NOE Measurements Research Articles

“Quasi flexible” automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of ΔΔG of complexation and 1H‐NMR NOE correlation

The purpose of this work is to apply the global molecular interaction evaluation ("Glob-MolInE") computational protocol to the study of two molecular complexes characterized by a chiral selector and a couple of enantiomeric selectands experimentally known to give large difference in the free energy of complexation much higher than the experimental error normally associated to the molecular mechanic calculations. We have considered the well known diastereomeric complexes between the selector (S)-N-(3,5-dinitrobenzoyl)-leucine-n-propylamide (S)-1 and the selectands (R) or (S)-N-(2-naphthyl)-alanine methyl ester 2, widely studied by enantioselective HPLC, NMR and X-ray. The experimental difference of free energy of complexation between [(S)-1*(R)-2] and [(S)-1*(S)-2] (-1.34 kcal/mol) was reproduced by the new computational protocol with an excellent confidence error. Detailed results about the conformational search, the "quasi-flexible" docking and the thermodynamic estimation are presented in this work. A remarkable correlation between the theoretical results and experimental data (NOE measurements, X-ray crystallographic structure of the [(S)-1*(S)-2] complex and the free energy of complexation) supports the validity of the computational approach and underline the importance of the conformational multiplicity in the definition of the macroscopic properties of the complex in solution.

Solution structure and equilibrium of new calix[4]resorcinarene complexes—prototype of molecular machines. NMR data

Association properties and molecular machine application of water soluble calix[4]resorcinarene (1) with two aromatic guests (2-naphthol (2) and 1,5-naphthalenediamine (3)) have been investigated by various NMR methods (chemical shift, nOe and diffusion measurements) in aqueous solution at different concentrations and pH range. In neutral solution 1 strongly associates with 2, while only moderately associating with 3. Increase in concentration causes an increase in the stability of 1 + 3 and 1 + 2 + 3 complexes and produces high order complexes. The decrease of pH does not have an influence on 1 + 2 association, but disrupts 1 + 3 assembly. 1 can be used for the separation of 2 + 3 mixture in aqueous solution at moderate concentrations. The pH dependency of the association properties of the 1 + 3 system makes these compounds prime candidates for pH-responsive molecular machines applications.

Synthesis, Reactivity, Spectroscopic Characterization, X-ray Structures, PGSE, and NOE NMR Studies of (η5-C5Me5)-Rhodium and -Iridium Derivatives Containing Bis(pyrazolyl)alkane Ligands

Rhodium(III) and iridium(III) complexes containing bis(pyrazolyl)methane ligands (pz = pyrazole, L' in general; specifically, L1 = H2C(pz)2, L2 = H2C(pzMe2)2, L3 = H2C(pz4Me)2, L4 = Me2C(pz)2), have been prepared in a study exploring the reactivity of these ligands toward [Cp*MCl(mu-Cl)]2 dimers (M = Rh, Ir; Cp* = pentamethylcyclopentadienyl). When the reaction was carried out in acetone solution, complexes of the type [Cp*M(L')Cl]Cl were obtained. However, when L1 and L2 ligands have been employed with excess [Cp*MCl(mu-Cl)]2, the formation of [Cp*M(L')Cl][Cp*MCl3] species has been observed. PGSE NMR measurements have been carried out for these complexes, in which the counterion is a cyclopentadienyl metal complex, in CD2Cl2 as a function of the concentration. The hydrodynamic radius (rH) and, consequently, the hydrodynamic volume (VH) of all the species have been determined from the measured translational self-diffusion coefficients (Dt), indicating the predominance of ion pairs in solution. NOE measurements and X-ray single-crystal studies suggest that the [Cp*MCl3]- approaches the cation, orienting the three Cl-legs of the "piano-stool" toward the CH2 moieties of the bis(pyrazolyl)methane ligands. The reaction of 1 equiv of [Cp*M(L')Cl]Cl or [Cp*M(L')Cl][Cp*MCl3] with 1 equiv of AgX (X = ClO4 or CF3SO3) in CH2Cl2 allows the generation of [Cp*M(L')Cl]X, whereas the reaction of 1 equiv of [Cp*M(L')Cl] with 2 equiv of AgX yields the dicationic complexes [Cp*M(L')(H2O)][X]2, where single water molecules are directly bonded to the metal atoms. The solid-state structures of a number of complexes were confirmed by X-ray crystallographic studies. The reaction of [Cp*Ir(L')(H2O)][X]2 with ammonium formate in water or acetone solution allows the generation of the hydride species [Cp*Ir(L')H][X].

Structure and Dynamics of ASC2, a Pyrin Domain-only Protein That Regulates Inflammatory Signaling

Structure and Dynamics of ASC2, a Pyrin Domain-only Protein That Regulates Inflammatory Signaling

Conformationally Biased Selective Alkylation of trans‐Cyclohexane‐1,2‐bis(sulfonamide) Assisted by Solvent‐Tuned Protecting Groups: Applications to the Synthesis of a Large Optically Active Polyazamacrocycle

AbstractThe selective alkylation of (R,R)‐cyclohexane‐1,2‐bis(sulfonamide) with trityl bromoalkyl ethers has been studied in detail. The major formation of either mono‐ or dialkylated compounds clearly depends on the right combination of protecting groups and the reaction solvent. An exhaustive study suggests that this effect can be reasonably explained by the conformational preferences of the monoalkylated compounds, which also depend on the reaction medium, solvophobic effects and weak intramolecular interactions. Structural analysis by NOE measurements showed the presence of folded conformations in solution for all the tested examples. Monte Carlo conformational searches supported this proposal, showing a very good correlation between the fraction of folded species and the selectivity towards monoalkylation. Finally, tuning of the reaction conditions, leading to either extended or folded conformations of the monoalkylated synthetic intermediates, was exploited for the efficient synthesis of a large optically active polyazamacrocycle. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Chiral α-Branched Benzylic Carbocations: Diastereoselective Intermolecular Reactions with Arene Nucleophiles and NMR Spectroscopic Studies

The chiral benzylic alcohols 1-6 were prepared and subjected to S(N)1-type displacement reactions with various arene nucleophiles in acidic medium. Under optimized conditions (HBF(4).OEt(2), CH(2)Cl(2), -78 degrees C --> r.t.) the corresponding 1,1-diarylalkanes 11-18 and 20 were obtained in good chemical yields (48-99%). The facial diastereoselectivity of the reaction is high (d.r. = 91/9-97/3) when the substrate bears a stereogenic carbon center -CHtBuMe in the alpha-position to the electrophilic carbon atom. If the starting material was enantiomerically pure, no significant racemization was observed (94% ee --> 92% ee). The reactions proceed stereoconvergently as demonstrated by the conversion of the separated diastereoisomers syn-1a and anti-1a in separate reactions to the same product syn-11 (d.r. = 97/3). Further evidence for long-lived chiral benzylic carbocations as reaction intermediates was obtained from NMR studies in superacidic medium. The chiral cation 24 was generated in SO(2)ClF as the solvent at -70 degrees C employing SbF(5) as the Lewis acid and characterized by its (1)H and (13)C NMR spectra. NOE measurements suggest a preferred conformation in which the diastereotopic faces of the cation are differentiated by the two carbon substituents R and Me at the stereogenic carbon center in the alpha-position. The hypothesis is further supported by the observation that the diastereoselectivity of the substitution reaction decreases if the bulky tert-butyl (R = tBu) substituent in the substrate 1a is replaced by a smaller ethyl group (2a, R = Et).

The effect of pendant-arm modification and ring size on the dynamics of cyclic polyamines

Carbon-13 relaxation studies have been performed on two cyclic polyamines—1,4,8,11-tetraazacyclotetradecane, N4R4_H, (cyclam) and 1,4,7,10,13,16-hexaazacyclooctadecane, N6R6_H, (hexacyclen), and on two synthesized N-substituted cyclam derivatives—1,4,8,11-tetrahexanoyl-1,4,8,11-tetraazacyclotetradecane, N4R4_CO(CH 2) 4CH 3, with aliphatic and 1,4,8,11-tetranaftalenesulfonyl-1,4,8,11-tetraazacyclotetradecane, N4R4_SO 2C 10H 7, with aromatic substituents. Longitudinal T 1 relaxation and NOE measurements were performed in extreme narrowing region for basic polyamines and outside extreme narrowing region for substituted derivatives at room temperature and for magnetic strengths 400 and 500 MHz. The main ring and the pendant-arms in substituted compounds were considered separately. The obtained relaxation rates and NOE factors for N4R4_CO(CH 2) 4CH 3 and N4R4_SO 2C 10H 7 molecules were fitted to overall and internal correlation times and order parameters using Lipari–Szabo ‘model-free’ formalism. The chemical shift anisotropy was determined for N4R4_SO 2C 10H 7 compound. The meaningful differences were observed between carbons in the main part of molecules and carbons from pendant-arms.

Nuclear Spin Relaxation Driven by Intermolecular Dipolar Interactions: The Role of Solute−Solvent Pair Correlations in the Modeling of Spectral Density Functions

Nuclear spin relaxation provides useful information related to the dynamics of molecular systems. When relaxation is driven by intermolecular dipolar interactions, the relevant spectral density functions (SDFs) also have significant contributions, in principle, from distant spins all over the dynamic range typically probed by NMR experiments such as NOESY. In this work, we investigate the intermolecular dipolar spin relaxation as driven by the relative diffusion of solvent and solute molecules taking place under a central force field, and we examine the relevant implications for (preferential) solvation studies. For this purpose, we evaluate the SDFs by employing a numerical approach based on spatial discretization of the time-propagation equation, and we supply an analytical solution for the simplest case of a steplike mean-field potential. Several situations related to different solute-solvent pair correlation functions are examined in terms of static/dynamic effects and relaxation modes, and some conclusions are drawn about the interpretation of NOE measurements. While we confirm previous results concerning the spoiling effect of long-range spins (Halle, B. J. Chem. Phys. 2003, 119, 12372), we also show that SDFs are sufficiently sensitive to pair correlation functions that useful, yet rather complicated, inferences can be made on the nature of the solvation shell.

Comparison of Structure and Dynamics of Micelle-bound Human α-Synuclein and Parkinson Disease Variants

Three point mutations (A30P, E46K, and A53T) as well as gene triplication genetically link the 140-residue protein alpha-synuclein (aS) to the development of Parkinson disease. Here, the structure and dynamics of micelle-bound aS(A30P) and aS(A53T) are described and compared with wild-type aS, in addition to describing the aS-micelle interaction. A53T is sensed only by directly adjacent residues and leaves the backbone structure and dynamics indistinguishable from the wild type. A30P interrupts one helix turn (Val26-Ala29) and destabilizes the preceding one. A shift in helix register following A30P disturbs the canonical succession of polar and hydrophobic residues for at least two turns. The shortened helix-N adopts a slightly higher helical content and is less bent, indicating that strain was present in the micelle-bound helix. In the vicinity of the A30P-induced perturbations, the underlying micelle environment has rearranged, but nevertheless all aS variants maintain similar interrelationships with the micelle. Moreover, aS-micelle immersion correlates well with fast and slow aS backbone dynamics, allowing a rare insight into protein-micelle interplay.

Systematic Assignment of the Configuration of Flexible Natural Products by Spectroscopic and Computational Methods: The Bistramide C Analysis

[reaction: see text] The combination of NMR NOE, chemical shift, and J-coupling measurements with molar rotation and circular dichroism (CD) determinations, including RI-DFT BP86/aug-cc-pVDZ calculations, reduced a candidate pool of 1024 possible stereoisomers of (+)-bistramide C to a single absolute configuration assignment for the 10 stereogenic carbons of the marine natural product.

Preparation of 2-amino-5-methyl-7H-1,3,4-thiadiazolo[3,2-α]pyrimidin-7-ones

2-Amino substituted 7H-1,3,4-thiadiazolo[3,2-α]pyrimidin-7-ones 11a-e were prepared by the reaction of 2-bromo-5-amino-1,3,4-thiadiazole (1b) and diketene (8), subsequent cyclocondensation (9b 3b) and displacement of the bromo substituents by the reaction with primary or secondary amines (3b 11a-e). The hydrogen atom 6-H in the heterobicycle 3b is replaced by a Cl or Br atom in the transformation of 3b 14a,b. The 2-bromo-6-chloro compound 14a reacts chemoselectively in the 2-position with dimethylamine (14a 15). The structure elucidations are based on one- and two-dimensional NMR techniques including a heteronuclear NOE measurement.

Facial Stereoselectivity in the Diels−Alder Reactions of (Arylethynyl)ethoxycarbenes of Group 6 with 1,2,3,4,5-Pentamethylcyclopenta-1,3-diene and Unusual Rearrangement of Strained Norbornadienyl Fischer Carbene Complexes of Chromium(0)

A study of reactivity and facial selectivity in Diels−Alder reactions of the Fischer carbene complexes (CO)5MC(C⋮CC6H4R)OCH2CH3 (1a, M = Cr, R = H; 1b, M = Cr, R = p-OCH3; 1c, M = Cr, R = p-CH3; 2, M = W, R = H; 3, M = Mo, R = H), with 1,2,3,4,5-pentamethylcyclopenta-1,3-diene (4) was carried out. The cycloadditions were found to be highly π-facial stereoselective, favoring the anti adduct. Among these complexes, 3 was the most reactive dienophile. The stereochemical assignment of the adducts 5−7 was supported by NOE measurements; structures of the anti cycloadducts 5a and 6 were established by single-crystal X-ray diffraction. A [4 + 2] cycloaddition/benzannulation/rearrangement cascade reaction was observed for the chromium carbene complexes 1a−c with 4 under thermal conditions, resulting in the naphthofurandione derivatives 9−11.

Protein Dynamics in Living Cells

A protein's structure is most often used to explain its function, but function also depends on dynamics. To date, protein dynamics have been studied only in vitro under dilute solution conditions where solute concentrations are typically less than 10 g/L, yet proteins function in a crowded environment where the solute concentration can exceed 400 g/L. Does the intracellular environment affect protein dynamics? The answer will help in assessing the biological significance of the NMR-derived dynamics data collected to date. We investigated fast protein dynamics inside living Escherichia coli by using in-cell NMR. The backbone dynamics of apocytochrome b5 were quantified using {1H}-15N nuclear Overhauser effect (nOe) measurements, which characterize motions on the pico- to nanosecond time scale. The overall trend of backbone dynamics remains the same in cells. Some of the nOe values differ, but most of the differences track the increased intracellular viscosity rather than a change in dynamics. Therefore, it appears that dilute solution steady-state {1H}-15N nOe measurements provide biologically relevant information about pico- to nanosecond backbone motion in proteins.

Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7‐SH2/erbB2 peptide complex

Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%-30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T(1), T(2), and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature.

Structure and Dynamics of Micelle-bound Human α-Synuclein

Misfolding of the protein alpha-synuclein (aS), which associates with presynaptic vesicles, has been implicated in the molecular chain of events leading to Parkinson's disease. Here, the structure and dynamics of micelle-bound aS are reported. Val3-Val37 and Lys45-Thr92 form curved alpha-helices, connected by a well ordered, extended linker in an unexpected anti-parallel arrangement, followed by another short extended region (Gly93-Lys97), overlapping the recently identified chaperone-mediated autophagy recognition motif and a highly mobile tail (Asp98-Ala140). Helix curvature is significantly less than predicted based on the native micelle shape, indicating a deformation of the micelle by aS. Structural and dynamic parameters show a reduced helical content for Ala30-Val37. A dynamic variation in interhelical distance on the microsecond timescale is complemented by enhanced sub-nanosecond timescale dynamics, particularly in the remarkably glycine-rich segments of the helices. These unusually rich dynamics may serve to mitigate the effect of aS binding on membrane fluidity. The well ordered conformation of the helix-helix connector indicates a defined interaction with lipidic surfaces, suggesting that, when bound to larger diameter synaptic vesicles, it can act as a switch between this structure and a previously proposed uninterrupted helix.

NMR Relaxation Study of the Protonated Form of 1,8-Bis(dimethylamino)naphthalene in Isotropic Solution: Anisotropic Motion outside of Extreme Narrowing and Ultrafast Proton Transfer

The protonated form of 1,8-bis(dimethylamino)naphthalene (DMANH(+)) consists of a rigid, aromatic framework, substituted by two amino groups that are connected by a strong, symmetric (on the NMR time-scale) hydrogen bond bridge. The reorientational motion of the molecule in dimethylformamide-d7 solution was characterized by T(1) and NOE measurements for aromatic (13)C nuclei. Treating the reorientation of DMANH(+) as anisotropic rotational diffusion of a rigid body, the diffusion tensor was determined with good accuracy. Measurements and interpretation of (15)N T(1) and NOE indicate that the proton transfer between potential minima in the hydrogen bond bridge is faster than the molecular reorientation.

The conformation of the cytoplasmic helix 8 of the CB1 cannabinoid receptor using NMR and circular dichroism

The cytoplasmic helix domain (fourth cytoplasmic loop, helix 8) of numerous GPCRs such as rhodopsin and the β-adrenergic receptor exhibits unique structural and functional characteristics. Computational models also predict the existence of such a structural motif within the CB1 cannabinoid receptor, another member of the G-protein coupled receptor superfamily. To gain insights into the conformational properties of this GPCR component, a peptide corresponding to helix 8 of the CB1 receptor with a small contiguous segment from transmembrane helix 7 (TM7) was chemically synthesized and its secondary structure determined by circular dichroism (CD) and solution NMR spectroscopy. Our studies in DPC and SDS micelles revealed significant α-helical structure while in an aqueous medium, the peptide exhibited a random coil configuration. The relative orientation of helix 8 within the CB1 receptor was obtained from intermolecular 31P– 1H and 1H– 1H NOE measurements. Our results suggest that in the presence of an amphipathic membrane environment, helix 8 assumes an alpha helical structure with an orientation parallel to the phospholipid membrane surface and perpendicular to TM7. In this model, positively charged side chains interact with the lipid headgroups while the other polar side chains face the aqueous region. The above observations may be relevant to the activation/deactivation of the CB1 receptor.

The conformational free-energy map for solvated neocarrabiose

A Ramachandran map of the conformational potential of mean force (pmf) for neocarrabiose in water was obtained using molecular dynamics (MD) simulations with umbrella sampling. The potential energy map calculated in a previous study for this molecule in vacuum exhibited a global minimum located at ( φ=81°, ψ=−141°). However, the global minimum on the new pmf map in aqueous solution is located in an area centered around ( φ=175°, ψ=180°), indicating a considerable solvent shift. This new global minimum-energy solution conformation was found to correspond to the experimental value obtained from NMR–NOE measurements, and is also consistent with the experimental crystal structure for neocarrabiose and the fiber diffraction conformation for ι-carrageenan. The global minimum of the solution pmf and its local topology were found to be approximately reproduced by quick vacuum conformational energy mapping using several approximations that mimic solvation effects by de-emphasizing intramolecular hydrogen bonding.

Photochemical formation of 64.4.49(1,3,5)cyclophanes from 1,3,5-tris(3-phenylpropenoyl)benzenes

Irradiation of 1,3,5-tris(3-phenylpropenoyl)benzene (1a) yields in solution a dimer 2a by a threefold head-to-head/anti [2π+2π]cycloaddition. The stereochemistry of this [4.4.4](1,3,5)cyclophane was determined by 1H and 13C NMR studies including NOE measurements and a calculation of the AA′MM′ spin pattern of the methine protons. In contrast to the solution photochemistry, which is presumably controlled by the arrangement of an excimer, the irradiation in the crystalline state leads by a topochemical control to a dimer 3a, which contains a single four-membered ring.

Photochemical formation of [4.4.4](1,3,5)cyclophanes from 1,3,5-tris(3-phenylpropenoyl)benzenes

Irradiation of 1,3,5-tris(3-phenylpropenoyl)benzene ( 1a ) yields in solution a dimer 2a by a threefold head-to-head/ anti [2π+2π]cycloaddition. The stereochemistry of this [4.4.4](1,3,5)cyclophane was determined by 1H and 13C NMR studies including NOE measurements and a calculation of the AA′MM′ spin pattern of the methine protons. In contrast to the solution photochemistry, which is presumably controlled by the arrangement of an excimer, the irradiation in the crystalline state leads by a topochemical control to a dimer 3a , which contains a single four-membered ring.