Nuclear Overhauser Effect Studies Research Articles

Optimizing the Local Chemical Environment on a Bifunctional Helical Peptide Scaffold Enables Enhanced Enantioselectivity and Cooperative Catalysis.

We describe a proof-of-concept study in which peptide-bound enamine and thiourea catalysts are used to facilitate the conjugate addition of cyclohexanone to nitroolefins. Our bifunctional peptide scaffold is modified to optimize the local environment around both catalysts to enhance both reactivity and enantioselectivity, affording selectivities of ≤95% ee. Circular dichroism, nuclear magnetic resonance nuclear Overhauser effect studies, and molecular dynamics simulations verify the helical structure of our catalyst in solution and the importance of the secondary structure in catalysis.

A study of the biologically active conformation of the cholecystokinin-4 dipeptide analogue GB-115

The conformational analysis with 1H NMR spectroscopy method in solution and the structure-activity relationship study of a series sterically restricted analogs allowed to detect the possible biologically active conformation of N-(6-phenylhexanoyl)glycyl-tryptophan amide (GB-115), a highly active dipeptide cholecystokinin-4 analog with anxiolytic activity. The structure-activity relationship study of GB-115 and the series of its' glycine- and proline-containing analogs with different C-terminal substitute detected the anxiolytic activity of compounds with beta-turn like conformation and inactivity of compounds with gamma-turn like conformation. So, the GB-115 biologically active conformation is beta-turn. The results of nuclear Overhauser effect study permitted to qualify the betaII-turn conformation as GB-115 biologically active conformation. The following synthesis of sterically restricted GB-115 analogs (2S)-2-{(3R)-3-[(6-phenylhexanoyl)amino]-2-oxopyrrolidin-1-yl}-3-(1H-indol-3-yl)propionic acid ethyl ester, N-(6-phenylhexanoyl)glycyl-N(alpha)(methyl)-tryptophan ethyl ester, (2S)-2-[10,11-dihydro-5H-dibenzo[b,f] azepin-5-carbonyl)-amino]-3-(1H-indol-3-yl)propionic acid methyl ester and (2S)-2-[({3-[(ethoxycarbonyl)amino]-10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl}carbonyl)amino]-3-(1H-indol-3-yl)propionic acid methyl ester confirmed the estimated type of GB-115 biologically active conformation.

13CO2H-labeled semirubin: hydrogen bonding and pK a

13CO2H-Labeled [6]-semirubin, 9-(6-[13C]-5-carboxypentyl)-2,3,7,8-tetramethyl-(10H)-dipyrrin-2-one, and its 91-oxo analog were synthesized from 2,3,7,8-tetramethyl-(10H)-dipyrrin-2-one. 13C NMR T1 measurements of the 13CO2H carbon were run in CDCl3, dioxane, (CH3)2SO and aqueous solvents and compared with those from the corresponding methyl esters. The data as well as those from nuclear Overhauser effect (NOE) studies indicate intramolecular hydrogen bonding between the CO2H and dipyrrinone groups. Studies of the acids in aqueous solvent predict (1) intramolecular hydrogen bonding over a wide range of pH and (2) a pK a of ~4.4.

Substituted 1,3,5-Triazaadamantanes: Biocompatible and Degradable Building Blocks

Substituted 1,3,5-Triazaadamantanes: Biocompatible and Degradable Building Blocks

X-ray crystal structure and nuclear Overhauser effect studies of cerium(IV) complexes with Schiff bases obtained from N, N′-(1 R,2 R)(−)-1,2-cyclohexanediamine and benzaldehyde derivatives

Schiff bases, obtained by condensation of N, N′-(1 R,2 R)-cyclohexanediamine with 2-hydroxy-5-chlorobenzaldehyde or 2-hydroxy-3,5-dichlorobenzaldehyde and of (±)cyclohexanediamine and salicylaldehyde, have been used as ligands for cerium(IV). The complexes were characterized by circular dichroism (CD), 1H NMR, 13C NMR and nuclear Overhauser effect (NOE) studies. X-ray crystal structures determined for: [Ce(IV)((1 R,2 R)(−)chxn(3,5-diClba) 2) 2] and [Ce(IV)(±)(chxn(salal) 2) 2] revealed different orientation of a pair of Schiff base ligands in the coordination sphere. In [Ce(IV)((1 R,2 R)(−)chxn(3,5-diClba) 2) 2] two ligands form a sandwich with the cerium(IV) ion positioned between two layers of dichlorophenolic moieties. CD spectra in acetonitrile solution revealed exciton coupled π → π ∗ and LMCT transitions. CD data are characteristic for distortion of the chelate ring from planarity and λ conformation of the cyclohexane bridge. NOE difference spectroscopy for the Schiff bases (saturated – HC N–) demonstrate correlations of the azomethine protons with the protons of the phenyl ring and the cyclohexane’s CH protons, and a weak correlation with the hydroxyl group. In the case of the cerium(IV) complexes, the strongest NOE (saturated H–C N) was observed with the phenyl ring’s hydrogen atoms, a slightly weaker correlation to the cyclohexane’s CH 2 protons, and a much weaker NOE to the cyclohexyl’s CH 2 protons. Results of spectral analyses suggest central ions in a distorted square antiprism geometry with the two basal N 2O 2 chromophore group. The X-ray crystallography study also confirmed antiprismatic distortion from planarity in obtained complexes.

PH-Dependent Dimerization of the Carboxyl Terminal Domain of Cx43

Previous studies have demonstrated that the carboxyl terminus of the gap junction protein Cx43 (Cx43CT) can act as an independent, regulatory domain that modulates intercellular communication in response to appropriate chemical stimuli. Here, we have used NMR, chemical cross-linking, and analytical ultracentrifugation to further characterize the biochemical and biophysical properties of the Connexin43 carboxyl terminal domain (S255-I382). NMR-diffusion experiments at pH 5.8 suggested that the Connexin43 carboxyl terminus (CX43CT) may have a molecular weight greater than that of a monomer. Sedimentation equilibrium and cross-linking data demonstrated a predominantly dimeric state for the Cx43CT at pH 5.8 and 6.5, with limited dimer formation at a more neutral pH. NMR-filtered nuclear Overhauser effect studies confirmed these observations and identified specific areas of parallel orientation within Cx43CT, likely corresponding to dimerization domains. These regions included a portion of the SH3 binding domain, as well as two fragments previously found to organize in α-helical structures. Together, these data show that acidification causes Cx43CT dimer formation in vitro. Whether dimer formation is an important structural component of the regulation of Connexin43 channels remains to be determined. Dimerization may alter the affinity of Cx43CT regions for specific molecular partners, thus modifying the regulation of gap junction channels.

Self-assembly of dipeptidyl ureas: a new class of hydrogen-bonded molecular duplexes.

The dipeptidyl urea 1 composed of two dipeptide chains bearing the C-terminal pyridyl moiety (-L-Ala-L-Pro-NHPy) was prepared. Two molecules of 1 are revealed to be held together by six intermolecular hydrogen bonds to form a hydrogen-bonded duplex by the single-crystal X-ray structure determination. Proton magnetic resonance nuclear Overhauser effect (NOE) study indicates the hydrogen-bonded duplex even in solution. Furthermore, a shuttle-like molecular dynamics based on recombination of the hydrogen bonds was observed. The dipeptidyl urea composed of two dipeptide chains bearing the C-terminal pyrenyl moiety (-L-Ala-L-Pro-NHCH(2)Pyr) exhibited both monomer and eximer emissions in the fluorescence spectra, supporting the formation of a duplex. A combination of the C-terminal amide NH function in each side and the designed sequence of hydrogen-bonding sites are considered to be a crucial factor for the duplex formation.

Structure, modelling, and molecular dynamics studies of the inhibition of protein tyrosine phosphatase 1B by sulfotyrosine peptides

The protein tyrosine phosphatases comprise a class of enzymes that are crucial for the regulation of a number of cellular processes. Because of this, they are attracting increasing attention, not only as legitimate therapeutic targets, but also because of their relationship to many fundamental cellular processes. Certain sulfotyrosine peptides derived from casein are known to be good inhibitors of the protein tyrosine phosphatase, PTP1B. In this study, NMR transfer nuclear Overhauser effect studies have been used to ascertain the bound-state conformation adopted by the 12-amino acid residue casein-derived peptide, CAS200 (NANEEE(sY)SIGSA) and N-terminal truncated forms of this peptide, CAS203 and CAS205. Each of the peptides were found to bind in an extended beta-strand conformation. Extensive molecular modelling and molecular dynamics simulations of the PTP1B/peptide complexes, in a fully hydrated model, allowed a detailed description of the potential sources of the binding interactions to be developed. In agreement with the NMR studies, the modelling provided a picture of binding of CAS200 in which only the central (E203-I208) residues contributed significantly to the binding while the 3 N-terminal and 3 C-terminal residues were quite fluxional. Critical cationic surface residues, lying near to, but outside the active site pocket were the source of strong stabilizing forces that complemented the stabilizing interactions of the active site pocket. Electrostatic, hydrophobic, and hydrogen bonding interactions, in a residue specific manner, were all found to make significant contributions to the binding of these inhibitors.

Characterization of the Human Cytomegalovirus Protease As an Induced-Fit Serine Protease and the Implications to the Design of Mechanism-Based Inhibitors

The conformational properties of the N-tert-butylacetyl-l-tert-butylglycyl-l-Nδ,Nδ-dimethylasparagyl-l-alanyl methyl ketone (MK) 1 and its terminal N-isopropylacetyl analogue 2 were investigated. Whereas these compounds are weak (mM IC50 range) inhibitors of the human cytomegalovirus (HCMV) protease, their activated carbonyl analogues are >1000-fold more potent (e.g., trifluoromethyl ketone 3, IC50 = 1.1 μM). A combination of NMR techniques demonstrated that MK 2 exists in solution as a relatively rigid and extended peptide structure and that the bulky side chains, notably the P3 tert-butyl group, greatly contribute to maintaining this solution conformation. Furthermore, transferred nuclear Overhauser effect (TRNOE) studies provided an enzyme-bound conformation of MK 2 that was found to be similar to its free solution structure and compares very well to the X-ray crystallographic structure of a related peptidyl inhibitor complexed to the enzyme. The fact that ligands such as MK 2 exist in solution in the bioactive conformation accounts, in part, for the observed inhibitory activity of activated ketone inhibitors bearing comparable peptidyl sequences. Comparison of the X-ray structures of HCMV protease apoenzyme and that of its complex with a related peptidyl α-ketoamide inhibitor allowed for a detailed analysis of the previously reported conformational change of the enzyme upon complexation of inhibitors such as 1 and 3. The above observations indicate that HCMV protease is a novel example of a serine protease that operates by an induced-fit mechanism for which complexation of peptidyl ligands results in structural changes which bring the enzyme to a catalytically active (or optimized) form. Kinetic and fluorescence studies are also consistent with an induced-fit mechanism in which a considerable proportion of the intrinsic ligand-binding energy is used to carry out the conformational reorganization of the protease. Issues related to the rational design of both mechanism- and nonmechanism-based inhibitors of HCMV protease, notably in light of the peptidyl ligand-induced optimization of its catalytic functioning, are discussed.

Transferred nuclear Overhauser effect study of macrolide–ribosome interactions: correlation between antibiotic activities and bound conformations

The study of macrolide–ribosome interactions has been investigated using two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY). A new medically important macrolide antibiotic, roxithromycin, with the replacement of the 9-keto group in erythromycin by a 9-oxime chain, was studied in the complex state with the bacterial ribosome. Analysis of transferred nuclear Overhauser effect (TRNOE) experiment resulted in a set of constraints for all protons pairs. These constraints were used in structure determination procedures based on molecular modelling to obtain a bound structure compatible with the experimental NMR data. The results compared with the conformational analysis of the substrate in solution indicate that only one specific conformation is preferred in the bound state while in the free state the sugar ring moities were relatively disordered. The bioactive macrolide antibiotics studied roxithromycin and erythromycin which displayed a strong NMR response, are metabolized in RU39001 and erythralosamine respectively which do not retain antimicrobial activity. The inactive major metabolites were used to define if TRNOEs observation may be characteristic of a biological activity. These control experiments gave essentially blank TRNOESY spectra. This study shows that Mg 2+ does not play a direct role for the low affinity binding site studied by TRNOE what is in agreement with an hypothesis of two distinct binding levels, with a low affinity binding level necessary for the tight binding one.

1H-NMR and NOE studies of 2-cephems and 3-cephems

The(1)H-NMR signals of 2-cephems and 3-cephems have been assigned and the Nuclear Overhauser Effect (NOE) study of these compounds was undertaken.

Temperature dependence of backbone dynamics in loops of human mitochondrial heat shock protein 10.

A highly flexible, yet conserved polypeptide loop of Hsp10 mediates binding to Hsp60 in the course of chaperonin-dependent protein folding. Previous transferred nuclear Overhauser effect (trNOE) studies with peptides based on the mobile loop of the Escherichiacoli and bacteriophage T4 Hsp10s suggested that the mobile loop adopts a characteristic hairpin turn upon binding to the E. coli Hsp60 GroEL. In this paper, we identify the sequence and characterize the nascent structure and dynamics of the 18-residue mobile loop in the 15N-enriched human Hsp10. We also identify four residues of another flexible loop, the roof beta hairpin. The mobile loop and/or roof beta hairpin of several subunits are absent from the X-ray crystal structure of human Hsp10. NMR data suggest that the mobile loop of Hsp10 preferentially samples a hairpin conformation despite the fact that the backbone motion resembles that of a disordered polypeptide. Analysis of backbone dynamics by measurement of 15N relaxation times, T1 and T2, and the 1H-15N nuclear Overhauser effect (1H-15N NOE) indicates that motion is greatest near the center of the loop. Inversion of the temperature dependence of the T1 near the center of the loop marks a transition to motion with a dominant time scale of less than 3 ns. Analysis of the relaxation data by spectral density mapping shows that subnanosecond motion increases uniformly along the loop at elevated temperatures, whereas nanosecond motion increases near the ends of the loop and decreases near the center of the mobile loop. The transition to dominance by fast motion in the center of the loop occurs at a distance from the well-structured part of Hsp10 that is equal to the persistence length of an unstructured polypeptide. Simulation of the spectral density function for the 15N resonance and its temperature dependence using the Lipari-Szabo formalism suggests that the dominant time scales of loop motion range from 0.6 to 18 ns. For comparison, the time scale for molecular rotation of the 70 kDa Hsp10 heptamer is estimated to be 37 ns. Complex behavior of the T2 relaxation time indicates that motion also occurs on longer time scales. All of the modes of loop motion are likely to have an impact on Hsp10/Hsp60 interaction and therefore affect Hsp10/Hsp60 function as a chaperonin.

Synthetic, Fungicidal Unsaturated-γ-lactones Attached to Furanosidic Systems. Configurational Determination by Nuclear Overhauser Effect1

Abstract Stereoselective synthesis of a butenolide sugar derivative was possible by reaction of the appropriate sugar epoxide with the dilithium salt of phenylselenoacetic acid, followed by oxidation of the α-phenylselenobutanolide obtained with hydrogen peroxide in the presence of catalytic amounts of acetic acid. On the other hand, synthesis of an exocyclic α,β-unsaturated lactone was accomplished by Reformatsky reaction on the appropriate sugar carbonyl groups with ethyl bromomethylacrylate and activated zinc, leading to the introduction of this ring at position 2 or 4 of a furanose ring. Nuclear Overhauser effect studies led to the unambiguous determination of the configuration of the new chiral centre formed by the Reformatsky reaction. The fungicidal efficacy of some unsaturated lactone sugar derivatives is given.

A Proton NMR and Nuclear Overhauser Effect (NOE) Study of Human Plasma Prealbumin, Including the Development and Application to Spectral Assignment of a Combined Ring Current Shift and NOE Prediction Program

A Proton NMR and Nuclear Overhauser Effect (NOE) Study of Human Plasma Prealbumin, Including the Development and Application to Spectral Assignment of a Combined Ring Current Shift and NOE Prediction Program

1H NMR and NOE studies of 6α-bromopenicillanates

The1H NMR signals of three 6α-bromopenicillanates have been assigned and the Nuclear Overhauser Effect(NOE) study of these compounds was undertaken.

The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides.

Crystallographic, isotopic labeling nmr and transferred nuclear Overhauser effect studies have highlighted the extended conformation as a very important element of secondary structure at the binding site of many peptide/protein complexes including peptide inhibitors-enzymes, B-cell epitopes-antibodies, and T-cell epitopes-major histocompatibility complex (MHC) of class I and II complexes. This paper discusses the peptide ligand conformation consequences of these findings particularly in view of the identification of the PII conformation (left-handed extended polyproline II) in free solution.

Transferred nuclear Overhauser effect study of the C-terminal helix of yeast phosphoglycerate kinase: NMR solution structure of the C-terminal bound peptide.

Two-dimensional 1H nuclear magnetic resonance spectroscopy is used to determine the structure of the C-terminal complementary peptide (404-415) bound to a mutant phosphoglycerate kinase (1-403). Conformational changes in the peptide induced by the formation of the peptide-protein complex are followed by transferred nuclear Overhauser effect spectroscopy. Measurement of transferred NOEs and molecular modeling reveal an alpha-helix fold in the 405-409 region. This fold is in good agreement with the corresponding helix XIV of the crystallographic structure of wild-type PGK (Watson et al., 1982). The role of the alpha-helix from the C-terminal peptide in the recovery of catalytic activity in the mutant PGK is discussed.

Synthetic and conformational studies on dehydrovaline-containing model peptides

To explore the conformational preferences of αs-dehydrovaline (ΔVal) residue, three model dipeptide N-methylamides containing ΔVal were synthesized. Conformational investigations using 300 MHz NMR spectroscopy were based on delineation of intramolecularly hydrogen-bonded NH groups and Nuclear Overhauser Effect (NOE) studies. Temperature and solvent dependence studies in (CD3)2SO and CDC13-(CD3)2SO mixtures showed the absence of any intramolecular hydrogen bonding which suggests that all the three peptides have an extended conformation in solution. Dilution studies in CHC13 conducted using IR spectroscopy further supported the above conclusions. NOE studies also ruled out the existence of any type of discernible secondary structure for these peptides. Conformational behaviour of these dehydrovaline peptides is in contrast with corresponding peptides containing ΔzPhe and ΔzLeu, both of which stabilize s-turn (type-II) structure. These results highlight the importance of steric factors in deciding the conformational properties of dehydropeptides.

Synthesis and assignments of regioisomeric cyanoimidazole esters

Regioassignments of ethyl cyanoimidazolecarboxylates have been performed by the nuclear Overhauser effect(NOE) studies on the regioisomeric monocyanoimidazoles obtained by the hydrolysis of the esters followed by decarboxylation. Alternately, regioassignment could also be carried out by comparing the chemical shifts of the N-methyl groups.

Role of the NH2-terminal domain of angiotensin II (ANG II) and [Sar1]angiotensin II on conformation and activity. NMR evidence for aromatic ring clustering and peptide backbone folding compared with [des-1,2,3]angiotensin II.

The role of the NH2 termini of angiotensin II (ANG II) and [Sar1]ANG II on conformation and activity were examined by proton NMR two-dimensional-J-correlated spectroscopy and one-dimensional nuclear Overhauser effect studies in the relatively nonpolar "receptor-simulating" environment provided by dimethyl sulfoxide-d6, using the biologically inactive COOH-terminal pentapeptide [des1,2,3]ANG II as control. Irradiation of C alpha H, C2H, and C4H proton resonances in ANG II and [Sar1]ANG II resulted in enhancements of Tyr and Phe ring proton resonances, indicating that the three aromatic rings cluster together. Very strong enhancements (17-22%) of the C alpha Y proton resonance in ANG II and [Sar1]ANG II upon irradiation of the C alpha H proton resonance, and vice versa, revealed that a Tyr-Ile-His bend is a predominant feature of the conformation of the two agonists. In contrast, saturation of the C alpha H and C alpha Y proton resonances in the control pentapeptide [des-1,2,3]ANG II did not produce, respectively, any C alpha Y or C alpha H proton nuclear Overhauser effect enhancement, illustrating the absence of a Tyr-Ile-His bend in the truncated ANG II peptide. The present findings indicate that the NH2-terminal domain of ANG II appears to have an essential role in generating the biologically active charge relay conformation of the hormone.