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1.
Conformational preferences of 1,4,7-trithiacyclononane were studied using a highly efficient sampling technique based on local nonstochastic deformations and the MM2(91) force field. The results show that conformers that the molecule adopts in the crystal state were found to be low-energy conformers (LECs) within 5 kcal mol(-1) of the global minimum. A conformation with C1 symmetry was the global minimum and the C3 and C2 conformations were calculated to be 0.03 and 1.78 kcal mol(-1) higher in energy, respectively. The structures were further minimized using Density Functional Theory (DFT) calculations with two different functionals. The C2 and the C1 conformations were found to be LECs with the C3 conformation more than 4.0 kcal mol(-1) above the global minimum. The relative energies and structural ordering obtained using the BP86 functional are in agreement with the previously reported relative energies calculated using second-order Moller-Plesset (MP2) ab initio calculations. With the energy ordering being dependent on the molecular mechanics force field used, the approach of MM-->DFT (searching exhaustively the available conformational space at the MM level followed by generating the energy ordering through DFT calculations) appears to be appropriate for thiacrown ethers.  相似文献   

2.
The tripeptide N-formyl-L-Met-L-Leu-L-Phe-OMe (FMLP-OMe) crystallizes in the orthorhombic system, space group P 2(1)2(1)2(1), with the following unit-cell parameters: a = 21.727, b = 21.836, c = 5.133 A, Z = 4. The structure has been solved and refined to a final R of 0.068 for 1838 independent reflexions with I greater than 2 omega (I). The peptide backbone is folded at the Leu residue (phi L = -67.7, psi L = -49.1 degrees) without intramolecular hydrogen bonds. Considering each peptide plane, the Leu side-chain is oriented on the same side of that of the Phe residue and on the opposite side of that of the Met residue, respectively. The crystal conformation differs from all the other conformations proposed for FMLP-OMe and the anionic form of N-formyl-L-Met-L-Leu-L-Phe-OH (FMLP) in solution accounts for the amphiphilic character of the peptide, giving rise, through intermolecular hydrogen bonds, to a stacking of molecules which could be maintained in the aggregation states experimentally observed in solvents of low polarity. Intramolecular potential energy calculations have been carried out in order to compare the energies of the various backbone conformers.  相似文献   

3.
The conformational preferences of azaphenylalanine-containing peptide were investigated using a model compound, Ac-azaPhe-NHMe with ab initio method at the HF/3-21G and HF/6-31G(*) levels, and the seven minimum energy conformations with trans orientation of acetyl group and the 4 minimum energy conformations with cis orientation of acetyl group were found at the HF/6-31G(*) level if their mirror images were not considered. An average backbone dihedral angle of the 11 minimum energy conformations is phi=+/-91 degrees +/-24 degrees , psi =+/-18 degrees +/-10 degrees (or +/-169 degrees +/-8 degrees ), corresponding to the i+2 position of beta-turn (delta(R)) or polyproline II (beta(P)) structure, respectively. The chi(1) angle in the aromatic side chain of azaPhe residue adopts preferentially between +/-60 degrees and +/-130 degrees, which reflect a steric hindrance between the N-terminal carbonyl group or the C-terminal amide group and the aromatic side chain with respect to the configuration of the acetyl group. These conformational preferences of Ac-azaPhe-NHMe predicted theoretically were compared with those of For-Phe-NHMe to characterize the structural role of azaPhe residue. Four tripeptides containing azaPhe residue, Boc-Xaa-azaPhe-Ala-OMe [Xaa=Gly(1), Ala(2), Phe(3), Asn(4)] were designed and synthesized to verify whether the backbone torsion angles of azaPhe reside are still the same as compared with theoretical conformations and how the preceding amino acids of azaPhe residue perturb the beta-turn skeleton in solution. The solution conformations of these tripeptide models containing azaPhe residue were determined in CDCl(3) and DMSO solvents using NMR and molecular modeling techniques. The characteristic NOE patterns, the temperature coefficients of amide protons and small solvent accessibility for the azapeptides 1-4 reveal to adopt the beta-turn structure. The structures of azapeptides containing azaPhe residue from a restrained molecular dynamics simulation indicated that average dihedral angles [(phi(1), psi(1)), (phi(2), psi(2))] of Xaa-azaPhe fragment in azapeptide, Boc-Xaa-azaPhe-Ala-OMe were [(-68 degrees, 135 degrees ), (116 degrees, -1 degrees )], and this implies that the intercalation of an azaPhe residue in tripeptide induces the betaII-turn conformation, and the volume change of a preceding amino acid of azaPhe residue in tripeptides would not perturb seriously the backbone dihedral angle of beta-turn conformation. We believe such information could be critical in designing useful molecules containing azaPhe residue for drug discovery and peptide engineering.  相似文献   

4.
An X-ray study of 3,20-dioxo-4-pregnene-[16 alpha,17 alpha-d]--2',2'-dimethylthiazolidine (I) and 3 beta-hydroxy-20-oxo-5--pregnene-[16 alpha,17 alpha-d]-2',2'- dimethylthiazolidine (II) has been carried out. Two independent molecules in crystal II have significantly different conformations of the D and E rings, although according to the atom-atom potential calculations the energy of interaction of these molecules with their neighbors in crystal is the same. The calculation of conformational energy of 3,20-dioxo-4-pregnene-[17 alpha,16 alpha-d]-2',2'--dimethyloxathiolane (III) by the molecular mechanics method (MMM) indicates a possibility of existence of two similar conformers also for this molecule. The MMM calculation shows also that the conformation of molecule III (as well as progesterone) with the 17 beta-acetyl group torsion angle C(16)C(17)C(20)0(20) close to -120 degrees is possible.  相似文献   

5.
The protocol of conformational analysis applied here to ribonucleotide oligomers combines conformational search in the space of torsion angles and energy minimization using the AMBER4.1 force field with a continuum treatment of electrostatic solute-solvent interactions. RNA fragments with 5′-GGGCGNNAGCCU-3′ sequences commonly fold into hairpins with four-membered loops. The combinatorial search for acceptable conformations using the MC-SYM program was restricted to loop nucleotides and yielded roughly 1500 structures being compatible with a double-stranded stem. After energy minimization by the JUMNA program (without applying any experimental constraints), these structures converged into an ensemble of 74 different conformers including 26 structures which contained the sheared G-A base pair observed in experimental studies of GNRA tetraloops. Energetic analysis shows that inclusion of solvent electrostatic effects is critically important for the selection of conformers that agree with experimentally determined structures. The continuum model accounts for solvent polarization by means of the electrostatic reaction field. In the case of GNRA loop sequences, the contributions of the reaction field shift relative stabilities towards conformations showing most of the structural features derived from NMR studies. The agreement of computed conformations with the experimental structures of GAAA, GCAA, and GAGA tetraloops suggests that the continuum treatment of the solvent represents a definitive improvement over methods using simple damping models in electrostatic energy calculations. Application of the procedure described here to the evaluation of the relative stabilities of conformers resulting from searching the conformational space of RNA structural motifs provides some progress in (non-homology based) RNA 3D-structure prediction. Received: 20 January 1999 / Revised version: 4 June 1999 / Accepted: 10 June 1999  相似文献   

6.
The synthesis and the solution behavior of the linear peptides containing a beta-homo (beta-H) leucine residue-Boc-Leu-beta-HLeu-Leu-OMe, Boc-beta-HLeu-Leu-beta-HLeu-Leu-OMe, and Boc-Leu-beta-HLeu-Leu-beta-HLeu-Leu-OMe-as well as the solid structure of the tripeptide, are reported. The conformational behavior of the peptides was investigated in solution by two-dimensional nmr. Our data support the existence in solution with different families of conformers in rapid interchange. The crystals of the tripeptide are orthorhombic, space group P2(1)2(1)2, with a = 15.829(1) A, b = 29.659(1) A, c = 6.563(1) A, and Z = 4. The structure has been solved by direct methods and refined to final R1 and wR2 indexes of 0.0530 and 0.1436 for 2420 reflections with I > 2sigma(I). In the solid state, the tripeptide does not present intramolecular H bonds, and the peptide backbone of the two leucine residues adopts a quasi-extended conformation. For the beta-HLeu residue, the backbone conformation is specified by the torsion angles straight phi(2) = -120.9(4) degrees, mu(2) = 56.7(4) degrees, psi(3) = -133.2(4) degrees. The side chains of the three residues assume the same conformation (g(-), g(-), trans), and all peptide bonds, except the urethane group at the N-terminus, are in the trans conformation. Preliminary conformational energy calculations carried out on the Ac-NH-beta-HAla-NHMe underline that the conformations with mu angle equal to 180 degrees and 60 degrees assume lower energy with respect to the others. In addition, we found a larger conformational freedom for the psi angle with respect to the straight phi angle.  相似文献   

7.
The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.  相似文献   

8.
Endomorphin-2 (EM-2) is a putative endogenous mu-opioid receptor ligand. To get insight into the important role of C-terminal amide group of EM-2, we investigated herein a series of EM-2 analogs by substitution of the C-terminal amide group with -NHNH(2), -NHCH(3), -N(CH(3))(2), -OCH(3), -OCH(2)CH(3), -OC(CH(3))(3), and -CH(2)-OH. Their binding affinity and bioactivity were determined and compared. Despite similar (analogs 1, 4, and 7) or decreased (analogs 2, 3,5, and 6) mu affinity in binding assays, all analogs showed low guinea pig ileum (GPI) and mouse vas deferens (MVD) potencies compared to their parent peptide. Interestingly, as for analogs 2 and 3 (a single and double N-methylation of C-terminal amide), the potency order with the K(i) (mu) values was 2>3; for the C-terminal esterified analogs 4-6, the potency order with the K(i) (mu) values was 4>5>6. Thus, we concluded that the steric hindrance of C-terminus might play an important role in opioid receptor affinity. We further investigated the conformational properties of these analogs by 1D and 2D (1)H NMR spectroscopy and molecular modeling. Evaluating the ratios of cis- and trans-isomers, aromatic interactions, dihedral angles, and stereoscopic views of the most convergent conformers, we found that modifications at the C-terminal amide group of EM-2 affected these analog conformations markedly, therefore changed the opioid receptor affinity and in vitro bioactivity.  相似文献   

9.
The crystal structure of a tetrahydrated form of L-arginyl-glycyl-L-aspartic acid (RGD), the consensus sequence for binding of fibrinogen to cell surface receptors, has been determined from diffractometer data. The tripeptide was crystallized in double zwitterionic form via hanging drop vapor diffusion experiments at a pH near 6.5. The orthorhombic unit cell contains four formula units in space group P2(1)2(1)2(1) with lattice parameters a = 4.852(4), b = 11.376(3), c = 34.083(8)A at RT. The structure was solved by direct methods and refined to a final R = 0.067 based upon 1345 observations with I greater than or equal to 2 sigma(I). Peptide bonds both are trans, omega 2 = 174.2(6) degrees and omega 3 = -169.3(6) degrees. The backbone bends at glycine with phi 2 = -85.5(8) degrees. One of the water molecules sits between the arginyl side chain and the C-terminal carboxylate, forming an intramolecular hydrogen bond to the glycyl carboxyl and linking adjacent molecules through two other H-bond interactions. Comparison of the structure to RGD sequences extracted from 3-D protein structures reveals a diversity of conformations for this tripeptide sequence.  相似文献   

10.
Lee SG  Breeze L  Bohn RK  True NS 《Chirality》2002,14(2-3):232-240
Allyl nitrite, O=NOCH(2)CH=CH(2), can exist in conformations which include syn (S) and anti (A) configurations of O=N-O-C, anti or gauche (G) configurations of N-O-C-C, and syn or skew (Sk) configurations of O-C-C=C. Four of them have been observed and characterized by their microwave spectra and quantum chemical calculations to have AGSk' (0.0 kcal/mol), AGSk (0.2(2) kcal/mol), SASk (0.2(2) kcal/mol), and SAS (0.9(2) kcal/mol) configurations about the three successive dihedral angles. All four are observed in microwave studies of the vapor at 300 and 200 K and the first three are seen in pulsed-jet beams. The SAS form apparently relaxes to the SASk conformer during expansion in the pulsed-jet. Quantum chemical calculations reveal that the two possible conformers with anti-anti configurations of the O=N-O-C-C fragment, AAS and AASk, are transition states, unstable configurations, or of marginal stability, consistent with structures observed in this and other previously studied alkyl nitrites. The remaining four possible conformers are predicted to have relative energies within 1 kcal/mol of the observed conformers but were not observed experimentally.  相似文献   

11.
Ab initio MO calculations were carried out at the MP2/6-311++G(d,p) level to investigate the conformational energy of 2-substituted oxanes and 1,3-dioxanes. It has been found that the Gibbs free energies of the axial conformers are smaller than those of the corresponding equatorial conformers in every case when the 2-substituent Z is electron withdrawing (OCH(3), F, Cl, Br). The difference in Gibbs energy between the equatorial and axial conformers DeltaG(eq-ax) increases from Z=OCH(3) to F, Cl, and then to Br. In the axial conformers, the interatomic distance between Z and the axial C-H, separated by four covalent bonds, has been found to be appreciably shorter than the van der Waals distance, suggesting the importance of the five-membered CH/n (CH/O or CH/halogen) hydrogen bond in stabilizing these conformations. Natural bonding orbital (NBO) charges of the relevant atoms have been shown to be different between the two conformers: more positive for H and more negative for C in the axial conformers than in the corresponding equatorial conformers. In view of the above findings, we suggest that the CH/n hydrogen bond plays an important role in stabilizing the axial conformation in 2-substituted oxanes and 1,3-dioxanes, and by implication, in the anomeric effect in carbohydrate chemistry.  相似文献   

12.
Considerable clinical interest in neuropeptides and peptide hormones has stimulated recent research and development of peptide-based drugs. This process differs from most classical drug discovery procedures because peptide molecules have considerable inherent flexibility. In the present paper, to identify lowest energy and metastable conformers for drug design, and to develop protocols for such studies, conformational search algorithms, incorporating empirical energy calculations, have been applied in the analysis of the peptide oxytocin. Energy minimization in torsion angle space was carried out from a variety of starting conformations, including published structures, in all-atom mode and all with distance constraints for disulphide bond formation. The energy-minimized conformations have been further optimized by a mapping method. Complementary simulations have been performed in united-atom mode and a model representing the effects of water using dummy sites has been developed and tested for this representation. Several of the preferred conformers together with de novo conformations have been used as starting points in molecular dynamics simulations; 28 low potential energy conformations were located at a temperature of 4 K. Conformations are analysed to identify hydrogen bonds, phi-psi angle distributions and the RMS values relative to the X-ray structure of deamino-oxytocin. The modelled structure of lowest energy in the molecular mechanics calculations was also that of least RMS deviation from the crystal structure; whilst structures of lower energy but larger deviation were identified by molecular dynamics techniques. A metastable structure has been identified which satisfies existing criteria for the "active form", and this model is tested by a theoretical residue-substitution technique, to provide clues on the agonist/antagonist relationship at the atomic level.  相似文献   

13.
The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2(1),2(1),2(1), with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)A. V = 5,884 (3) A3, Z = 8, R = 0.086. VALa crystallises in space group P2(1) with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) A, beta = 95.84 (8) degrees , V = 3,040(4) A3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel beta-sheet arrangement in both the structures. Several of the Calpha hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand. An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and alphaL conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed alphaR conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.  相似文献   

14.
4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained alpha-amino acid residue that exhibits promising conformational characteristics, i.e., helical and beta-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The C(alpha) carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 3(10), and alpha(L) helical structures.  相似文献   

15.
Empirical conformational energy calculations have been carried out on the molecule retro-all-D -methionine enkephalin. Low-energy conformers were found by energy minimization and conformational search procedures. The lowest energy conformers wee found toi have some stereochemical relationship to the calculated normal met-enkephalin conformers, but they were not retro-all-D -equivalent to the Met-enkephalin structures. The retro-all-D -equivalent conformations were ~10 kcal/mol higher energy than the low-energy conformers found here. A structural comparison between the retro-all-D -conformers and the met-enkephalin conformers shows hat one cannot rely solely on topochemical analysis to predict biological activity for linear retro-all-D -peptides.  相似文献   

16.
17.
A crystal of the potent opioid agonist ketobemidone [1-methyl-4-(3-hydroxyphenyl)-4-propionylpiperidine] HCl was analyzed by X-ray crystallography. The crystal was monoclinic, space group P21/n with four molecules in the unit cell. In agreement with MM2 calculations (J. Med. Chem. 25:1127–1133, 1982), the crystal contains mirror image conformers in which the phenyl ring is equatorial to the piperidine ring. The conformers are enantiomers since they are not superimposable. One conformer is predicted to be responsible for the typical morphine-like activity of the compound since it closely matches the preferred conformer of the morphine-like (+)-phenylmorphan whereas the other conformer resembles the preferred conformers of (+)-β-prodine and (?)-phenylmorphan which have atypical opioid properties and/or structure–activity relationships. The importance of considering the conformational enantiomers of a nonchiral receptor ligand in centrosymmetric crystal structures is emphasized. © 1993 Wiley-Liss, Inc.  相似文献   

18.
A structural feature of aureobasidins, cyclic depsipeptide antibiotics produced by Aureobasidium pullulans R106, is the N-methylation of four out of seven amide bonds. In order to investigate possible relationship between the molecular conformation and the amide N-methylation, aureobasidin A (AbA), which exhibits the potent antifungal activity, was subjected to X-ray crystal analysis. The crystal, recrystallized from ether (orthorhombic, space group P2(1)2(1)2(1), a = 21.643 (3) A, b = 49.865(10) A, c = 12.427 (1) A, z= 8), contained two independent conformers per asymmetric unit and they took on a similar arrowhead-like conformation. The conformation consisted of three secondary structures of antiparallel beta-sheet, and beta- and gamma-turns, and was stabilized by three intramolecular and transannular N-H O=C hydrogen bonds. The beta-hydroxy-N-methyl-l-valine residue, which is indispensable for its bioactivity, was located at the tip of the corner. Since a nearly identical conformation has been observed for aureobasidin E, a related cyclic depsipeptide, this arrowhead-like conformation may be energetically stable and important for biological activity. The contribution of the amide N-methylation to the conformation was investigated by model building and energy calculations. The energy-minimizations of AbA analogs, in which some (one to four) of four N-methylated amide bonds were replaced with usual amide bond, led to some conformers which are fairly different from the arrowhead form of AbA, although they are stabilized by three intramolecular N-H...O=C hydrogen bonds. This result explains the reason why four out of the seven amide bonds have to be methylated to manifest biological activity, i.e. the high N-methylation of aureobasidin is necessary to form only one well-defined conformation.  相似文献   

19.
The crystal and molecular structure of a ribavirin acyclic analogue, 1-(2-hydroxyethoxymethyl)-1,2,4-triazole-3-carboxamide, has been determined by X-ray diffraction method. The space group is P1, unit cell parameters: a = 5,237, b = 6,960, c = 11,483 A, alpha = 93,89, beta = 97,43, gamma = 94,26 degrees; Z = 2. The structure was solved by the direct method and refined by least-squares procedure to R = 3.7%. Two molecular conformers statistically coexist in the unit cell, differing in the hydroxyethoxymethyl group conformation. Trans-conformation about O4'-C4' bond and gauche about C4'-C5' bond are observed in both molecules. C1'-O4' bond is approximately perpendicular to the aglicon.  相似文献   

20.
Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6(1)22 and two structures in space groups P2(1)2(1)2(1) and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P2(1). While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Calpha rmsd of 0.54-0.79 A) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Calpha rmsd values of 0.28-0.37 A). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure.  相似文献   

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