NMR Methods (nmr + methods)

Distribution by Scientific Domains
Distribution within Chemistry


Selected Abstracts


NMR methods for studying membrane-active antimicrobial peptides

CONCEPTS IN MAGNETIC RESONANCE, Issue 2 2004
Erik Strandberg
Abstract NMR is a versatile tool for studying interactions between antimicrobial peptides and lipid membranes. Different approaches using both liquid state and solid state NMR are outlined here, with an emphasis on solid state NMR methods, to study the structures of antimicrobial peptides in lipid bilayers as well as the effect of these peptides on model membranes. Different NMR techniques for observing both peptides and lipids are explained, including 2H, 13C, 15N, and 19F labels, or natural abundance 1H, 13C, or 31P. Previous studies in the field are extensively reviewed in easily accessible tables. 2004 Wiley Periodicals, Inc. Concepts Magn Reson 23A: 89,120, 2004. [source]


NMR Investigation of the Bound Conformation of Natural and Synthetic Oligomannosides to Banana Lectin

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2007
Caroline Clavel
Abstract The conformational behaviour of three mannose-containing oligosaccharides, namely, the ,1,3[,1,6] trisaccharide, a heptasaccharide with ,1,2, ,1,3 and ,1,6 linkages and a tetrasaccharide consisting of ,1,3 and ,1,2 linkages, when bound to banana lectin (BanLec) has been evaluated by trNOE NMR methods and docking calculations. It was found that the molecular recognition event involves a conformational selection process with only one of the conformations present in the free state of the sugar being recognised at the lectin binding site. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]


Structural studies of the capsular polysaccharide and lipopolysaccharide O-antigen of Aeromonas salmonicida strain 80204-1 produced under in vitro and in vivo growth conditions

FEBS JOURNAL, Issue 22 2004
Zhan Wang
Aeromonas salmonicida is a pathogenic aquatic bacterium and the causal agent of furunculosis in salmon. In the course of this study, it was found that when grown in vitro on tryptic soy agar, A. salmonicida strain 80204-1 produced a capsular polysaccharide with the identical structure to that of the lipopolysaccharide O-chain polysaccharide. A combination of 1D and 2D NMR methods, including a series of 1D analogues of 3D experiments, together with capillary electrophoresis-electrospray MS (CE-ES-MS), compositional and methylation analyses and specific modifications was used to determine the structure of these polysaccharides. Both polymers were shown to be composed of linear trisaccharide repeating units consisting of 2-acetamido-2-deoxy- d -galacturonic acid (GalNAcA), 3-[(N -acetyl-L-alanyl)amido]-3,6-dideoxy- d -glucose{3-[(N -acetyl- l -alanyl)amido]-3-deoxy- d -quinovose, Qui3NAlaNAc} and 2-acetamido-2,6-dideoxy- d -glucose (2-acetamido-2-deoxy- d -quinovose, QuiNAc) and having the following structure: [,3)- , - d -GalpNAcA-(1,3)- , - d -QuipNAc-(1,4)- , - d -Quip3NAlaNAc-(1-]n, where GalNAcA is partly presented as an amide and AlaNAc represents N -acetyl- l -alanyl group. CE-ES-MS analysis of CPS and O-chain polysaccharide confirmed that 40% of GalNAcA was present in the amide form. Direct CE-ES-MS/MS analysis of in vivo cultured cells confirmed the formation of a novel polysaccharide, a structure also formed in vitro, which was previously undetectable in bacterial cells grown within implants in fish, and in which GalNAcA was fully amidated. [source]


Synthesis and stereochemical studies of 2-substituted thiazolidine-4-carboxamide derivatives

JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 6 2000
Bernard Refouvelet
A series of new 2-substituted thiazolidine-4-carboxamide derivatives which have potentially useful immunological properties, have been synthesized in a stereoselective manner by coupling 2-subsituted thiazolidine-4-carboxylic acids with amines or amino esters. The structure of these compounds was established by combination of NMR methods and by X-ray analysis. [source]


Physical image vs structure relation: part 12 , structure of 2,2,5,5-tetramethyl-dihydro-furan-3-one oxime and its protonated forms through isomerization and NMR spectra,

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2007
Ryszard B. Nazarski
Abstract The study of an isomeric A/B mixture of the title oxime 1, by photolytic or thermal E,Z -isomerization and NMR measurement including 1H{1H}-NOE difference spectra, led to assignment of the E configuration to its predominating form A. The 1H/13C data were interpreted in terms of steric overcrowding of both forms, especially of the thermolabile photoproduct B. Four classical (empirical) NMR methods of elucidating the oxime geometry were critically tested on these results. Unexpected vapor-phase photoconversion A,B in the window glass-filtered solar UV and spectroscopic findings on their protonated states were discussed, as well. The kinetically controlled formation of the N- protonated species (Z)- 5+ was proved experimentally. In addition, some 1H NMR assignments reported for structurally similar systems were rationalized (3 and 4) or revised (1 and 7,9) with the GIAO-DFT(B3LYP) and/or GIAO-HF calculational results. Copyright 2007 John Wiley & Sons, Ltd. [source]


The addition reaction of diamides to 1,2,5-thiadiazole 1,1-dioxide derivatives,

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2004
Jos A. Caram
Abstract The reactions of several derivatives of 1,2,5-thiadiazole 1,1-dioxide [3,4-diphenyl-(1a), 3,4-bis(p -methoxyphenyl)-(1b), phenanthro[9,10- c]-(1c) and acenaphtho[1,2-c]-1,2,5-thiadiazole 1,1-dioxide (1d), 3,4-diphenyl-1,2,5-thiadiazoline 1,1-dioxide (2a) and 4-ethoxy-5-methyl-3,4-diphenyl-1,2,5-thiadiazoline 1,1-dioxide (2b)], with reagents possessing two nucleophilic nitrogen atoms (urea, N,N,-dimethylurea, thiourea, N -methylthiourea, N -ethylthiourea, N -allylthiourea, N,N,-diethylthiourea, N,N,-diphenylthiourea, dithioxamide and sulfamide), were followed by cyclic voltammetry (CV) and UV,visible spectrophotometry in aprotic solvent solution. The products were isolated, characterized by IR, 1H NMR and 13C NMR methods and their structure was confirmed by single-crystal x-ray diffraction. Several substrate,nucleophile combinations (1a,d and 2a with some ureas and thioureas) reacted to give good yields of new compounds formed by the addition reaction of the two nitrogen atoms of the nucleophile to the two >CN, double bonds of the 1,2,5-thiadiazole 1,1-dioxide ring. Some systems (1a,dithioxamide and 2b,thiourea) did not react, whereas in others (e.g. 1a,sulfamide) a monoaddition equilibrium reaction was observed. Copyright 2004 John Wiley & Sons, Ltd. [source]


Long-range substituent and temperature effect on prototropic tautomerism in 2-(acylmethyl)quinolines

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 4 2001
Ryszard Gawinecki
Abstract Tautomeric equilibria between 2-(cinnamoylmethyl)quinoline, (Z)-1,2-dihydro-2-(cinnamoylmethylene)quinoline and (Z)-4-phenyl-1-(2-quinolyl)-1,3-butadien-2-ol were studied by 1H, 13C and 15N NMR methods. The ,CHCH, fragment conjugated with phenyl and a strong electron donor p -(1-pyrrolidine) substituent were found to favour the enolimine tautomer. This undergoes fast exchange (on the NMR time-scale) with the enaminone form. The amount of the latter tautomer was found to increase at low temperatures. Copyright 2001 John Wiley & Sons, Ltd. [source]


Acid-labile, thermoresponsive (meth)acrylamide polymers with pendant cyclic acetal moieties

JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 13 2008
Xiao-Nan Huang
Abstract Acid-labile, thermoresponsive polymers with pendant six-membered cyclic acetal groups were prepared by radical polymerization of two monomers, N -(2,2-dimethyl-1,3-dioxan-5-yl) methacrylamide (NDMM) and N -(2,2-dimethyl-1,3-dioxan-5-yl) acrylamide (NDMA). The aqueous solution properties of the polymers, PNDMM and PNDMA, were studied by turbidimetry, 1H NMR, fluorescence, and DSC measurements. It is found that both polymers show sensitive and reversible phase transitions with distinct lower critical solution temperatures (LCST). Below their LCSTs, there are still some polymer aggregates as evidenced by measurements of pyrene excitation spectra and urea effects on the cloud points (CP) of polymers. The salting effect of six inorganic sodium salts on the phase transition behavior of PNDMM was investigated by turbidimetric approach. The salting-out to salting-in effect is in the order of SO42, > F, > Cl, > Br, > I, > SCN,, following the Hofmeister's series. pH-dependent hydrolysis of PNDMM and PNDMA was studied by turbidimetric and 1H NMR methods. They are both pH-sensitive and their hydrolysis rates significantly increase with decreasing pH value. The CP of PNDMM gradually increases with the acid-triggered hydrolysis of the acetal groups and the hydrolyzed polymer with , 30% hydrolysis degree does not show thermally induced phase transition. 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4332,4343, 2008 [source]


Detection of platinum dihydride bisphosphine complexes and studies of their reactivity through para -hydrogen-enhanced NMR methods

MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2008
Cyril Godard
Abstract In-situ NMR studies on the reactions of Pt{CH2 = CHSi(Me)2}2O)(PCy3) with phosphines, HSiEt3 and - hydrogen or Pt(L)(L,)(Me)2 alone enable the detection of cis -Pt(L)(L,)(H)2 [L = PCy3 and L, = PCy2H, PPh3 or PCy3] which then undergo hydride site interchange and H2 reductive elimination on the NMR timescale. Copyright 2008 John Wiley & Sons, Ltd. [source]


The use of unsymmetrical indirect covariance NMR methods to obtain the equivalent of HSQC-NOESY data

MAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2007
Kirill A. Blinov
We have recently demonstrated that unsymmetrical indirect covariance NMR methods can be used to mathematically calculate the equivalent of low sensitivity, hyphenated NMR experiments by combining data from a pair of higher sensitivity experiments. The present report demonstrates the application of this method to the combination of HSQC and NOESY spectra to provide results comparable to HSQC-NOESY data, albeit with greater sensitivity and with considerably less spectrometer time. Copyright 2007 John Wiley & Sons, Ltd. [source]


Structural elucidation by 1D and 2D NMR of three isomers of a carotenoid lysophosphocholine and its synthetic precursors

MAGNETIC RESONANCE IN CHEMISTRY, Issue 4 2004
Bente Jeanette Foss
Abstract A carotenoic acid was used to obtain a long-chain unsaturated lysophosphocholine. The carotenoid lysophosphocholine was synthesized by two methods. The first method resulted in mixtures of regioisomers for each step in the synthetic route. Homo- and heteronuclear 1D and 2D NMR methods were employed to elucidate the structures of the individual isomers and their intermediates. The pure regioisomer [1-(,-apo-8, -carotenoyl)-2-lyso- glycero -3-phosphocholine] was obtained by a second method, but in low yield. The 1D 1H NMR subtraction spectrum of the mixture and the pure regioisomer was used to interpret the 1H shifts of the unsaturated acyl moieties. The 1H and 13C signals of the acyl chain show characteristic shifts depending on the positions of the choline and the acyl group attached to the glycerol backbone. Therefore, the unsaturated acyl chain signals have diagnostic values for the identification of isomers of unsaturated (lyso)phosphocholines. Chemical shifts and indirect coupling constants are reported for each of the major components of the mixtures. The methods used were 1D (1H, 13C and 31P) and 2D (H,H-COSY, HMBC, HSQC and HETCOR) NMR. Copyright 2004 John Wiley & Sons, Ltd. [source]


NMR methods for studying the structure and dynamics of oncogenic and antihistaminic peptides in biomembranes

MAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2004
Christina Sizun
Abstract We present several applications of both wide-line and magic angle spinning (MAS) solid-state NMR of bicelles in which are embedded fragments of a tyrosine kinase receptor or enkephalins. The magnetically orientable bicelle membranes are shown to be of particular interest for studying the functional properties of lipids and proteins in a state that is very close to their natural environment. Quadrupolar, dipolar and chemical shielding interactions can be used to determine minute alterations of internal membrane dynamics and the orientation of peptides with respect to the membrane plane. MAS of bicelles can in turn lead to high-resolution proton spectra of hydrated membranes. Using deuterium,proton contrast methods one can then obtain pseudo-high-resolution proton spectra of peptides or proteins embedded in deuterated membranes and determine their atomic 3D structure using quasi-conventional liquid-state NMR methods. Copyright 2004 John Wiley & Sons, Ltd. [source]


Complete 1H and 13C NMR assignment for aryl diisoprenes

MAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2003
Jorge L. Zambrano
Abstract The characterization of four aryl diisoprenes was carried out by 1D- and 2D-NMR methods, which permitted the assignment of the signals of all protons and all carbon atoms. Copyright 2003 John Wiley & Sons, Ltd. [source]


NMR methods applied to anisotropic diffusion

MAGNETIC RESONANCE IN CHEMISTRY, Issue 13 2002
Istvn Fur
Abstract The methodology of NMR experiments intended to measure anisotropic diffusion is reviewed. Experiments of this kind preferably require oriented samples and/or orientation-dependent spin coupling and/or magnetic field gradients in different directions. One strategy of diffusion experiments in anisotropic systems with broad NMR lines employs line narrowing techniques, thereby allowing for efficient gradient encoding/decoding. Depending on the nuclei, spin couplings and samples, the preferred methods vary from decoupling through echo techniques to magic angle sample orientation and spinning. Another avenue to efficient gradient encoding/decoding is through very strong magnetic field gradients. Either way, anisotropic diffusion reveals new structural features as illustrated by a few selected examples in liquid crystals and in biological tissues. Copyright 2002 John Wiley & Sons, Ltd. [source]


Total assignment of 1H and 13C NMR spectra of three triterpene saponins from roots of Silene vulgaris (Moench) Garcke

MAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2002
Sabine Bouguet-Bonnet
Abstract The assignments of 1H and 13C NMR spectra for three new triterpene saponins from Silene vulgaris (gypsogenin 3- O -glucuronide, quillaic acid 3- O -glucuronide, and gypsogenin 3- O -glycoside) are reported. In addition to 1D NMR methods, 2D NMR techniques (COSY, HSQC, HMBC, and HSQC-TOCSY) were used for the assignments. Copyright 2002 John Wiley & Sons, Ltd. [source]


Identification of isomeric dicaffeoylquinic acids from Eleutherococcus senticosus using HPLC-ESI/TOF/MS and 1H-NMR methods

PHYTOCHEMICAL ANALYSIS, Issue 6 2002
Ari Tolonen
Abstract Liquid chromatography,electrospray time-of-flight mass spectrometry (HPLC-ESI/TOF/MS) and a novel NMR technique, developed to maximise the sensitivity obtained from the standard NMR spectrometer, have been applied to the identification of the phenolic constituents of Eleutherococcus senticosus. In addition, molecular modelling and dihedral bond angle calculations based on the vicinal 3JHH -coupling constants have been used in the unambiguous assignment of signals in the 1H-NMR spectra. 5,- O -Caffeoylquinic acid and three isomeric compounds, 1,,5,- O -dicaffeoylquinic acid, 3,,5,- O -dicaffeoylquinic acid and 4,,5,- O -dicaffeoylquinic acid, have been isolated and identified from a sample. The isolation and structure determination of the latter two compounds are reported for the first time from this plant. Copyright 2002 John Wiley & Sons, Ltd. [source]


Synthesis and NMR characterization of 6-Phenyl-6-deoxy-2,3-di- O -methylcellulose,

POLYMERS FOR ADVANCED TECHNOLOGIES, Issue 6 2002
Dr Navzer (Nozar) D. Sachinvala
Abstract Cellulose (1) was converted for the first time to 6-phenyl-6-deoxy-2,3-di- O -methylcellulose (6) in 33% overall yield. Intermediates in the five-step conversion of 1 to6 were: 6- O -tritylcellulose (2), 6- O -trityl-2,3-di- O -methylcellulose (3), 2,3-di- O -methylcellulose (4); and 6-bromo-6-deoxy-2,3-di- O -methylcellulose (5). Elemental and quantitative carbon-13 analyses were concurrently used to verify and confirm the degrees of substitution in each new polymer. Gel permeation chromotography (GPC) data were generated to monitor the changes in molecular weight (DPw) as the synthesis progressed, and the compound average decrease in cellulose DPw was , 27%. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were used to characterize the decomposition of all polymers. The degradation temperatures (,C) and percent char at 500,C of cellulose derivatives 2 to 6 were 308.6 and 6.3%, 227.6,C and 9.7%, 273.9,C and 30.2%, 200.4,C and 25.6%, and 207.2,C and 27.0%, respectively. The glass transition temperature (Tg) of6- O -tritylcellulose by dynamic mechanical analysis (DMA) occurred at 126.7,C and the modulus (E,, Pa) dropped 8.9 fold in the transition from ,150,C to,+,180,C (6.6,,109 to 7.4,,108 Pa). Modulus at 20,C was 3.26,,109 Pa. Complete proton and carbon-13 chemical shift assignments of the repeating unit of the title polymer were made by a combination of the HMQC and COSY NMR methods. Ultimate non-destructive proof of carbon,carbon bond formation at C6 of the anhydroglucose moiety was established by generating correlations between resonances of CH26 (anhydroglucose) and C1,, H2,, and H6, of the attached aryl ring using the heteronuclear multiple-bond correlation (HMBC) method. In this study, we achieved three major objectives: (a) new methodologies for the chemical modification of cellulose were developed; (b) new cellulose derivatives were designed, prepared and characterized; (c) unequivocal structural proof for carbon,carbon bond formation with cellulose was derived non-destructively by use of one- and two-dimensional NMR methods. Copyright 2002 John Wiley & Sons, Ltd. [source]


Pre-structured motifs in the natively unstructured preS1 surface antigen of hepatitis B virus

PROTEIN SCIENCE, Issue 10 2007
Seung-Wook Chi
Abstract The preS1 surface antigen of hepatitis B virus (HBV) is known to play an important role in the initial attachment of HBV to hepatocytes. We have characterized structural features of the full-length preS1 using heteronuclear NMR methods and discovered that this 119-residue protein is inherently unstructured without a unique tertiary structure under a nondenaturing condition. Yet, combination of various NMR parameters shows that the preS1 contains "pre-structured" domains broadly covering its functional domains. The most prominent domain is formed by residues 27,45 and overlaps with the putative hepatocyte-binding domain (HBD) encompassing residues 21,47, within which two well-defined pre-structured motifs, formed by Pro32,Ala36 and Pro41,Phe45 are found. Additional, somewhat less prominent, pre-structured motifs are also formed by residues 11,18, 22,25, 37,40, and 46,50. Overall results suggest that the preS1 is a natively unstructured protein (NUP) whose N-terminal 50 residues, populated with multiple pre-structured motifs, contribute critically to hepatocyte binding. [source]


Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination

PROTEIN SCIENCE, Issue 5 2006
Linda Columbus
Abstract Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be greatly facilitated by biophysical techniques that are capable of evaluating and assessing the fold and oligomeric state of these proteins solubilized in detergent micelles. In this study, an approach to the characterization of detergent-solubilized integral membrane proteins is presented. Eight Thermotoga maritima membrane proteins were screened for solubility in 11 detergents, and the resulting soluble protein,detergent complexes were characterized with small angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD) spectroscopy, and chemical cross-linking to evaluate the homogeneity, oligomeric state, radius of gyration, and overall fold. A new application of SAXS is presented, which does not require density matching, and NMR methods, typically used to evaluate soluble proteins, are successfully applied to detergent-solubilized membrane proteins. Although detergents with longer alkyl chains solubilized the most proteins, further characterization indicates that some of these protein,detergent complexes are not well suited for NMR structure determination due to conformational exchange and protein oligomerization. These results emphasize the need to screen several different detergents and to characterize the protein,detergent complex in order to pursue structural studies. Finally, the physical characterization of the protein,detergent complexes indicates optimal solution conditions for further structural studies for three of the eight overexpressed membrane proteins. [source]


Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy

PROTEIN SCIENCE, Issue 12 2001
Wei Li
Abstract Translation initiation factor 1A (aIF-1A) from the archaeon Methanococcus jannaschii was expressed in Escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional NMR methods. The protein was found to be a member of the OB-fold family of RNA-associated proteins, containing a barrel of five beta-strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1A (eIF-1A), as well as the prokaryotic translation initiation factor IF1. External to the , barrel, aIF-1A contains an ,-helix at its C-terminal and a flexible loop at its N-terminal, features that are qualitatively similar to those found in eIF-1A, but not present in prokaryotic IF1. The structural model of aIF-1A, when used in combination with primary sequence information for aIF-1A in divergent species, permitted the most-conserved residues on the protein surface to be identified, including the most likely candidates for direct interaction with the 16S ribosomal RNA and other components of the translational apparatus. Several of the conserved surface residues appear to be unique to the archaea. Nitrogen-15 relaxation and amide exchange rate data were used to characterize the internal motions within aIF-1A, providing evidence that the protein surfaces that are most likely to participate in intermolecular interactions are relatively flexible. A model is proposed, suggesting some specific interactions that may occur between aIF-1A and the small subunit of the archaeal ribosome. [source]


Designed protein G core variants fold to native-like structures: Sequence selection by ORBIT tolerates variation in backbone specification

PROTEIN SCIENCE, Issue 2 2001
Scott A. Ross
Abstract The solution structures of two computationally designed core variants of the ,1 domain of streptococcal protein G (G,1) were solved by 1H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native G,1 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between G,1's ,-helix and ,-sheet was increased by 15% relative to native G,1. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core ,1 angles in both variants, five of six ,2 angles in the threefold mutant and four of seven ,2 angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior. [source]


The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus

PROTEIN SCIENCE, Issue 5 2000
Gary S. Thompson
Abstract The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35 0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two ,-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. [source]


Solution structure of the cyclic peptide contryphan-Vn, a Ca2+ -dependent K+ channel modulator

BIOPOLYMERS, Issue 3 2004
Tommaso Eliseo
Abstract The solution structure of contryphan-Vn, a cyclic peptide with a double cysteine S,S bridge and containing a D -tryptophan extracted from the venom of the cone snail Conus ventricosus, has been determined by NMR spectroscopy using a variety of homonuclear and heteronuclear NMR methods and restrained molecular dynamics simulations. The main conformational features of backbone contryphan-Vn are a type IV ,-turn from Gly 1 to Lys 6 and a type I ,-turn from Lys 6 to Cys 9. As already found in other contryphans, one of the two prolines,the Pro4,is mainly in the cis conformation while Pro7 is trans. A small hydrophobic region probably partly shielded from solvent constituted from the close proximity of side chains of Pro7 and Trp8 was observed together with a persistent salt bridge between Asp2 and Lys6, which has been revealed by the diagnostic observation of specific nuclear Overhauser effects. The salt bridge was used as a restraint in the molecular dynamics in vacuum but without inserting explicit electrostatic contribution in the calculations. The backbone of the unique conformational family found of contryphan-Vn superimposes well with those of contryphan-Sm and contryphan-R. This result indicates that the contryphan structural motif represents a robust and conserved molecular scaffold whose main structural determinants are the size of the intercysteine loop and the presence and location in the sequence of the D -Trp and the two Pro residues. 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source]


New structural insights from Raman spectroscopy of proteins and their assemblies

BIOPOLYMERS, Issue 4-5 2002
George J. Thomas Jr.Article first published online: 9 MAY 200
Abstract Protein structure and stability are sensitive to and dependent on the local interactions of amino acid side chains. A diverse and important type of side-chain interaction is the hydrogen bond. Although numerous hydrogen bonds are resolved in protein 3-dimensional structures, those of the cysteine sulfhydryl group (S H) are elusive to high-resolution X-ray and NMR methods. However, the nature and strength of sulfhydryl hydrogen bonds (SH,X) are amenable to investigation by Raman spectroscopy. The power of the Raman method for characterizing SH,X interactions is illustrated by resolving the Raman SH stretching band for each of the eight cysteines per 666-residue subunit in the trimeric tailspike of icosahedral bacteriophage P22. The Raman sulfhydryl signatures of the wild-type tailspike and eight single-site cysteine to serine mutants reveal a heretofore unrecognized diversity of SH hydrogen bonds in a native protein. The use of Raman spectroscopy to identify the non-hydrogen-bonded state of the tyrosine phenoxyl group is also described. This unusual and unexpected state occurs for all tyrosines in the assembled capsids of filamentous viruses Ff and Pf1. The Raman spectral signature of the non-hydrogen-bonded tyrosine phenoxyl, which is characterized by an extraordinary Raman Fermi doublet intensity ratio (I850/I830 = 6.7), extends and refines the existing correlation for hydrogen-bonded tyrosines. Finally, a novel Raman signature for tryptophan in the Pf3 filamentous virus is identified, which is proposed as diagnostic of "cation,, interaction" involving the guanidinium group of Arg 37 as a cation donor and the indolyl ring of Trp 38 as a ,-electron acceptor. These studies demonstrate the power of Raman spectroscopy for investigating the interactions of key side chains in native protein assemblies. 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 214,225, 2002 [source]


High-Resolution Solid-State NMR Studies on Uniformly [13C,15N]-Labeled Ubiquitin

CHEMBIOCHEM, Issue 9 2005
Karsten Seidel
Abstract Understanding of the effects of intermolecular interactions, molecular dynamics, and sample preparation on high-resolution magic-angle spinning NMR data is currently limited. Using the example of a uniformly [13C,15N]-labeled sample of ubiquitin, we discuss solid-state NMR methods tailored to the construction of 3D molecular structure and study the influence of solid-phase protein preparation on solid-state NMR spectra. A comparative analysis of13C,,13C,, and13C, resonance frequencies suggests that13C chemical-shift variations are most likely to occur in protein regions that exhibit an enhanced degree of molecular mobility. Our results can be refined by additional solid-state NMR techniques and serve as a reference for ongoing efforts to characterize the structure and dynamics of (membrane) proteins, protein complexes, and other biomolecules by high-resolution solid-state NMR. [source]


Self-Assembled Ionophores from Isoguanosine: Diffusion NMR Spectroscopy Clarifies Cation's and Anion's Influence on Supramolecular Structure

CHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2007
Tamar Evan-Salem
Abstract Cation-templated self-assembly of the lipophilic isoguanosine (isoG,1) with different monovalent cations (M+=Li+, Na+, K+, NH4+, and Cs+) was studied in solvents of different polarity by using diffusion NMR spectroscopy. Previous studies that did not use diffusion NMR techniques concluded that isoG,1 forms both pentamers (isoG,1)5,M+ and decamers (isoG,1)10,M+ in the presence of alkali-metal cations. The present diffusion NMR studies demonstrate, however, that isoG,1 does not form (isoG,1)5,M+ pentamers. In fact, the diffusion NMR data indicates that both doubly charged decamers of formula (isoG,1)10,2,M+ and singly charged decamers, (isoG,1)10,M+, are formed with lithium, sodium, potassium, and ammonium tetraphenylborate salts (LiB(Ph)4, KB(Ph)4, NaB(Ph)4 and NH4B(Ph)4), depending on the isoG,1:salt stoichiometry of the solution. In the presence of CsB(Ph)4, isoG,1 affords only the singly charged decamers (isoG,1)10,Cs+. By monitoring the diffusion coefficient of the B(Ph)4, ion in the different mixtures of solvents, we also concluded that the anion is more strongly associated to the doubly charged decamers (isoG,1)10,2,M+ than to the singly charged decamers (isoG,1)10,M+. The (isoG,1)10,2,M+ species can, however, exist in solution without the mediation of the anion. This last conclusion was supported by the finding that the doubly charged decamers (isoG,1)10,2,M+ also prevail in 1:1 CD3CN:CDCl3, a solvent mixture in which the B(Ph)4, ion does not interact significantly with the self-assembled complex. These diffusion measurements, which have provided new and improved structural information about these decameric isoG,1 assemblies, demonstrate the utility of combining diffusion NMR techniques with conventional NMR methods in seeking to characterize labile, multicomponent, supramolecular systems in solution, especially those with high symmetry. [source]


Determination of absolute configurations by X-ray crystallography and 1H NMR anisotropy

CHIRALITY, Issue 5 2008
Nobuyuki Harada
Abstract To determine the absolute configurations of chiral compounds, many spectroscopic and diffraction methods have been developed. Among them, X-ray crystallographic Bijvoet method, CD exciton chirality method, and the combination of vibrational circular dichroism and quantum mechanical calculations are of nonempirical nature. On the other hand, X-ray crystallography using a chiral internal reference, and 1H NMR spectroscopy using chiral anisotropy reagents are relative and/or empirical methods. In addition to absolute configurational determinations, preparations of enantiopure compounds are strongly desired. As chiral reagents useful for both the preparation of enantiopure compounds by HPLC separation and the simultaneous determination of their absolute configurations, we have developed camphorsultam dichlorophthalic acid (CSDP acid) for X-ray crystallography and 2-methoxy-2-(1-naphthyl)propionic acid (M,NP acid) for 1H NMR spectroscopy. In this review, the principles and applications of these X-ray and NMR methods are explained using mostly our own data. Chirality, 2008. 2007 Wiley-Liss, Inc. [source]