobic moieties (butyl or benzyl groups) to the streptose do not markedly further strengthen the interactions of the molecule with phosphatidylinositol. (ii) Even though some derivatives (e.g. dideguanylstreptomycylamine) bind as tightly to phospholipids as gentamicin, they remain much less inhibitory towards lysosomal phospholipases.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural analogies between protein kinase C activators

Phorbol esters and diacylglycerols activate protein kinase C but specific structural parameters appear to be required for the enzyme activation. We have analyzed the conformation of potent and not potent diacylglycerols and phorbol esters. The orientation of the CH20H group at C3 of 1,2 diolein is remarkably similar to that of the same group at C-20 of 4 beta phorbol didecanoate and crucial for potency in activating the enzyme. Our data suggest that the new conformational approach here described could be used to rationally design specific inhibitors preventing the effects of tumor promoters and to predict the structure of potential tumor promoters.

Sequence of ionophore conformational changes induced by a simulated membrane/water interface

We demonstrate how the progressive passage through an interface simulated by a linear increase in dielectric constant may mediate a reversible transconformation of Na+/X537A (lasalocid A) from a cyclic to an extended structure. During the passage through the interface, the complex adopts progressively a more extended conformation favorable to the Na+ complexation or decomplexation at the interface.

Conformational analysis of 6-cis- and 6-trans-leukotriene B4-calcium complexes

We present a computational description of the conformation of a pair of two isomeric molecules (6-cis-and 6-trans-leukotriene B4) forming a complex with one calcium ion. Our theoretical prediction of the membrane-water interface conformation and of the bulk lipid phase conformation of the two different isomeric complexes are in excellent agreement with experimental data on the leukotriene-mediated calcium ionophoresis in liposomes. The two isomers lead to vastly different conformations in the presence of Ca2+, and the most probable conformation of the permeant species shows a globular conformation able to cross a lipid membrane.

Conformational properties of the pentapeptide fragment [32-36] of the thymic hormone thymopoietin

The conformational energy for the pentapeptide Arg-Lys-Asp-Val-Tyr (TP5) is calculated using empirical potential functions. Calculation of the local interactions for each independent residue gives a local energy term for which the probabilities as a function of phi, psi are plotted on Ramachandran-type maps. The interaction energy between residues is calculated only for these points in the maps with maximum probability. The most probable conformation for TP5 is found to have an extended backbone arrangement having the Arg and Tyr sidechains folded over the backbone. 13C n.m.r. spin lattice relaxation time measurements show no increase in T1 of the alpha-carbons at the first and terminal amino acids. The increase in T1 along the sidechain as found for Lys does not occur for Arg and Tyr. These signs of reduced mobility are consistent with a set of folded conformations in which the Arg and Tyr sidechains have hindered internal rotations. The vicinal NH-C alpha H couplings agree well with those calculated for the most probable conformer. This is not so for the C alpha H-C beta H couplings. These data are consistent with previous n.m.r. and structure activity studies.

Conformation and mobility of tyrosine side chain in tetrapeptides. Specific effects of cis- and trans-proline in Tyr-Pro- and Pro-Tyr-segments

We examined the properties of tyrosine in four free tetrapeptides: Ala-Ala-Tyr-Ala (AATA), Ala-Pro-Tyr-Ala (APTA), Ala-Tyr-Ala-Ala (ATAA) and Ala-Tyr-Pro-Ala (ATPA) by CD, n.m.r. and energy calculations. Experimental data (the aromatic 1Lb signal, rotamer populations around the C alpha-C beta bond (chi 1), rotations around C beta-C gamma(chi 2), chemical shifts of ortho- and meta-protons in the phenolic ring (in aqueous and Me2SO solutions), NH proton temperature coefficients and vicinal coupling constants 3JNH-C alpha H in the backbone (Me2SO solution) were compared with calculated minimum energy conformations. We find qualitative agreement between the results of the different techniques with respect to global tendencies of conformational behaviour: we present experimental evidence showing that the presence of proline in the sequence has a more pronounced effect on the side chain organization of the residues preceding it than on one succeeding it. This steric influence of proline on its immediate neighbor is even stronger in the cis isomer than in the more common trans isomer. The strong preference for Rotamer II (chi 1 = 180 degrees) over Rotamer I (chi 1 = -60 degrees) in ATPA (cis-form) concomitant with a noticeable deviation of chi 2 is a striking example.

Calcium transport by a beta-diketone in model membranes

The beta-diketone 1,1,1,2,2,3,3-heptafluoro-7,7-dimethyloctane-4,6-dione (FOD) translocates calcium from an aqueous medium into an organic phase. FOD is less efficient than but acts synergistically with A23187 in causing calcium translocation. The FOD-mediated process of calcium translocation is inhibited by NaCl, although the translocation of sodium by FOD is two to three orders of magnitude lower than that of calcium, when expressed relative to the concentration of these cations in the aqueous medium. At pH 7.4, FOD mediates calcium exchange-diffusion in fluid liposomes as efficiently as A23187. The extent of exchange-diffusion depends on the rigidity and cholesterol content of the liposomes. Conformational analysis of the complex formed by two molecules of FOD and one calcium atom at a simulated membrane interface reveals the existence of several interconvertible, asymmetrical and more-or-less planar configurations. The efficiency of FOD-mediated calcium ionophoresis thus appears to be regulated in a multifactorial manner by such factors as the concentration of calcium and monovalent cations, chemical composition and fluidity of the membrane, availability of other ionophoretic molecules and spatial configuration of the calcium complex.

Conformational analysis of phorbol esters at a simulated membrane/water interface

The conformation at a simulated membrane/water interface of four distinct phorbol esters, selected for their vastly different tumor-promoting potency, was predicted by a modification of the usual computing approach for the conformational analysis of macromolecules. In the modified procedure, the transfer energy of each part of the molecule in either a hydrophobic or hydrophilic domain was taken into account in order to define the orientation of the molecule at the simulated interface. The results of this study are compatible with known tensioactive properties of these phorbol esters, and may help to explain differences in their biological potency by the relative facility of their insertion in lipid bilayers.

Conformational analysis of the calcium-antagonist gallopamil

Conformational analysis of gallopamil was performed in order to gain insight into the molecular determinant of its calcium-antagonistic property. Whereas the neutral form of gallopamil was characterized by a single, largely predominant configuration, the protonated form of the drugs yielded several conformers, some of which were characterized by a readily accessible ionized site. The capacity of gallopamil to inhibit ionophore-mediated calcium translocation in a two-phase bulk system was inversely related to the pH of the aqueous phase. These findings indicate that the capacity of gallopamil to interfere with the transport of cations is critically dependent on the availability of a protonated configuration of the drug.

Homologous and hybrid calcium complexes of A23187 and hypoglycemic sulfonylureas: nuclear magnetic resonance and conformational analysis

Hypoglycemic sulfonylureas (e.g., gliclazide) are able to transport calcium across hydrophobic domains. Gliclazide and the ionophore A23187 act synergistically upon calcium transport. One calcium atom is complexed by either two molecules of sulfonylureas (or A23187) or one molecule each of sulfonylurea and A23187; the existence of such hybrid complexes has been documented by nuclear magnetic resonance. Conformation analysis of the calcium-gliclazide complex suggests close apposition of the toluyl groups in the gliclazide molecules.

Conformational analysis of the calcium--A23187 complex at a lipid--water interface

A possible conformation of the complex formed by one calcium ion and two molecules of the ionophore A23187 at a simulated lipid--water interface was predicted by a variant method for conformational analysis. This method takes into account, in addition to the Van der Waals energy, electrostatic interaction, and torsional potential, the alteration of electrostatic forces attributable to changes in dielectric constant at the interface and the transfer energy for each part of the complex as it moves through the lipid-water interface. The most probable conformer was characterized by a two-fold axial symmetry that was maintained during transition to the hydrophobic bulk conformation. Minor changes in the interfacial structure were sufficient to achieve the configuration characteristic of the hydrophobic bulk phase.