Semi empirical calculations of cyclo-(L-threonyl-L-histidyl) conformations.

The conformations of cyclo-(L-Thr-L-His) have been calculated by semi-empirical method without taking account on the solvent. The Thr side chain is folded above the DKP ring with $\text{χ}{}^{\mathrm{I}}{}_1\text{= 60°}$; this conformation seems to be due to a specific interaction of the hydroxylated side chain with the DKP ring. The His side chain can be folded in order to interact with the Thr side chain. In the open forms, the His side chain interacts with the peptide backbone. The most stable conformations are the folded forms in which the unprotonated imidazole ring is in the N^ε-H^ε tautomeric form.     

Synthesis, crystal structure and molecular conformation of N-Ac-dehydro-Phe-L-Val-OH.

The peptide N-Ac-dehydro-Phe-L-Val-OH (C16H20N2O4) was synthesized by the usual workup procedure. The peptide crystallizes from its solution in acetonitrile at 4 degrees in hexagonal space group P6(5) with a = b = 11.874(2)A, c = 21.856(9) A, V = 2668(1) A3, Z = 6, dm = 1.151(3) g cm-3, dc = 1.136(4) g cm-3, CuK alpha = 1.5418 A, mu = 0.641 mm-1, F(000) = 972, T = 293 K. The structure was solved by direct methods and refined by least-squares procedure to an R value of 0.074 for 1922 observed reflections. In the dehydro-residue, the C1 alpha-C1 beta distance is 1.35(1) A while the bond angle C1 alpha-C1 beta-C1 gamma is 131.2(9) degrees. The backbone torsion angles are: omega 0 = 172(1) degrees, phi 1 = -60(2) degrees, psi 1 = -31(2) degrees, omega 1 = -179(1) degrees, phi 2 = 59(2) degrees. These values suggest that the peptide tends to adopt an alternating right-handed and left-handed helical conformation. The side chain torsion angles are: chi 1(1) = -6(2) degrees, chi 1(2.1) = -1(2) degrees, chi 1(2.2) = -178(2) degrees, chi 2(1.1) = 63(2) degrees and chi 2(1.2) = -173(1) degrees. These values show that the side chain of dehydro-Phe is planar whereas the valyl side chain adopts a sterically most preferred conformation. The molecules, linked by intermolecular hydrogen bonds and van der Waals forces, are arranged in helices along the c-axis. The helices are held side-by-side by van der Waals contacts.     

Structure and conformation of peptides containing the sulfonamide junction. II. Synthesis and conformation of cyclo[-MeTau-Phe-DPro-]

By applying the method of amino-acyl incorporation to sulfonamido peptides, cyclo(-MeTau-Phe-DPro-) 3 has been synthesized in high yield starting from Z-MeTau-Phe-Pro-OH. The crystal structure and the molecular conformation of 3 have been determined. Crystals are orthorhombic, s.g. P2(1)2(1)2(1), with a = 5.454, b = 13.486, c = 24.025 A. The structure has been solved by direct methods and refined to R = 0.039 for 1974 reflections with I greater than 1.5 sigma (I). The 10-measured cyclopeptide adopts a backbone conformation in the crystals characterized by Phe-DPro and DPro-MeTau peptide bonds in trans and cis conformation, respectively. Both the peptide bonds deviate significantly from planarity and the corresponding [delta omega[ values are ca. 12 degrees. The sulfonamide SO2NH junction adopts a cisoidal conformation with a C alpha 1-S1-N2-C alpha 2 torsion angle of 70.8 degrees. 13C n.m.r. data show that the trans geometry at the Phe-DPro junction found in the crystals is retained in DMSO solution. The 10-membered ring of 3 is characterized by a pseudo mirror-plane passing through the Phe nitrogen and the DPro carbonylic carbon. The DPro ring adopts a half-chair conformation. The Phe side chain conformation corresponds to the statistically most favored g- rotamer (chi 1 = -68.6 degrees). The crystal packing is characterized by a weak intermolecular hydrogen bond between NH group and the MeTau O1' oxygen.     

Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine.

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".     

Pulse fluorometry of cyclo-(glycyl-L-tryptophyl).

The fluorescence of cyclo-(glycyl-L-tryptophyl) in trimethyl phosphate has been studied in a temperature range varying from room temperature to -85 degrees C. At room temperature, the fluorescence decay is the sum of two exponentials, the relative amplitude of which depends on the emission wavelength. This can be explained by the presence of the two following emitting molecular states: on one hand the unfolded state, the fluorescence decay time and the emission spectrum of which are close to these of skatole; on the other hand the folded state which has a shorter decay time and a blue-shifted spectrum. By lowering the temperature, the fluorescence spectrum shifts to the blue, while the skatole spectrum shifts to the red. This behavior corresponds to an increase of the folded conformation concentration in agreement with the NMR results. Furthermore the rate of exchange between the folded and the unfolded conformations decreases. Accordingly the wavelength dependence of the fluorescence decay lessens. There are two possible values of the conformational angle x2 differing by 180 degrees, which correspond to the folded state; due to the indole asymmetry, the interactions between the indole and diketopiperazine rings differ in these conformers. Consequently the fluorescence decay remains biexponential even at -85 degrees C.     

Effects of proline ring conformation on theoretical pi-pi* absorption and CD spectra of helical poly(L-proline) forms I and II

Absorption and CD spectra of the pi-pi* transition near 200 nm are calculated for helical (Pro)10 forms I and II with a variable proline ring conformation characterized by torsion angle chi 2 in the range -60 degrees to 60 degrees. The spectra for poly(Pro) I are not sufficiently sensitive to chi 2 to suggest a preferred ring conformation. The spectra for poly(Pro) II are more sensitive to chi 2, and suggest preferred ring conformations near either or both of the chi 2 regions -50 +/- 10 degrees and 50 +/- 10 degrees.     

Synthesis, crystal structure, and molecular conformation of peptide N-Boc-L-Pro-dehydro-Phe-L-Gly-OH

The peptide N-Boc-L-Pro-dehydro-Phe-L-Gly-OH was synthesized by the usual workup procedure and finally coupling the N-Boc-L-Pro-dehydro-Phe to glycine. The peptide crystallizes in monoclinic space group P2(1) with a = 8.951(4) A, b = 5.677(6) A, c = 21.192(11) A, beta = 96.97(4) degrees, V = 1069(1) A3, Z = 2, dm = 1.295(5) Mgm-3, and dc = 1.297(4) Mgm-3. The structure was determined by direct methods using SHELXS86. The structure was refined by the block-diagonal least-squares procedure to an R value of 0.074 for 1002 observed reflections. The C alpha 2-C beta 2 distance of 1.33(2) A is an appropriate double bond length. The angle C alpha 2-C beta 2-C gamma 2 is 133(1) degrees. The peptide backbone torsion angles are theta 1 = -167(1) degrees, omega 0 = 179(1) degrees, phi 1 = -48(1) degrees, psi 1 = 137(1) degrees, omega 1 = 175(1) degrees, phi 2 = 65(2) degrees, psi 2 = 15(2) degrees, omega 2 = -179(1) degrees, and phi 3 = -166(1) degrees. These values show that the Boc group has a trans-trans conformation while the peptide backbone adopts a beta-turn II conformation, which is stabilized by an intramolecular hydrogen bond of length of 3.05(1) A. The structures of dehydro-Phe containing peptides suggest that the dehydro-Phe promotes the beta-turn II conformation. The five-membered pyrrolidine ring of the Pro residue adopts an ideal C gamma-exo conformation with torsion angles chi 1(1) = -24(1) degrees, chi 2(1) = 34(1) degrees, chi 3(1) = -30(1) degrees, chi 4(1) = 15(1) degrees, and theta 0(1) = 6(1) degrees. The side-chain torsion angles in dehydro-Phe are chi 1(2) = -1(2) degrees, chi 2,1(2) = -176(1) degrees, and chi 2,2(2) = 8(2) degrees. The plane of C alpha 2-C beta 2-C gamma 2 is rotated with respect to the plane of the phenyl ring at 7(1) degrees, which indicates that the atoms of the side chain of dehydro-Phe are essentially coplanar. The molecules form a 2(1) screw axis related hydrogen-bonded rows along the b axis.     

Statistical and energetic analysis of side-chain conformations in oligopeptides

The distributions of side-chain conformations in 258 crystal structures of oligopeptides have been analyzed. The sample contains 321 residues having side chains that extend beyond the C beta atom. Statistically observed preferences of side-chain dihedral angles are summarized and correlated with stereochemical and energetic constraints. The distributions are compared with observed distributions in proteins of known X-ray structures and with computed minimum-energy conformations of amino acid derivatives. The distributions are similar in all three sets of data, and they appear to be governed primarily by intraresidue interactions. In side chains with no beta-branching, the most important interactions that determine chi 1 are those between the C gamma H2 group and atoms of the neighboring peptide groups. As a result, the g- conformation (chi 1 congruent to -60 degrees) occurs most frequently for rotation around the C alpha-C beta bond in oligopeptides, followed by the t conformation (chi 1 congruent to 180 degrees), while the g+ conformation (chi 1 congruent to 60 degrees) is least favored. In residues with beta-branching, steric repulsions between the C gamma H2 or C gamma H3 groups and backbone atoms govern the distribution of chi 1. The extended (t) conformation is highly favored for rotation around the C beta-C gamma and C gamma-C delta bonds in unbranched side chains, because the t conformer has a lower energy than the g+ and g- conformers in hydrocarbon chains. This study of the observed side-chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations.     

Effect of conformation on the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH to its cyclic imide degradation product.

The objective of this study was to explain the increased propensity for the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH (1), a vitronectin-selective inhibitor, to its cyclic imide counterpart cyclo-(1,7)-Gly-Arg-Gly-Asu-Ser-Pro-Asp-Gly-OH (2). Therefore, we present the conformational analysis of peptides 1 and 2 by NMR and molecular dynamic simulations (MD). Several different NMR experiments, including COSY, COSY-Relay, HOHAHA, NOESY, ROESY, DQF-COSY and HMQC, were used to: (a) identify each proton in the peptides; (b) determine the sequential assignments; (c) determine the cis-trans isomerization of X-Pro peptide bond; and (d) measure the NH-HCalpha coupling constants. NOE- or ROE-constraints were used in the MD simulations and energy minimizations to determine the preferred conformations of cyclic peptides 1 and 2. Both cyclic peptides 1 and 2 have a stable solution conformation; MD simulations suggest that cyclic peptide 1 has a distorted type I beta-turn at Arg2-Gly3-Asp4-Ser5 and cyclic peptide 2 has a pseudo-type I beta-turn at Ser5-Pro6-Asp7-Gly1. A shift in position of the type I beta-turn at Arg2-Gly3-Asp4-Ser5 in peptide 1 to Ser5-Pro6-Asp7-Gly1 in peptide 2 occurs upon formation of the cyclic imide at the Asp4 residue. Although the secondary structure of cyclic peptide 1 is not conducive to succinimide formation, the reaction proceeds via neighbouring group catalysis by the Ser5 side chain. This mechanism is also supported by the intramolecular hydrogen bond network between the hydroxyl side chain and the backbone nitrogen of Ser5. Based on these results, the stability of Asp-containing peptides cannot be predicted by conformational analysis alone; the influence of anchimeric assistance by surrounding residues must also be considered.     

Serine and threonine residues bend alpha-helices in the chi(1) = g(-) conformation

The relationship between the Ser, Thr, and Cys side-chain conformation (chi(1) = g(-), t, g(+)) and the main-chain conformation (phi and psi angles) has been studied in a selection of protein structures that contain alpha-helices. The statistical results show that the g(-) conformation of both Ser and Thr residues decreases their phi angles and increases their psi angles relative to Ala, used as a control. The additional hydrogen bond formed between the O(gamma) atom of Ser and Thr and the i-3 or i-4 peptide carbonyl oxygen induces or stabilizes a bending angle in the helix 3-4 degrees larger than for Ala. This is of particular significance for membrane proteins. Incorporation of this small bending angle in the transmembrane alpha-helix at one side of the cell membrane results in a significant displacement of the residues located at the other side of the membrane. We hypothesize that local alterations of the rotamer configurations of these Ser and Thr residues may result in significant conformational changes across transmembrane helices, and thus participate in the molecular mechanisms underlying transmembrane signaling. This finding has provided the structural basis to understand the experimentally observed influence of Ser residues on the conformational equilibrium between inactive and active states of the receptor, in the neurotransmitter subfamily of G protein-coupled receptors.     

Conformation of histidine model peptides. I. Conformational energy calculations for L-alanyl-L-histidine diketopiperazine

Semiempirical conformational energy calculations were carried out for the cyclic dipeptide L -alanyl-L -histidine diketopiperazine. The results indicate that electrostatic effects are probably significant in determining the conformation assumed by this molecule. When the imidazole group is in its uncharged state the most stable conformations of the molecule are those with the imidazole ring folded over the diketopiperazine ring (χ¹ = 60°). Upon protonation of the imidazole group the folded conformation may be destabilized relative to conformations characterized by χ¹ positions near 180°.     

Crystal structure and conformation of 5-fluorouridine: conformational preferences for 5-fluorinated pyranosides

Crystals of 5-fluorouridine (5FUrd) have unit cell dimensions a = 7.716(1), b = 5.861(2), c = 13.041(1)A, alpha = gamma = 90 degrees, beta = 96.70 degrees (1), space group P2(1), Z = 2, rho obs = 1.56 gm/c.c and rho calc = 1574 gm/c.c The crystal structure was determined with diffractometric data and refined to a final reliability index of 0.042 for the observed 2205 reflections (I > or = 3sigma). The nucleoside has the anti conformation [chi = 53.1(4) degrees] with the furanose ring in the favorite C2'-endo conformation. The conformation across the sugar exocyclic bond is g+, with values of 49.1(4) and -69.3(4) degrees for phi(theta c) and phi (infinity) respectively. The pseudorotational amplitude tau(m) is 34.5 (2) with a phase angle of 171.6(4) degrees. The crystal structure is stabilized by a network of N-H...O and O-H...O involving the N3 of the uracil base and the sugar 03' and 02' as donors and the 02 and 04 of the uracil base and 03' oxygen as acceptors respectively. Fluorine is neither involved in the hydrogen bonding nor in the stacking interactions. Our studies of several 5-fluorinated nucleosides show the following preferred conformational features: 1) the most favored anti conformation for the nucleoside [chi varies from -20 to + 60 degrees] 2) an inverse correlation between the glycosyl bond distance and the chi angle 3) a wide variation of conformations of the sugar ranging froni C2'-endo through C3'-endo to C4'-exo 4) the preferred g+ across the exocyclic C4'-C5' bond and 5) no role for the fluorine atom in the hydrogen bonding or base stacking interactions.     

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.     

Structure and conformation of linear peptides. VIII. Structure of t-Boc-glycyl-L-phenylalanine

The crystal structure of t-Boc-glycyl-L-phenylalanine (C14H22N2O5, molecular weight = 298) has been determined. Crystals are monoclinic, space group P2(1), with a = 7.599(1) A, b = 9.576(2), c = 12.841(2), beta = 97.21(1) degrees, Z = 2, Dm = 1.149, Dc = 1.168 g X cm-3. Trial structure was obtained by direct methods and refined to a final R-index of 0.064 for 1465 reflections with I greater than 1 sigma. The peptide unit is trans planar and is nearly perpendicular to the plane containing the urethane moiety. The plane of the carboxyl group makes a dihedral angle of 16.0 degrees with the peptide unit. The backbone torsion angles are omega 0 = -176.9 degrees, phi 1 = -88.0 degrees, psi 1 = -14.5 degrees, omega 1 = 176.4 degrees, phi 2 = -164.7 degrees and psi 2 = 170.3 degrees. The phenylalanine side chain conformation is represented by the torsion angles chi 1 = 52.0 degrees, chi 2 = 85.8 degrees.     

Crystal structure and molecular conformation of the peptide N-Boc-L-Gly-dehydro-Phe-NHCH3

The peptide N-Boc-L-Gly-dehydro-Phe-NHCH3 was synthesized by the combination of N-Boc-L-Gly-dehydro-Phe azlactone and methylamine. The peptide crystallizes in orthorhombic space group P2(1)2(1)2(1) with a = 5.679(2) A, b = 16.423(9) A, c = 19.198(10) A, V = 1791(2) A3, Z = 4, dm = 1.212(5) Mg m-3, dc = 1.237(1) Mg m-3. The structure was determined by direct methods using SHELXS 86. The structure was refined by full-matrix least squares procedure to an R value of 0.049 for 1509 observed reflections. The molecular dimensions are, in general, in good agreement with the standard values. The bond angle C alpha-C beta-C gamma in the dehydro-Phe residue is 133.6(5) degrees. The peptide backbone torsion angles are theta 1 = -171.4(4) degrees, omega 0 = 178.2(4) degrees, phi 1 = -57.2(6) degrees, psi 1 = 141.2(4) degrees, omega 1 = -174.4(4) degrees, phi 2 = 71.5(6) degrees, psi 2 = 7.2(6) degrees, and omega 2 = -179.8(5) degrees. These values show that the backbone adopts the beta-bend type II conformation. The Boc group has a trans-trans conformation. The side-chain torsion angles in dehydro-Phe are chi 2 = 1.6(9) degrees, chi 2(2, 1) = 0.5(9) degrees, and chi 2(2, 2) = 179.8(6) degrees. The plane of C2 alpha-C2 beta-C2 gamma is rotated with respect to the plane of the phenyl ring at 0.5(6) degrees, which indicates that the atoms of the side chain of the dehydro-Phe residue are essentially coplanar.(ABSTRACT TRUNCATED AT 250 WORDS)     

A novel cytotoxic ternary copper(II) complex of 1,10-phenanthroline and L-threonine with DNA nuclease activity

A novel ternary copper(II) complex, [Cu(phen)(L-Thr)(H2O)](ClO4) (phen=1,10-phenanthroline, L-Thr=L-threonine), has been synthesized and structurally characterized. The complex crystallized in a triclinic system with space group P1 , a=7.526(15) A, b=11.651(2) A, c=12.127(2) A, alpha=115.41(3) degrees , beta=102.34(3) degrees and gamma=91.33(3) degrees . The copper(II) center is situated in a distorted square-pyramidal geometry. At a concentration of 10(-6) mol L(-1), the complex exhibited potent cytotoxic effects against human leukemia cell line HL-60 and human stomach cancer cell line SGC-7901 with inhibition rates of over 90%, however, less pronounced effects were observed for human liver carcinoma cell line BEL-7402 and human non-small-cell lung cancer cell line A-549. The complex was shown to bind DNA by intercalation and cleave pBR322 DNA in the presence of ascorbate.     

Cyclo(L-prolyl-L-N-methylphenylalanyl). Conformation in solution and in the crystal.

Detailed analysis of the proton and carbon-13 NMR spectra of cyclo(L-prolyl-L-N-methylphenylalanyl) in chloroform and methanol in relation to its nonmethylated analog provided information on the conformation of the title compound in solution as well as on the effect of N-methylation and solvation. The X-ray structure of the title compound in the crystalline state showed the same conformational features as the solution structure. The phenyl group folds over the diketopiperazine ring which resembles a flattened half-chair. Both amide bonds are considerably nonplanar. The pyrrolidine ring of proline shows a strong pucker at the ring junction with the largest chi 5 value hitherto observed.     

Resisting degradation by human elastase: commonality of design features shared by 'canonical' plant and bacterial macrocyclic protease inhibitor scaffolds

A previously unexplained difference in the resistance to enzymatic hydrolysis of 11-mer Bowman-Birk-type inhibitors of human leukocyte elastase that differ in P1 is found to correlate with the strength of a particular intramolecular hydrogen bond within the inhibitor. This transannular hydrogen bond stabilizes the side chain of the conserved P2 Thr in a 'canonical' +60 degrees -rotamer chi(1) conformation and thereby directs it for a close interaction with the enzyme's catalytic His. As the implications of this NMR analysis are neither limited to this macrocyclic scaffold derived from plant proteins nor to a particular serine protease, we present a unified analysis with inhibitory bacterial depsipeptides of 7-12 residues in length that share key design features for which we propose communal functional explanations.     

Crystal Structure and Molecular Conformation of the Cyclic Hexapeptide cyclo-(Gly-Aib-Gly)2

We have synthesized and crystallized the cyclic peptide (Gly-Aib-Gly) ₂. Its structure has been determined by conventional X-ray diffracti on methods. In the crystal it adopts a conformation with one β-turn (type I) and its mirror image at the other side of the ring. All conformation al angles are similar to those reported for these amino acid residues. In particular the Aib residue has a conformation intermediate between α- and 3₁₀-helical conformations. The ring is an adequate model for the β-turn conformation. A molecule of formic acid is found in the crystal which shows a very short hydrogen bond with one of the glycine carbonyl groups.     

Structure and conformation of peptides involving prolyl residue. IV. L-Prolyl-L-leucine monohydrate

The dipeptide, L-prolyl-L-leucine monohydrate (C11H20N2O3.H2O, molecular weight, 246.3) crystallizes in the monoclinic space group P2(1), with cell constants: a = 6.492(2)A, b = 5.417(8)A, c = 20.491(5)A, beta = 96.59(2) degrees, Z = 2, Do = 1.15 g/cm3, and Dc = 1.142 g/cm3. The structure was solved by SHELX-86 and refined by full matrix least squares methods to a final R-factor of 0.081 for 660 unique reflections (I greater than 2 sigma (I)) measured on an Enraf Nonius CAD-4 diffractometer (CuK alpha, lambda = 1.5418 A, T = 293 K). The peptide linkage exists in the trans conformation. The pyrrolidine ring exists in the envelope conformation. The values of the sidechain torsion angles are: chi 1 = -59.3(13) degrees, chi 21 = -63.1(16) degrees and chi 22 = 174.8(15) degrees for leucine (C-terminal). The crystal structure is stabilised by a three-dimensional network of N-H ... O, O-H ... O, and C-H ... O hydrogen bonds.