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PubMed1991

[Conformational analysis of N-terminal O-glycopeptide sequences of interleukin-2].

The preferred conformations of eight O-glycopeptide sequences from the N-terminus of interleukin-2 containing two to ten amino acids, monoglycosylated at Thr3 with a 2-acetamido-2-deoxy-alpha-D-galactopyranosyl group, were determined by means of n.m.r. spectroscopic methods. The preferred conformation of the N-terminal sequence, L-Ala-L-Pro-[alpha-D-GalpNAc-(1----3)]-L-Thr-L-Ser, including the O-glycosidically linked 2-acetamido-2-deoxy-alpha-D-galactopyranosyl group is not substantially influenced by the linkage of additional amino acids at the C-terminal end. Extended conformations were observed for all peptide units. Measurements of the relaxation times of the 13C atoms showed that the 2-acetamido-2-deoxy-D-galactose bound to the central amino acids has the lowest mobility, whereas the terminal amino acid residues and peptide side-chains are flexible. Calculations with the force-field program AMBER yielded conformations of minimized energies that were in good agreement with the n.m.r. spectroscopic data. This was only true when n.m.r. parameters that can be used as starting values for the calculations were available. Comparison with a nonglycosylated, N-terminal tetrapeptide sequence analog did not suggest changes in the peptide conformation when Thr3 is glycosylated with a 2-acetamido-2-deoxy-alpha-D-galactopyranosyl group.

Amino Acid Sequence↗
PubMed2002

A novel class of endothelin-A receptor antagonists, (R)-2-(benzo[1,3]dioxol-5-yl)-6-isopropyloxy-2H-chromene-3-carboxylic acids (S-1255). Conformational analysis of basic structure, crucial for ET(A) antagonism, in solution and solid states.

Conformational studies of potent and selective endothelin-A (ET(A)) receptor antagonists, 4-substituted (R)-2-(benzo[1,3]-dioxol-5-yl)-6-isopropoxy-2H-chromene-3-carboxylic acids, are reported. X-ray crystallography and NMR studies of the 4-anisyl derivative 2 (S-1255), the stable atropisomers 3 and the 4-n-butyl derivative 4 reveal that the A-, B- and C-rings in these compounds adopt a L-like conformation in both solution and solid states. Molecular mechanics calculation shows that this L-like conformation is an inevitable conformation as determined by intramolecular steric repulsions. These 2H-chromene derivatives bound to an ET(A) receptor with IC(50) values of less than 1 nM, whereas the dihydro compounds 7 and 9 not having the L-like conformation showed weaker affinities. These results suggest that the L-like conformation is specifically recognized by the active site of the ET(A) receptor. The roles of the L-like conformation in the receptor binding are discussed.

Acids, Heterocyclic↗
PubMed1986

Conformational analysis of cyclic partially modified retro-inverso enkephalin analogues by proton NMR.

The conformations of five cyclic retro-inverso enkephalin analogues have been probed by proton NMR. After assignment of peaks, intramolecularly hydrogen-bonded amide protons were detected by temperature perturbation. Carbonyl hydrogen-bond acceptors were surmised from the computer simulations of minimum energy conformations of Hassan and Goodman [Hassan, M., & Goodman, M. (1986) Biochemistry (preceding paper in this issue)]. Hydrogen bonds were identified in dimethyl-d6 sulfoxide solutions and monitored as H2O was added. One hydrogen bond was observed in each of the retro-inverso-modified enkephalin analogues although in the parent analogue H-Tyr-c-(D-A2bu-Gly-Phe-Leu) two were detected. The change in solvent altered the conformations of two of the analogues.

Amino Acid Sequence↗
PubMed1978

Conformational analysis of the molecule luteinizing hormone-releasing hormone. 3. Analogue inhibitors and antagonists.

Conformational energy calculations have been carried out on analogues of luteinizing hormone-releasing hormone which have been shown to be potent inhibitors of the release of luteinizing hormone and follicle-stimulating hormone. The analogues included in this study have D-amino acid substitutions in the 2 and/or 3 positions, such as [D-X2]-LH-RH, [D-X2,D-Y3]-LH-RH, [D-X2,Pro3]-lh-rh, and [D-X2,Leu3]-LH-RH. A configurational property which was common to the low-energy conformers of all the analogues is the directional change of the cis-peptide bond of the pyroglutamate ring. Further, there was no overall structural change in the analogues relative to the conformation of native LH-RH, and the orientation of the aromatic side chains relative to one another remained the same throughout this series of analogues.

Gonadotropin-Releasing Hormone↗
PubMed1995

Optimization of lyophilization conditions for recombinant human interleukin-2 by dried-state conformational analysis using Fourier-transform infrared spectroscopy.

PURPOSE: Examination of the dried-state conformation of interleukin-2 (IL-2) was used to determine the pH conditions and stabilizers that provide optimal storage stability for the lyophilized product. METHODS: Fourier-transform infrared spectroscopy and accelerated stability studies which examined solubility, aggregate formation, and covalent cross-linking were used. RESULTS: Varying the pH in the absence of excipients resulted in dramatic differences in the dried state conformation of IL-2. At pH 7, IL-2 unfolds extensively upon lyophilization while at pH below 5 it remains essentially native. Additional unfolding was observed upon incubation at elevated temperatures. A strong direct correlation between the retention of the native (aqueous) structure during freeze-drying and enhanced stability is demonstrated. IL-2 prepared at pH 5 is approximately an order of magnitude more stable than at pH 7 with regard to formation of soluble and insoluble aggregates. A similar pH profile was observed in the presence of excipients, although the excipients alter the overall stability profile. Additional accelerated stability studies examined the stabilizers necessary for optimal stability. CONCLUSIONS: Excipients with the capacity to substitute for water upon dehydration better preserve the native structure resulting in enhanced stability. Those that have high glass transition temperatures provide the highest level of stability during storage, although they do not prevent dehydration induced unfolding.

Drug Stability↗
PubMed1995

Conformational analysis and biological activity of leptocarpin and leptocarpin acetate.

This paper deals with the conformational study in solution of leptocarpin, a germacranolide with the heliangolide structure isolated from Leptocarpha rivularis D.C. The results obtained agree with the single crystal X-ray diffraction studies. Leptocarpin and leptocarpin acetate show 50% inhibition of [35S]-methionine uptake without affecting the (methyl-3H)thymidine and (5,6-3H)uridine incorporation, when assayed in HeLa cells.

4-Butyrolactone↗
PubMed1987

Conformational analysis of pepstatin and related renin inhibitors by 400 MHz 1H n.m.r. spectroscopy.

The conformational behaviour of pepstatin (Iva-Val-Val-Sta-Ala-Sta) and of two derived renin inhibitors, Boc-Phe-Nle-Sta-Ala-Sta-OMe, 1, and Boc-Phe-Nle-X-Ala-Sta-OMe, 2 (X = -NH-CH(iPr)-CHOH-CH2-CO-) was assessed in DMSO-d6 at various temperatures and in deuteriopyridine at -35 degrees. Complete assignment of almost all proton signals was achieved by 2D COSY, 2D NOESY and selective NOE experiments. The three compounds show similar extended conformations in both solvents, with the hydrophobic lateral chains extending away from the peptide backbone. In the case of pepstatin the solvated conformation is closely related to the structure found in the crystal of the pepstatin-Rhizopus chinensis complex. Strong NOE effects and precise determination of vicinal coupling constants show the lack of large structural differences between 1 and 2 at the level of the internal Sta or X residues, which are assumed to interact with the aspartyl residues of the renin active-site. This suggests that the 100-fold lower inhibitory potency of 2 is mainly due to unfavorable close contacts of the beta-branched residue X with constituent amino acids of the enzyme.

Dimethyl Sulfoxide↗
PubMed2006

Conformational analysis and vibrational assignments of 2,2,3,3-tetrafluoro-1-propanol CHF2CF2CH2OH as three-rotors system.

The conformational stability of 2,2,3,3-tetrafluoro-1-propanol was investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The calculated potential energy curves of the molecule at DFT-B3LYP level were consistent with five distinct minima that correspond to gauche(-)-gauche-gauche (G1gg), trans-trans-gauche (Ttg), trans-gauche-gauche (Tgg), trans-gauche-gauche(-) (Tgg1) and gauche(-)-gauche-trans (G1gt) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3-tetrafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 38% G1gg, 28% Ttg, 13% Tgg, 11% Tggt and 10% G1gt conformations at 298.15K. The vibrational frequencies of 2,2,3,3,-tetrafluoro-1-propanol in its five stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.

1-Propanol↗
PubMed1980

Conformational analysis of sterols: comparison of X-ray crystallographic observations with data from other sources.

Cystallographic data on over 400 steroids collected in the Atlas of Steroid Structure provide information concerning preferred conformations, relative stabilities and substituent influence of the interactive potential of steroid hormones. Analysis of these data indicates that observed conformational details are intramolecularly controlled and that the influence of crystal packing forces is negligible. Crystallographic data on the orientation of the progesterone side chain contradict published force-field calculations. In 84 of 88 structures having a 20-one substituent, the C(16)-C(17)-C(20)-O(20) torsion angle is between 0 degrees and -46 degrees. The 4 torsion angles that lie outside this range do so because of a 16 beta-substituent and not because of crystal packing forces. Not one of the 88 structures is found to have a conformation in which the C(16)-C(17)-C(20)-O(20) torsion angle is within +/- 15 degrees of the most commonly calculated minimum energy value. The narrow range of side chain conformations seen in very different crystalline environments in the 88 crystal structure determinations and the predictable substituent influence apparent in the data strongly suggest that crystallographically observed conformers seldom deviate from minimum energy positions, regardless of hypothetical broad energy minima, metastable states and small barriers to rotation. The 96 crystallographically independent determinations of the cholestane 17-side chain show that the chain has 4 principal conformations (A:B:C:D), occurring in the ratio 69:8:8:11. Although the fully extended side chain is clearly the energetically most favored one, in 16 observations of cholesterol itself only 6 are in the extended conformation. Some of the correlated conformational changes in the chains can be rationalized on the basis of model studies, but others apparently result from subtle intramolecular forces. The unsaturated B ring provides another element of flexibility in the structure of cholesterol. The 5-ene B ring is normally observed in an 8 beta, 9 alpha-half-chair conformation. However, in structures containing more than one molecular in the crystallographic asymmetric unit, at least one of the 2 molecules is found to differ significantly from this form. It may be that this inherent flexibility is responsible for the presence of conformationally distnct molecules in the same crystal. The intermolecular interaction observed in the crystal structure of cholesterol and its fatty acid derivatives illustrate the type of interaction between the steroid ring system and hydrocarbon chains that can be expected in membrane bilayers.

Cholestanes↗
PubMed1985

Conformational analysis of cyclized dipeptide models for specific types of beta-bends by two-dimensional nuclear Overhauser spectroscopy.

The solution conformations in DMSO-d6 of the two cyclized dipeptides, cyclo(L-alanyl-L-alanyl-epsilon-aminocaproyl) and cyclo(L-alanyl-D-alanyl-epsilon-aminocaproyl), have been analyzed by means of the two-dimensional nuclear Overhauser effect (2D-NOE). The preferred conformations for the two compounds have been deduced by comparing proton-proton distances, derived from the 2D-NOE data and relaxation-time measurements, with the corresponding distances in several possible computed low-energy conformations. The predominant conformations are a type III bend and a type II bend, respectively, for the two compounds. These conclusions agree with those deduced earlier on the basis of infrared and Raman spectra and circular dichroism measurements.

Magnetic Resonance Spectroscopy↗
PubMed1989

Chromophore conformational analysis in phycocyanin and in related chromopeptides by surface enhanced Raman spectroscopy.

Chromopeptides got from phycocyanin by proteolytic digestion do not preserve the extended chromophore conformations characteristic to the native protein. Chromophore conformations in the chromopeptides showed heterogenity varying between completely folded and semi-extended states. Indications were found that the silver sol-phycocyanin interaction involves the UV electronic transition of the biliprotein which may explain why the visible excited surface enhanced Raman spectra were similar not to the visible excited but to the UV-excited resonance Raman spectrum of phycocyanin.

Peptide Fragments↗
PubMed2004

Multiplex PCR amplimer conformation analysis for rapid detection of gyrA mutations in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates.

A new strategy known as multiplex PCR amplimer conformation was developed for detection of mutation in the gyrA gene of 138 clinical isolates of Mycobacterium tuberculosis. The method generated a single-stranded and heteroduplex DNA banding pattern of multiplex PCR amplimers of the region of interest that was extremely sensitive to specific mutations, thus enabling much more sensitive and reliable mutation analysis compared to the standard single-stranded conformation polymorphism technique. The genetic profiles of the gyrA gene of the 138 isolates as detected by MPAC were confirmed by nucleotide sequencing and were found to correlate strongly with the in vitro susceptibilities of the mutant strains to six fluoroquinolones (ofloxacin, levofloxacin, sparfloxacin, moxifloxacin, gatifloxacin, and sitafloxacin). All 32 isolates that contained gyrA mutations exhibited cross-resistance to the six fluoroquinolones (ofloxacin MIC for 90% of strains > 16 mg/liter), although moxifloxacin, gatifloxacin, and sitafloxacin (MIC for 90% of strains </= 4 mg/liter) were apparently more active than ofloxacin, levofloxacin, and sparfloxacin (MIC for 90% of strains >/==" BORDER="0"> 16 mg/liter). All gyrA mutations were clustered in codons 90, 91, and 94, and aspartic acid 94 was most frequently mutated. Twenty-three isolates without gyrA mutations were also found to exhibit reduced susceptibility to ofloxacin (MIC for 90% of strains = 4 mg/liter), but largely remained susceptible to other drugs (MIC for 90% of strains </= 1 mg/liter). Another 83 isolates without mutations were fully susceptible to all six fluoroquinolones (ofloxacin MIC for 90% of strains = 1 mg/liter). In conclusion, high-level phenotypic resistance to fluoroquinolones among M. tuberculosis clinical isolates, which appears to be predominantly due to gyrA mutations, may be readily detected by genotyping techniques such as multiplex PCR amplimer conformation.

Anti-Infective Agents↗
PubMed2007

Statistical and conformational analysis of the electron density of protein side chains.

Protein side chains make most of the specific contacts between proteins and other molecules, and their conformational properties have been studied for many years. These properties have been analyzed primarily in the form of rotamer libraries, which cluster the observed conformations into groups and provide frequencies and average dihedral angles for these groups. In recent years, these libraries have improved with higher resolution structures and using various criteria such as high thermal factors to eliminate side chains that may be misplaced within the crystallographic model coordinates. Many of these side chains have highly non-rotameric dihedral angles. The origin of side chains with high B-factors and/or with non-rotameric dihedral angles is of interest in the determination of protein structures and in assessing the prediction of side chain conformations. In this paper, using a statistical analysis of the electron density of a large set of proteins, it is shown that: (1) most non-rotameric side chains have low electron density compared to rotameric side chains; (2) up to 15% of chi1 non-rotameric side chains in PDB models can clearly be fit to density at a single rotameric conformation and in some cases multiple rotameric conformations; (3) a further 47% of non-rotameric side chains have highly dispersed electron density, indicating potentially interconverting rotameric conformations; (4) the entropy of these side chains is close to that of side chains annotated as having more than one chi(1) rotamer in the crystallographic model; (5) many rotameric side chains with high entropy clearly show multiple conformations that are not annotated in the crystallographic model. These results indicate that modeling of side chains alternating between rotamers in the electron density is important and needs further improvement, both in structure determination and in structure prediction.

Algorithms↗
PubMed2004

Restriction of a peptide turn conformation and conformational analysis of guanidino group using arginine-proline fused amino acids: application to mini atrial natriuretic peptide on binding to the receptor.

Compounds (2S,4S)- and (2S,4R)-4-(2'-guanidinoethyl)proline have been synthesized as a conformationally restricted arginine. Their backbones fit the i + 1 position in a turn, and the side chains are restricted compared to that of arginine. These analogues were incorporated into mini atrial natriuretic polypeptide, which has an important turnlike conformation at Gly(6)-Arg(7)()-Met(8)-Asp(9). Structural analysis revealed that the size of the conformational space of Arg(7) on binding to the receptor was approximately one-third of the entire conformational space.

Animals↗
PubMed1991

Conformational analysis of bacitracin A, a naturally occurring lariat.

The proton nmr spectra of bacitracin A in H2O and DMSO-d6 have been assigned and the conformational behavior of the peptide in the two solvents has been compared. Although bacitracin A shows a conformational equilibrium between at least two conformations differing in the relative position of the cyclic and linear domains of the molecule, the spectra in water can be interpreted in terms of a preferred conformation in which the linear part is folded over the cyclic moiety and a turn is present around Ile(8)-DPhe(9).

Amino Acid Sequence↗
PubMed1985

Conformational analysis of some alpha-phenylpropionic acids with anti-inflammatory activity.

CNDO/2 quantum mechanical conformational calculations, as well as 13C and 1H NMR measurements, have been carried out for the propionic acid residues of 2-(p-isobutylphenyl)propionic acid (ibuprofen) and 2-methyl-2-(p-isobutylphenyl)propionic acid. A relationship between the conformational angle of the propionic acid residue and the anti-inflammatory activity appears to exist. The more open the Ph--C alpha--COOH dihedral angle, the larger the anti-inflammatory activity.

Animals↗
PubMed2004

X-ray and conformational analysis of methyl 3-amino-2,3-dideoxy-alpha-D-arabino-hexopyranoside.

The structure, conformation and configuration of methyl 3-amino-2,3-dideoxy-alpha-d-arabino-hexopyranoside were confirmed by (1)H NMR, (13)C NMR and IR spectroscopy, as well as by optical rotation. The structure of the compound studied was also determined by single crystal X-ray crystallography at 293 K and refined to a final R=0.0521 based on 1798 independent reflections. The title compound crystallized in the tetragonal space group P4(3) with a=6.572(1) angstrom, b=6.572(1) angstrom, c=41.161(8) angstrom, D(c)=1.324 Mgcm(-3) and V=1777.8(5) angstrom(3) for Z=8. The packing arrangement in the unit cell displayed a stratified structure. Moreover, medium-strength N-H. . .O and O-H. . .O hydrogen bonds, which stabilized the 3-D structure of compound I, were observed.

Carbohydrate Conformation↗