Conformations of angiotensin II and enkephalin related to N.M.R.

Statistical samples of conformations for Angiotensin II and Enkephalin, obtained from a Monte-Carlo method, are models proposed to simulate the behavior of these hormones under different physico-chemical conditions. Analysis of molecular conformations shows that, for the two peptides, extended conformations are more likely to be present in acidic solutions used for N.M.R. measurements and folded conformations due to interactions of charged terminal groups are favoured at neutral pH.     

Sodium and chlorine ions as part of the DNA solvation shell.

The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C(5)T(5)). (A(5)G(5)) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B-DNA conformations are discussed.     

Multiple solution conformations and internal rotations of the decapeptide gramicidin S.

The conformations of every C alpha H-C beta H2 moiety of the peptide gramicidin S are reported. Internal rotation occurs, but distinct preferences for one side chain rotamer, greater than 80%, are found for the D-phenylalanine and ornithine residues. Leucine and valine exhibit more extensive averaging while proline is shown to be at least 90% in the Ramachandran B conformation. The data are consistent with the coexistence of many tertiary conformations of gramicidin S; the statistical weights of the twelve major tertiary conformations consistent with the rotamer populations are reported. The relative statistical weights of the tertiary conformers depend upon temperature and solvent. A comparison of the conclusions from this publication and conformations derived by energy minimization procedures is made. Partial agreement was found, but the calculations have not yet predicted the wealth of coexisting tertiary conformations nor accounted for the subtle effects of solvent. It is proposed that a more complete picture of the conformational dynamics of gramicidin S and other peptides will result from calculations which use as a basis the extensive data reported here.     

Theoretical studies on peptidoglycans. II. Conformations of the disaccharide–peptide subunit and the three-dimensional structure of peptidoglycan

Possible conformations of the disaccharide–peptide subunit of peptidoglycan (of Staphylococcus aureus or Micrococcus luteus) have been studied by an energy-minimization procedure. The favored conformation of the disaccharide N-acetyl-glucosaminyl-β(1–4)-N-acetylmuramic acid (NAG-NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three-dimensional arrangement of peptidoglycan in the bacterial cell wall.     

Noncontact dipole effects on channel permeation. II. Trp conformations and dipole potentials in gramicidin A

The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their side chain conformations should therefore be important, but the energies of different conformations are unknown. A conformational search for the right-handed helix based on molecular mechanics in vacuo yielded 46 conformations within 20 kcal/mol of the lowest energy conformation. The two lowest energy conformations correspond to the solid-state and solution-state NMR conformations, suggesting that interactions within the peptide determine the conformation. For representative conformations, the electrostatic potential of the Trp side chains on the channel axis was computed. A novel application of the image-series method of. Biophys. J. 9:1160-1170) was introduced to simulate the polarization of bulk water by the Trp side chains. For the experimentally observed structures, the CHARm toph19 potential energy (PE) of a cation in the channel center is -1.65 kcal/mol without images. With images, the PE is -1.9 kcal/mol, demonstrating that the images further enhance the direct dipole effect. Nonstandard conformations yielded less favorable PEs by 0.4-1.1 kcal/mol.     

Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate

As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles ? and ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche–gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.     

Conformational studies of 13 trinucleoside bisphosphates by 360-MHz 1H-NMR spectroscopy. 1. Ribose protons

The ribose protons of 13 trinucleoside bisphosphates (trimers) were studied, using 360-MHz proton nuclear magnetic resonance spectroscopy. Complete assignments and analyses of the NMR signals of these protons were carried out by the methods of homonuclear decoupling and computer line-shape simulations. It was shown that the trinucleotides preferred the anti, 3' endo, gamma +, beta t and epsilon t/epsilon- conformations for the glycosidic torsions, the ribose rings, the C4'-C5' bonds, the C5'-O5' bonds, and the C3'-O3' bonds, respectively. It was also found that the trimers, especially those which had noticeable population of 'bulged' structures, did not necessarily have a higher population of these preferred local conformations than their component dimers. The overall conformations of the trinucleotides are classified into two categories. The conformations in the first category involve the nearest-neighbor interactions. Each dinucleotide moiety can assume one of the four stable conformations (I, I', II and III) or the open forms of dinucleoside monophosphates. However, due to steric hindrance, there are only four cases in which both dinucleotide moieties can assume one of the four stable conformations at the same time. These four combinations of conformations are I-I, I'-I', I-II and III-I', where the first Roman numeral represents the conformation of the NpN'p-moiety and the second one, that of the -pN'pN' moiety of the trimers. Among them, I-I and I'-I' are helical structures, capable of forming a double helix. The second category contains conformations with bulged structures which have the two dinucleotide moieties in open forms (i.e. no nearest-neighbor interactions) and the bases of the two terminal residues stacking on each other while the middle residue is bulged out. These bulged conformations may serve as structural models for frame-shift mutations.     

Conformational energy calculations of enzyme-substrate complexes of lysozyme. I. Energy minimization of monosaccharide and oligosaccharide inhibitors and substrates of lysozyme

Conformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid-search method was used to locate all of the low-energy conformational regions for N-acetyl-β-D -glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N-acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the —CH₂OH group. The positions of the two vicinal cis —OH groups are determined predominantly by interactions with either the —CH₂OH or the N-acetyl group. The most stable conformations of β-N-acetylmuramic acid (NAM) were determined from the study of the low-energy conformations of NAG. In the two stable orientations for the D -lactic acid side chain, the O—C—C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low-energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups. The conformational preferences of the α-anomers of NAG and NAM were also explored. The calculated conformation of the N-acetyl group for α-NAG was quite close to that determined by X-ray analysis. Two of the three lowest energy conformations of α-NAM are similar to the corresponding conformations of the β-anomer. A third low-energy structure, which has a hydrogen bond from the NH of the N-acetyl group to the C?O of the lactic acid group, corresponds very closely to the X-ray structure of this molecule. The preferred conformations of the disaccharides NAG–NAG, NAM–NAG and NAG–NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C₃ of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH₂OH (donor) of residue i + 1 and the C?O of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence.     

Stereochemical studies on nucleic acid analogues. I. Conformations of alpha-nucleosides and alpha-nucleotides: interconversion of sugar puckers via O4'-exo.

The preferred conformations of ribo and deoxyribo alpha-nucleosides and alpha-nucleotides, the stereoisomers of the naturally occurring beta-isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their beta counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of P values are found to be energetically less favorable, with the barrier to anti in equilibrium with syn interconversion being higher especially in alpha-ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1'-exo range of sugars are highly unfavorable for alpha-nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by beta-isomers. While both trans congruent to 180 degrees and skew congruent to 270 degrees conformations around the C3'-O3' (phi') bond are favored for alpha-3'-nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of phi'. Most interestingly and in sharp contrast to beta-stereoisomers, an energy barrier is encountered at P values corresponding to O4'-endo sugars. This suggests that the possible sugar pucker interconversion between C2'-endo/C3'-exo and C3'-endo/C2'-exo in alpha-anomers could take place only through the O4'-exo region. Likewise the possible path of anti in equilibrium with syn interconversion in alpha-nucleosides is not via high anti, in sharp contrast to beta-nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in alpha-nucleosides and those containing them from nmr investigations. Comparison of the results with beta-anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of alpha-stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.     

Conformational behaviour of the architectural units of peptides and proteins. Assessment of current understanding by ab initio quantum mechanical methods and refinement of the dipeptide energy surface.

The conformational energy surfaces of analogues of the dipeptide unit of polypeptides and proteins are calculated by ab initio methods using extended basis sets.The calculations are not particularly sensitive to the choice of (extended) basis set.The calculations are shown to support a particular empirical method parameterized with respect to crystal data. Non-hydrogen bonded conformations agree to within 3 kcal mol^?1, even for conformations in which quite considerable degrees of atomic overlap occur.Hydrogen bonded conformations, are, however, in less satisfactory agreement and it is the ab initio calculations which appear to be at fault.A simple correction is applied to the ab initio energy for hydrogen bonded conformations, and with the use of the empirical energy surface a full quantum mechanical conformational energy map is interpolated for the alanyl dipeptide.The effect of flexibility in the peptide backbone is taken into account, and supports recent empirical findings that distortions in valence angles must be considered in calculations of the conformational behaviour of peptides.     

Molecular orbital studies on the conformation of phospholipids. II. Preferred conformations of hydrocarbon chains and molecular organization in biomembranes.

The preferred conformations of the nonpolar β and γ (hydrocarbon) chains in phospholipids have been derived using EHT and CNDO calculations. These calculations indicate that the possible conformations of phospholipids are highly restricted. The calculations find support from X-ray diffraction studies and NMR measurements on model compounds. When considering conformations relevant to structures in cell membranes, a further selection is possible because of the fact that in aqueous solutions hydrophobic interactions stabilize an arrangement where the hydrocarbon chains (β and γ) are stacked almost parallel to one another, leading to a bilayer structure. The various models for β and γ-chains which satisfy this condition have been compared and it has been shown that of these only four are favoured by energy considerations. These arrangements differ from one another in the orientation of the β-chain and γ-chains in the interior of the bilayer structure. A low energy pathway connects these conformations and thus the molecule can easily flip from one stable bilayer arrangement to another. The possible conformations of the polar group (α) are likewise restricted. The proposed model provides explanations to a number of dynamic and static properties of phospholipids, in particular to the observed NMR coupling constants, ¹H and ¹³C relaxation times, studies based on ESR spin labels and the observed X-ray diffraction results on model compounds.     

Conformational properties of trans Ac-Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in dimethylsulfoxide and in water determined by multinuclear n.m.r. spectroscopy

Vicinal coupling constants between various nuclei provide backbone and side-chain conformational information for a series of asparagine- and tyrosine-containing peptides in DMSO and in H2O. By enriching Tyr of Ac-Asn-Pro-Tyr-NHMe with 15N, it has been possible to distinguish between the resonances of the two side-chain beta protons of Tyr. Analysis of the coupling constants in terms of the distributions of side-chain conformations in these peptides indicates that the addition of Asn to the Pro-Tyr sequence leads to a less random conformational distribution. When compared to the side-chain rotamer distribution of Ac-Asn-NHMe and Ac-Tyr-NHMe, particular Asn and Tyr side-chain conformations of Ac-Asn-Pro-Tyr-NHMe are stabilized in dimethylsulfoxide solution. The interaction(s) which stabilize a unique Tyr side-chain conformation of Ac-Asn-Pro-Tyr-NHMe in dimethylsulfoxide are not present in Ac-Ala-Pro-Tyr-NHMe and are unaffected by the addition of Val-Pro to the C-terminus of Asn-Pro-Tyr. In water, a preferential stabilization of one Asn side-chain conformation of Ac-Asn-Pro-Tyr-NHMe is also observed, while the Tyr side-chain rotamer distribution is similar to that of Ac-Tyr-NHMe. An interaction between the Asn side chain and the Pro-Tyr-NHMe backbone was previously shown to stabilize a beta-bend conformation at Pro-Tyr in water. Data are also presented for Ac-Tyr-Pro-Asn-NHMe, for which local interactions do not stabilize particular backbone conformations in dimethylsulfoxide or in water. The conformations of the peptides studied here are relatively insensitive to temperatures between 27 degrees and 62 degrees, both in dimethylsulfoxide and in water. The sequences Asn-Pro-Tyr and Tyr-Pro-Asn occur in ribonuclease A, and these tripeptides serve as models for the interactions involved in the folding of this protein.     

Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units

The general conformations of a system of three linked peptide units are studied, and it is found that there are three types of conformations which contain NH…O hydrogen bonding between the first and the third units. One of them is part of a 3₁₀-helix, while the other two arc nonhelical. The two nonhelical conformations are very similar, and in both the cases the peptide chain turns around, reversing the direction of progress. Such a conformation can therefore occur in the region where a polypeptide chain folds back on itself, as in the cross-β structure. The method of representing these interesting tripeptide conformations in a (?,ψ) map is described. Examples of such hydrogen-bonded, nonhelical conformations which occur in peptides and proteins are discussed—e.g., in cyclohexaglyeyl, an open tetrapeptide Gly-L -Pro-L -Leu-Gly, and in parts of the lysozyme chain.     

Conformational features responsible for the binding of cyclic analogues of enkephalin to opioid receptors. III. Probable binding conformations of mu-agonists with phenylalanine in position 3.

Theoretical conformational analysis was carried out for several tetrapeptide analogues of beta-casomorphin and dermorphin containing a Phe residue in position 3. Sets of low-energy backbone structures of the mu-selective peptides [N-Me-Phe3, D-Pro4]-morphiceptin and Tyr-D-Orn-Phe-Asp-NH2 were obtained. These sets of structures were compared for geometrical similarity between themselves and with the low-energy conformations found for the delta-selective peptide Tyr-D-Cys-Phe-D-Pen-OH and nonactive peptide Tyr-Orn-Phe-Asp-NH2. Two pairs of geometrically similar conformations of mu-selective peptides, sharing no similarity with the conformations of peptides showing low affinity to the mu-receptor, were selected as two alternative models of probable mu-receptor-bound backbone conformations. Both models share geometrical similarity with the low-energy structures of the linear mu-selective peptide Tyr-D-Ala-Phe-Phe-NH2. Putative binding conformations of Tyr1 and Phe3 side chains are also discussed.     

Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains

A combined geometric and potential-energy analysis has been carried out to identify the torsional arrangements of the nucleic acid chain that can accommodate the intercalation of small planar moieties. In contrast to previous theoretical efforts, which detail local conformations after adjacent bases are positioned in space, the likely geometries are found here on the basis of the base orientations that result from all feasible combinations of the nine torsional variables of the basic dinucleotide intercalation unit. The relatively mobile nature of the sugar-phosphate backbone, together with the fairly long stretches of chemical bonds between adjacent units, is apparently responsible for the large number of feasible binding geometries. Some previously overlooked conformations with unusual sugar-puckering combinations and various phosphodiester arrangements are found in the survey. A large proportion of the energetically favored intercalation states are closely related to the backbone conformations of familiar double-helical models such as A-, B-, and Z-DNA, as well as the Watson-Crick model. Moreover, the intercalated forms are found to interconvert smoothly along a continuous conformational pathway. The intercalation structures derived from x-ray crystallographic analyses of drug-oligonucleotide complexes, in contrast, are stiff three-dimensional forms essentially frozen in a single domain of conformation space. Specific ligand-nucleic acid interactions that may be responsible for the experimental observations are not included in this study. The classical intramolecular potential energies reported here are highly approximate, providing only rough gauges of the relative importance of the many competing conformations.     

Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.

The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.     

Stereochemistry of nucleic acids and polynucleotides. V. Conformational energy of a ribose-phosphale unit

The potential energy calculations on the sugar-phosphate unit for different puckerings of the sugar are reported in this paper. The results obtained here essentially confirm our earlier predictions made by using criteria of contact distances (hard-sphere potential) and are also supported by observed conformation in crystal structures. The minimum energy conformations of the sugar phosphate unit, along with the preferred orientations of the base with respect to the sugar given in the previous paper, determine the probable conformations of the monomer unit of a polynucleotide (or nucleic acid) chain.     

Conformational analysis of [Cpp1, Sar7, Arg8] vasopressin by 1H-NMR spectroscopy and molecular mechanics calculations.

A combined 1H-NMR and molecular mechanics study of [Cpp1, Sar7]AVP was performed in order to select the most probable conformations in DMSO solutions. The NMR constraints obtained were employed in the selection of starting conformations of the cyclic moiety of the analog. In particular, the diminished accessibility of the Asn5 NH proton to solvent and the close contact between Cpp1 and Cys6 C alpha H protons suggests a beta-turn conformation at the Phe3-Gln4 residues. Energy minimization was carried out both in the ECEPP/2 (rigid-valence geometry) and in the AMBER (flexible-valence geometry) force fields. Comparison of the experimental and calculated values of NMR characteristics has revealed that conformations containing type I, II, and III beta-turns at the Phe3-Gln4 residues are in reasonable agreement with the experimental data, with a dynamic equilibrium between the beta I (beta III) and beta II type structures of the cyclic part being the most probable. All of these conformations prefer the negative chirality of the disulfide bridge (theta 3 approximately -90 degrees). Five representative conformations were chosen for the acyclic tail: one with a beta I, one with a beta II'-turn at the Sar7-Arg8 residues, two extended-type conformations, and a conformation with a gamma-turn at Sar7. Because only high-energy extended conformations were in agreement with NMR data, it was concluded that the acyclic tail has considerable conformational flexibility in solution. The conformations obtained are discussed in terms of the structure-function relationship of the neurohypophyseal hormone analogs.     

Mechanism of action of aspartic proteases. III. Conformational characteristics of HIV-1 protease inhibitor JG-365]

A set of conformations was shown to be characteristic of the free-state spatial structure of substrate-like inhibitor JG-365 for aspartic protease from HIV-1. Among them, the lowest-energy conformations have a folded form of the peptide backbone. The inhibitor has a noncleavable hydroxyethylamine group with an additional chiral center in its structure. Our calculations showed that only the S-isomer of the inhibitor displays conformational characteristics that practically coincide with those of the native substrate for HIV-1 protease. One of the calculated conformations with a completely extended main chain and a relative energy of 9.5 kcal/mol very closely mimics the experimentally observed structure of the inhibitor in the enzyme-inhibitor complex. The realization of this structure is unlikely for a free inhibitor, because it has only a small number of interresidual noncovalent interactions in the extended conformation; these are presumably compensated for by intermolecular interactions at the active site of the enzyme.     

Recognition in cell adhesion. A comparative study of the conformations of RGD-containing peptides by Monte Carlo and NMR methods

Many of the proteins that mediate cell adhesion processes processes-fibronectin, fibrinogen, vitronectin, von Willebrand factor, osteopontin, laminin and various collagens--contain the amino acid sequence Arg-Gly-Asp. Short peptides that include this sequence have been shown to inhibit the interactions of cell adhesion proteins with their receptors and to have dramatic effects on developmental processes involving cellular recognition. In order to determine which conformations are accessible to Arg-Gly-Asp containing peptides, we analyzed tri-, tetra- and pentapeptides using molecular mechanics and Monte Carlo methods, and studied the solution conformations of the pentapeptide Gly-Arg-Gly-Asp-Ser using nuclear magnetic resonance techniques. The Monte Carlo method was used to: (a) identify the low energy conformations of the peptides and (b) evaluate their thermodynamic properties. In the case of the pentapeptide Gly-Arg-Gly-Asp-Gly, the four stable conformations include three with reverse turns and one open structure. The conformations found in this analysis are compatible with the nuclear magnetic resonance (nuclear Overhauser effect) data.