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.     

Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.

The analysis and prediction of non-canonical structural motifs in RNA is of great importance for an understanding of the function and design of RNA structures. A hierarchical method has been employed to generate a large variety of sterically possible conformations for a single-base adenine bulge structure in A -form DNA and RNA. A systematic conformational search was performed on the isolated bulge motif and neighboring nucleotides under the constraint to fit into a continuous helical structure. These substructures were recombined with double-stranded DNA or RNA. Energy minimization resulted in more than 300 distinct bulge conformations. Energetic evaluation using a solvation model based on the finite-difference Poisson-Boltzmann method identified three basic classes of low-energy structures. The three classes correspond to conformations with the bulge base stacked between flanking nucleotides (I), location of the bulge base in the minor groove (II) and conformations with a continuous stacking of the flanking helices and a looped out bulge base (III). For the looped out class, two subtypes (IIIa and IIIb) with different backbone geometries at the bulge site could be distinguished. The conformation of lowest calculated energy was a class I structure with backbone torsion angles close to those in standard A -form RNA. Conformations very close to the extra-helical looped out bulge structure determined by X-ray crystallography were also among the low-energy structures. In addition, topologies observed in other experimentally determined bulge structures have been found among low-energy conformers. The implicit solvent model was further tested by comparing an uridine and adenine bulge flanked by guanine:cytosine base-pairs, respectively. In agreement with the experimental observation, a looped out form was found as the energetically most favorable form for the uridine bulge and a stacked conformation in case of the adenine bulge. The inclusion of solvation effects especially electrostatic reaction field contributions turned out to be critically important in order to select realistic low-energy bulge structures from a large number of sterically possible conformations. The results indicate that the approach might be useful to model the three-dimensional structure of non-canonical motifs embedded in double-stranded RNA, in particular, to restrict the number of possible conformations to a manageable number of conformers with energies below a certain threshold.     

Structure-function organization of neurokinin A and neurokinin B molecules. I. Theoretical conformational analysis of neurokinin A

The spatial structure of the neurokinin A molecule was studied by the method of theoretical conformational analysis. On the basis of fragmental analysis, stable structures of the neurokinin A molecule under polar conditions were determined. The structures can be described by four families of low-energy conformations having a relatively labile tripeptide at the C-end and a conformationally rigid heptapeptide at the N-end. It was shown that two of these conformations are virtually isoenergetic structures. One of these is an alpha-helical structure and the other forms two beta-turns at the N-terminus, which change to the turn of the alpha-helix at the C-end.     

Conformational analysis of cysteine-containing peptides and prospects of their application to 213Bi chelating in antitumor therapy

The method of conformational analysis was applied to the spatial structures of peptide analogues of phytochelatins and some fragments of metallothioneins: (Cys-Gly)3, (Cys-Gly)3Asp, (Cys-Gly)3Glu, (Cys-betaAla)3, (Cys-gammaGlu)3, and (Cys-Gly-Gly)3. All the possible low-energy conformations of the molecules were revealed and the role of intra- and inter-residual interactions in the formation of their spatial structures was determined. A different tendency of the molecules under study for acceptance of conformations favorable for binding bismuth ions was shown. Low-energy structures providing an optimum binding of bismuth ion were shown to be most frequent for (Cys-betaAla)3 peptide. Among the analogues of peptide fragments of the metallothioneins, lacking in natural peptides, low-energy pentapeptide CCXXC fragments (where X = Gln, Asn, Phe, Tyr, and Gly) were revealed. In the alpha-helical conformations of these pentapeptides, the distance between the sulfur atoms corresponds to that in Bi2S3. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2006, vol. 32, no. 3; see also http://www.maik.ru.     

Determination of cyclopeptide conformations in solution using NMR data and conformational energy calculations

The three-dimensional structure of the cyclic analogs of bradykinin and substance P C-terminal hexapeptide was studied using conformational energy calculations. Initial conformations for energy minimization were selected with the aid of the measured intensities of local nuclear Overhauser effects (NOEs) and other 1H-NMR data. Expected values of the 1H-NMR parameters for low-energy conformations of the cyclopeptides were calculated and compared with those observed experimentally using semiquantitative gradation of NOE intensities. Several low-energy structures of the cyclic bradykinin analog, possessing similar backbone conformations stabilized by two beta-turns, are in agreement with experimental data. None of the low-energy conformations of the substance P cyclic hexapeptide were in satisfactory agreement with the experimental set of NOEs. The agreement was achieved only by averaging of the calculated 1H-NMR parameters over several combinations of the low-energy conformations.     

Influence of local interactions on protein structure. III. Conformational energy studies of N-acety-N′-methylamides of Gly-X and X-Gly dipeptides

Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N-acetyl- N′-methylamides of Gly-X and X-Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu-Gly. Each depeptde was found to have 25 or more low-energy minima, except Gly-Thr, which had only 11 low-energy minima because of the stable side chian-backbone hydrogen present in all low-energy conformation. As a group, the stble chain-backbone hydrogen bonds present in all low-energy conformations. As a group, the Gly-containing dipeptides were calculated in all low-energy prpensity for formation of bends than the Ala-containing depeptides. The X- Gly dipeptides were calculated to favor bends more than the Gly-X dipeptides, primarlly because of the high stability of the type II bend in X-Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x-ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results.     

Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data

An implementation of the variable-target-function procedure, first introduced by Braun and Go [W. Braun and N. Go, J. Mol. Biol. 186, 611-626 (1985)], has been used to generate conformations of the small protein bovine pancreatic trypsin inhibitor (BPTI), given a limited set of simulated data that could be obtained by nuclear magnetic resonance (NMR) techniques. A hybrid strategy was also used to calculate conformations of BPTI, given the same information. In the hybrid strategy, low-energy structures of medium-size fragments (decapeptides) of BPTI were generated using the variable-target-function method, followed by restrained energy optimization. The low-energy conformations were used as a basis to build up the complete fifty-eight-residue BPTI molecule. By using the variable-target-function approach, in which energy considerations were not introduced until full conformations of the entire BPTI molecule had been generated, it was not possible to obtain calculated structures with rms deviations from the X-ray conformation of less than 1.6 A for the alpha-carbons. On the other hand, with the hybrid strategy, which involved the consideration of realistic energy terms in the early stages of the calculations, it was possible to calculate low-energy conformations of BPTI with rms deviations from the X-ray structure of 1.06 to 1.50 A for the alpha-carbons. When the rms deviations were computed along the amino acid sequence, it was found that there was a good correlation between deviations among the calculated structures and deviations from the X-ray structure.     

The spatial organization and conformational flexibility of neuropeptides of the gallatostatin family

The spatial organization and conformational flexibility of neuropeptides of the gallatostatin family was studied by the method of theoretical conformational analysis. It was found that the spatial organization of neuropeptides allows the realization of folded helical structures of the C-terminal pentapeptide, and the flexibility of neuropeptides is due to a great number of low-energy states in the N-terminal fragment of the molecule.     

Variable-Target-Function and Build-up Procedures for the Calculation of Protein Conformation. Application to Bovine Pancreatic Trypsin Inhibitor Using Limited Simulated Nuclear Magnetic Resonance Data

Abstract

An implementation of the variable-target-function procedure, first introduced by Braun and Gō [W. Braun and N. Gō, J. Mol. Biol. 186, 611–626 (1985)], has been used to generate conformations of the small protein bovine pancreatic trypsin inhibitor (BPTI), given a limited set of simulated data that could be obtained by nuclear magnetic resonance (NMR) techniques. A hybrid strategy was also used to calculate conformations of BPTI, given the same information. In the hybrid strategy, low-energy structures of medium-size fragments (decapeptides) of BPTI were generated using the variable-target-function method, followed by restrained energy optimization. The low-energy conformations were used as a basis to build up the complete fifty-eight-residue BPTI molecule. By using the variable-target-function approach, in which energy considerations were not introduced until full conformations of the entire BPTI molecule had been generated, it was not possible to obtain calculated structures with rms deviations from the X-ray conformation of less than 1.6 Å for the α-carbons. On the other hand, with the hybrid strategy, which involved the consideration of realistic energy terms in the early stages of the calculations, it was possible to calculate low-energy conformations of BPTI with rms deviations from the X-ray structure of 1.06 to 1.50 Å for the α-carbons. When the rms deviations were computed along the amino acid sequence, it was found that there was a good correlation between deviations among the calculated structures and deviations from the X-ray structure.     

Refinement of the thrombin-bound structure of a hirudin peptide by a restrained electrostatically driven Monte Carlo method.

Energy refinement of the structure of a linear peptide, hirudin56-65, bound to thrombin was carried out using a conformational search method in combination with restrained minimization. Five conformations originated from nmr data and distance geometry calculations having a similar global folding pattern but quite different backbone conformations were used as the starting structures. As a result of this approach, a series of low-energy conformations compatible with a set of upper and lower bounds of interproton distances determined from transferred nuclear Overhauser effects were found. A comparison among the lowest energy conformations of each run showed that the combination of energy refinement plus distance constraints led to a very well-defined structure for both the backbone and the side chains of the last 7 residues of the polypeptide. Furthermore, the low-energy conformations generated with this technique contain a segment of 3(10)-helix involving the last 5 residues at the COOH terminal end.     

Conformational analysis of cysteine-containing peptides and prospects of their application to 213Bi chelating in antitumor therapy

The method of conformational analysis was applied to the spatial structures of peptide analogues of phytochelatins and some fragments of metallothioneins: (Cys-Gly)₃, (Cys-Gly)₃-Asp, (Cys-Gly)₃-Glu, (Cys-βAla)₃, (Cys-γGlu)₃, and (Cys-Gly-Gly)₃. All the possible low-energy conformations of the molecules were revealed and the role of intra-and interresidual interactions in the formation of their spatial structures was determined. A different tendency of the molecules under study for acceptance of conformations favorable for binding bismuth ions was shown. Low-energy structures providing an optimum binding of bismuth ion were shown to be most frequent for (Cys-βAla)₃ peptide. Among the analogues of peptide fragments of the metallothioneins, lacking in natural peptides, low-energy pentapeptide CCXXC fragments (where X = Gln, Asn, Phe, Tyr, or Gly) were revealed. In the α-helical conformations of these pentapeptides, the distance between the sulfur atoms corresponds to that in Bi₂S₃.     

Conformational features responsible for the binding of cyclic analogues of enkephalin to opioid receptors. II. Models of mu- and delta-receptor-bound structures for analogues containing Phe4

Models of mu- and delta-receptor-bound backbone conformations of enkephalin cyclic analogues containing Phe4 were determined by comparing geometrical similarity among the previously found low-energy backbone structures of [D-Cys2,Cys5]-enkephalinamide, [D-Cys2,D-Cys5]-enkephalinamide, [D-Pen2,L-Pen5]-enkephalin and [D-Pen2,D-Pen5]-enkephalin. The present mu-receptor-bound conformation resembles a beta-I bend in the peptide backbone centred on the Gly3-Phe4 region. Two slightly different models were found for the delta-receptor-bound conformation; both of them are more extended than the mu-receptor-bound conformation and include a gamma-turn (or a gamma-like turn) on the Gly3 residue. Energetically favourable rotamers of Tyr and Phe side chains were also determined for the mu- and delta-conformations. The present models of mu- and delta-conformations share geometrical similarity with the low-energy structures of Leu-enkephalin and the Tyr-D-Lys-Gly-Phe-analogue.     

Efficient conformational sampling of multiconformational cyclic molecules: application to 1,4,7,10,13-Pentaoxacyclopentadecane

The result of an exhaustive search of low-energy conformers of 1,4,7,10,13-Pentaoxacyclopentadecane is presented. The search method combines the generation of large number of trial conformers using local nonstochastic deformations known as the Conflex method, which is coupled to AMBER force field as the minimizer. The extent of the conformational space sampled was evaluated from the view point of the number of duplicates of each conformer, generation of inclusion type structures without considering the substrate and the spread of the allowed torsion angles visited during the search. It is shown that the conformational search is exhaustive and efficient as conformers, which the metal coordinated crown ether complexes adopt, were generated. Free energies using the AMBER structures were calculated using the model of Cramer and Truhlar. The study suggests that 1,4,7,10,13-Pentaoxacyclopentadecane exists as a mixture of conformers in solution. The results show the efficiency of the method and could be the method of choice in the design of synthetic macrocyclic receptors.     

DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies

Results are presented from density functional molecular dynamics (DFTMD) simulations, based on constant energy dynamics, of glucose and its cyclic form of 6-carbon epimers. Both in vacuo and an implicit solvent method (COSMO) were examined, including simulations of low-energy conformations of each molecule. Analysis of the DFTMD results includes the following: energies averaged over the simulation time, calculated anomeric ratios, hydroxyl and hydroxymethyl rotamer populations, and hydration energies. Hydrogen-bonding networks persistence times were examined, and the effects of solvation on rotamer populations were described. Anomeric ratios calculated from energy optimization of an ensemble of low-energy conformers are compared to those obtained from ensemble averages from molecular dynamics, with dynamics simulations giving populations in best agreement with experimental anomeric ratios. Ensemble results in vacuo were not in agreement with experimental anomeric ratios or hydroxymethyl populations, producing in some cases reversal of the α:β ratios. The difficulty in obtaining correct α:β ratios increases with the number of axial groups; the mono-axial epimers being best represented, epimers with two axial groups being more difficult, and the epimers with three axial hydroxyl groups being most difficult to analyze, the result of a large number of very strong hydrogen-bonding networks that form the ensemble of low-energy conformations in the multi-axial structures.     

Conformation-activity relationships of cyclic dermorphin analogues

A theoretical conformational analysis (molecular mechanics study) of nine cyclic tetrapeptides, structurally related to the highly mu-receptor-selective dermorphin analogue H-Tyr-D-Orn-Phe-Asp-NH2, was performed. These compounds display considerable diversity in their mu-receptor affinity and selectivity. A systematic search and subsequent energy minimization in absence of the exocyclic Tyr1 residue and Phe3 side chain revealed the constrained nature of the 11-13-membered ring structures contained in these analogues. No more than four low-energy conformers (within 2 kcal/mol of the lowest energy conformation) were found in each case. After attachment of the Tyr1 moiety and Phe3 side chain to the "bare" low-energy ring structures, a systematic search and energy minimization of these exocyclic moieties resulted in a limited number of low-energy conformational families for all compounds. Five analogues with high mu-receptor affinity--H-Tyr-D-Orn-Phe-Asp-NH2, H-Tyr-D-Orn-Phe-D-Asp-NH2, H-Tyr-D-Asp-Phe-Orn-NH2, H-Tyr-D-Asp-Phe-A2bu-NH2 (A2 bu: alpha, gamma-diaminobutyric acid) and H-Tyr-D-Cys-Phe-Cys-NH2--all showed a tilted stacking interaction between the Tyr1 and Phe3 aromatic rings in the lowest or second lowest energy conformation found. The same kind of stacking was not possible in low-energy conformers of the four analogues with poor affinity for the mu-receptor [H-Tyr-L-Orn-Phe-Asp-NH2, H-Tyr-D-Orn-D-Phe-Asp-NH2, H-Tyr-D-Orn-Phe(NMe)-Asp-NH2 [Phe(NMe): N alpha-methylphenylalanine], and H-Tyr-D-Orn-Phg-Asp-NH2 (Phg: phenylglycine)].(ABSTRACT TRUNCATED AT 250 WORDS)     

Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N′-methylamides of pro-X and X-pro dipeptides

Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N-acetyl-N′-methylamides of Pro-X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X-Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low-energy single-residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low-energy single-residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low-energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low-energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro-X dipeptides because ?_Pro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X-Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.     

Conformational analysis of the biologically active cyclic analog of beta-casomorphin H-Tyr-cyclo[D-OrnPheProGly].

A biologically active analog of beta-casomorphin, H-Tyr-cyclo[D-OrnPheProGly], was studied by theoretical conformational analysis. Random sampling was used to search the conformational space of allowed dihedral angles. Among 53 low-energy conformers with different folding of the peptide cyclic moiety, only those were selected which correspond to the low-energy area of the model linear tripeptide Ac-D-AlaAlaPro-NHMe. This peptide was used as the main chain "template" for the D-OrnPheProGly fragment of the studied cyclopeptide molecule. Only 15 conformers were chosen as potentially biologically active structures. The conformational possibilities of the Phe residue were constrained to the combined (A + G) region of the Ala residue phi,psi-map for linear peptides.     

Conformational analysis of biologically active RGD-containing cyclopentapeptides

The theoretical conformational analysis of the biologically active RGD-containing pentapeptide cyclo(-Arg-Gly-Asp-Phe-DVal-), an inhibitor of laminin P1 interaction with its receptor, was performed. The space of permissible torsional angles of the backbone of the molecule was studied by the Monte Carlo method. From the large number of predicted low-energy conformers with various packings of the cyclic moiety of this pentapeptide, only those were selected that corresponded to stable structures of the model linear tripeptide Ac-Ala-Gly-Asp-NHMe. This peptide simulated the spatial possibilities of the backbones of RGD-containing fragments of laminin, vitronectin, and fibronectin. We selected several dozen structures that may be potential biologically active conformers, but only a few of them were capable of forming stable intramolecular hydrogen bonds. We assumed that a biologically active conformer of cyclo(-Arg-Gly-Asp-Phe-DVal-) can be present in significant amounts in an equilibrium mixture in solution along with other conformers without necessarily dominating among them.     

Metastable and stable states of xanthan polyelectrolyte complexes studied by atomic force microscopy

The compaction of the semiflexible polysaccharide xanthan with selected multi- and polyvalent cations was studied. Polyelectrolyte complexes prepared at concentrations of 1-2 microg/ml were observed by tapping mode atomic force microscopy. High-molecular-weight xanthan compacted with chitosan yields a blend of mainly toroidal and metastable structures and a small fraction of rod-like species. Polyelectrolyte complexes of xanthan with polyethylenimine and trivalent chromium yielded similar structures or alternatively less well packed species. Racquet-type morphologies were identified as kinetically trapped states occurring on the folding path toward the energetically stable state of the toroids. Thermal annealing yielded a shift of the distribution of xanthan-chitosan morphologies toward this stable state. Ensembles of toroidal and rod-like morphologies of the xanthan-chitosan structures, collected using an asphericity index, were analyzed. The mean height of the toroids increased upon heating, with a selective increase in the height range above 2 nm. It is suggested that the observed metastable structures are formed from the high-molecular-weight fraction of xanthan and that these are driven toward the toroidal state, being a low-energy state, following annealing. Considered a model system for condensation of semiflexible polymers, the compaction of xanthan by chitosan captures the system at various stages in the folding toward a low-energy state and thus allows experimental analyses of these intermediates and their evolution.