Genomes and Genes
biomolecular nuclear magnetic resonance
Summary: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
- Chang C, Zhang L, Chen R, Kuo L, Huang J, Huang H, et al. Antioxidant and anti-inflammatory phenylpropanoid derivatives from Calamus quiquesetinervius. J Nat Prod. 2010;73:1482-8 pubmed publisher..6-8.4 ?M). Of the tested isolates, compounds 4-6 and 9 showed potent inhibition (IC(50) 9.2-29.5 ?M) of LPS-stimulated NO production when compared with a positive control substance, quercetin (IC(50) 34.5 ?M). ..
- Acuña U, Figueroa M, Kavalier A, Jancovski N, Basile M, Kennelly E. Benzophenones and biflavonoids from Rheedia edulis. J Nat Prod. 2010;73:1775-9 pubmed publisher..Compound 1 showed significant antioxidant activity in both DPPH and ABTS free radical scavenging assays, whereas compound 2 was inactive. ..
- Bosco D, Eisenmesser E, Clarkson M, Wolf Watz M, Labeikovsky W, Millet O, et al. Dissecting the microscopic steps of the cyclophilin A enzymatic cycle on the biological HIV-1 capsid substrate by NMR. J Mol Biol. 2010;403:723-38 pubmed publisher..The results illustrate that a quantitative analysis of catalysis using the biological substrates is critical when interpreting the effects of PPIase mutations in biological assays. ..
- Li H, Yang S, Wang H, Tian J, Gao W. Biosynthesis of the iridoid glucoside, lamalbid, in Lamium barbatum. Phytochemistry. 2010;71:1690-4 pubmed publisher..Based on the (13)C labeling pattern of lamalbid and the incorporation data, we deduce that the iridoid glucoside in L. barbatum is biosynthesized through the MEP pathway, whereas the classic MVA pathway is not utilized. ..
- Pieber B, Schober S, Goebl C, Mittelbach M. Novel sensitive determination of steryl glycosides in biodiesel by gas chromatography-mass spectroscopy. J Chromatogr A. 2010;1217:6555-61 pubmed publisher..On the given conditions high recovery rates ? 89% can be obtained. Evaluation of lab specific variance and intermediate precision underline the robustness of the method which will be further assessed by Round robin tests. ..
- Horita S, Ishibashi J, Nagata K, Miyakawa T, Yamakawa M, Tanokura M. Isolation, cDNA cloning, and structure-based functional characterization of oryctin, a hemolymph protein from the coconut rhinoceros beetle, Oryctes rhinoceros, as a novel serine protease inhibitor. J Biol Chem. 2010;285:30150-8 pubmed publisher..Although the target molecule of oryctin in the beetle hemolymph remains obscure, our results showed that oryctin is a novel single domain Kazal-type inhibitor and could play a key role in protecting against bacterial infections. ..
- Nam S, Gaudêncio S, Kauffman C, Jensen P, Kondratyuk T, Marler L, et al. Fijiolides A and B, inhibitors of TNF-alpha-induced NFkappaB activation, from a marine-derived sediment bacterium of the genus Nocardiopsis. J Nat Prod. 2010;73:1080-6 pubmed publisher..Fijiolide B did not affect QR1 activity, indicating the importance of the nitrogen substitution pattern for biological activity. On the basis of these data, fijiolide A is viewed as a promising lead for more advanced anticancer testing. ..
- Schneemann I, Kajahn I, Ohlendorf B, Zinecker H, Erhard A, Nagel K, et al. Mayamycin, a cytotoxic polyketide from a Streptomyces strain isolated from the marine sponge Halichondria panicea. J Nat Prod. 2010;73:1309-12 pubmed publisher..Mayamycin (1) exhibited potent cytotoxic activity against eight human cancer cell lines and showed activity against several bacteria including antibiotic-resistant strains. ..
- Lusceac S, Vogel M. (2)H NMR study of the water dynamics in hydrated myoglobin. J Phys Chem B. 2010;114:10209-16 pubmed publisher..The present results are discussed in the context of previous experimental findings for hydrated proteins. ..
- Wazawa T, Miyazaki T, Sambongi Y, Suzuki M. Hydration analysis of Pseudomonas aeruginosa cytochrome c551 upon acid unfolding by dielectric relaxation spectroscopy. Biophys Chem. 2010;151:160-9 pubmed publisher..It indicates that C1 is due to the hydration water of PA c551. Little change in the DR frequency of C1 and a 1.7-fold increase in hydration number were observed. ..
- Dong S, Zhang C, He X, Liu H, Wu Y, Yue J. Mesendanins A-J, limonoids from the leaves and twigs of Melia toosendan. J Nat Prod. 2010;73:1344-9 pubmed publisher..Ten new limonoids, namely, mesendanins A-J (1-10), together with 14 known compounds, have been isolated from the leaves and twigs of Melia toosendan. Their structures were established on the basis of spectroscopic data analysis...
- Mei W, Chen P, Wang H, Huang J, Dai H. Two new sesquiterpenes from endophytic fungus S49 of Cephalotaxus hainanensis. J Asian Nat Prod Res. 2010;12:582-5 pubmed publisher..Their structures were determined based on HR-ESI-MS and spectroscopic techniques (1D and 2D NMR)...
- Fattorusso C, Persico M, Calcinai B, Cerrano C, Parapini S, Taramelli D, et al. Manadoperoxides A-D from the Indonesian sponge Plakortis cfr. simplex. Further insights on the structure-activity relationships of simple 1,2-dioxane antimalarials. J Nat Prod. 2010;73:1138-45 pubmed publisher..For the manadoperoxides, either the endoperoxide linkage is inaccessible to the heme iron or the O1 radical cannot evolve to produce a C-centered radical...
- Xu J, Soong R, Im S, Waskell L, Ramamoorthy A. INEPT-based separated-local-field NMR spectroscopy: a unique approach to elucidate side-chain dynamics of membrane-associated proteins. J Am Chem Soc. 2010;132:9944-7 pubmed publisher..Therefore, using an appropriate model, it is possible to determine side-chain dynamics and provide additional information on the topology and function of a membrane protein in its native environment. ..
- Fawzi N, Ying J, Torchia D, Clore G. Kinetics of amyloid beta monomer-to-oligomer exchange by NMR relaxation. J Am Chem Soc. 2010;132:9948-51 pubmed publisher..The fraction of peptide within the "dark" oligomeric state undergoing exchange with free monomer is calculated to be approximately 3%. ..
- Cheng S, Chuang C, Wang S, Wen Z, Chiou S, Hsu C, et al. Antiviral and anti-inflammatory diterpenoids from the soft coral Sinularia gyrosa. J Nat Prod. 2010;73:1184-7 pubmed publisher..6 and 3.7 microM, respectively. In addition, compounds 1 and 2 showed significant anti-inflammatory activity by reducing the levels of the COX-2 protein (19.6 + or - 3.9% and 29.1 + or - 9.6%, respectively) in RAW 264.7 macrophages...
- Ren X, Lin J, Jin C, Xia B. Solution structure of the N-terminal catalytic domain of human H-REV107--a novel circular permutated NlpC/P60 domain. FEBS Lett. 2010;584:4222-6 pubmed publisher..As H-REV107 is highly similar to lecithin retinol acyltransferase, our study also provides structural insight to this essential enzyme in retinol metabolism. ..
- Bowman S, Bren K. Variation and analysis of second-sphere interactions and axial histidinate character in c-type cytochromes. Inorg Chem. 2010;49:7890-7 pubmed publisher..In summary, chemical shifts of the axial His and exogenous CN(-) bound trans to His are shown to be sensitive probes of the His-Fe(III) interaction in variants of Ht cyt c(552) and display trends that correlate with E(m). ..
- Bullock S, Ringel I, Ish Horowicz D, Lukavsky P. A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila. Nat Struct Mol Biol. 2010;17:703-9 pubmed publisher..Our study provides insights into the basis for RNA cargo recognition and reveals a key biological function encoded by A'-form RNA conformation. ..
- Tan M, Kitajima M, Kogure N, Nonato M, Takayama H. Isolation of pandamarilactonine-H from the roots of Pandanus amaryllifolius and synthesis of epi-pandamarilactonine-H. J Nat Prod. 2010;73:1453-5 pubmed publisher..Eleven known alkaloids were also isolated. Unambiguous assignment of the structure of 1a, including the absolute configuration, was accomplished by spectroscopic analysis and total synthesis of its enantiomer...
- Lind J, Lindahl E, Perálvarez Marín A, Holmlund A, Jornvall H, Mäler L. Structural features of proinsulin C-peptide oligomeric and amyloid states. FEBS J. 2010;277:3759-68 pubmed publisher..This leads to the conclusion that the oligomerization of C-peptide may be relevant also at low concentrations. ..
- Eckhardt B, Grosse W, Essen L, Geyer A. Structural characterization of a beta-turn mimic within a protein-protein interface. Proc Natl Acad Sci U S A. 2010;107:18336-41 pubmed publisher..As building blocks, ?-turn mimics capable of both backbone and side-chain mimicry may simplify the design of synthetic proteins. ..
- Strodel B, Lee J, Whittleston C, Wales D. Transmembrane structures for Alzheimer's A?(1-42) oligomers. J Am Chem Soc. 2010;132:13300-12 pubmed publisher..On the basis of these results, we suggest that A? pores may consist of tetrameric and hexameric ?-sheet subunits. These A? pore models are consistent with the results of biophysical and biochemical experiments. ..
- May E, Armen R, Mannan A, Brooks C. The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners. Proteins. 2010;78:2251-64 pubmed publisher..We propose that C-terminal flexibility is key for mediating the different functional states of the Z-protein. ..
- Zhao Q, Hua W, Zhang L, Guo T, Zhao M, Yan M, et al. Antitumor activity of two gelsemine metabolites in rat liver microsomes. J Asian Nat Prod Res. 2010;12:731-9 pubmed publisher..By the MTT method in vitro, the antitumor activities between gelsemine and its metabolites were compared in the HepG2 and HeLa cell lines. Moreover, the main metabolic pathway was further proposed...
- Miwa K, Furusho Y, Yashima E. Ion-triggered spring-like motion of a double helicate accompanied by anisotropic twisting. Nat Chem. 2010;2:444-9 pubmed publisher..Circular dichroism analysis suggests that the twisting doesn't affect the helicate's handedness. This anisotropic extension-contraction process is reversibly triggered by the successive addition and removal of sodium ions in solution. ..
- Mohankumar R, Ilango K, Santhanakrishnan V, Radhakrishnan V, Narasimhan S. Ethylenediamine: an effective reagent for deacetylation of natural products. J Asian Nat Prod Res. 2010;12:851-8 pubmed publisher..This method enables to deacetylate without affecting other functional groups such as ?,?-unsaturated ketone, ester, ether, etc. in certain tetranortriterpenoids and other acetate-containing natural compounds. ..
- Baldwin A, Religa T, Hansen D, Bouvignies G, Kay L. 13CHD2 methyl group probes of millisecond time scale exchange in proteins by 1H relaxation dispersion: an application to proteasome gating residue dynamics. J Am Chem Soc. 2010;132:10992-5 pubmed publisher..The methodology is applied to the gating residues of the T. acidiphilium proteasome that are shown to undergo extensive motion on the millisecond time scale...
- Mantsyzov A, Ivanova E, Birdsall B, Alkalaeva E, Kryuchkova P, Kelly G, et al. NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor. FEBS J. 2010;277:2611-27 pubmed publisher..Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination. ..
- Hou W, Su Z, Pi H, Yao G, Zhang P, Luo X, et al. Immunosuppressive constituents from Urtica dentata Hand. J Asian Nat Prod Res. 2010;12:707-13 pubmed publisher..Thus, 1 possessed specific immunosuppressive property by eliciting T regulatory cells, which may provide a potential treatment strategy for autoimmune diseases...
- Hass M, Keizers P, Blok A, Hiruma Y, Ubbink M. Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy. J Am Chem Soc. 2010;132:9952-3 pubmed publisher..It is concluded that paramagnetic relaxation dispersion could represent a sensitive method to probe protein dynamics. However, the selection of a rigid attachment site is of critical importance. ..
- Karlsson E, Johnson C, Sarda S, Iddon L, Iqbal M, Meng X, et al. High-performance liquid chromatography/mass spectrometric and proton nuclear magnetic resonance spectroscopic studies of the transacylation and hydrolysis of the acyl glucuronides of a series of phenylacetic acids in buffer and human plasma. Rapid Commun Mass Spectrom. 2010;24:3043-51 pubmed publisher
- Burz D, Shekhtman A. The STINT-NMR method for studying in-cell protein-protein interactions. Curr Protoc Protein Sci. 2010;Chapter 17:Unit 17.11 pubmed publisher..Applications of STINT-NMR, including an in-cell methodology to post-translationally modify interactor proteins and an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) are presented. ..
- Nudelman I, Akabayov S, Schnur E, Biron Z, Levy R, Xu Y, et al. Intermolecular interactions in a 44 kDa interferon-receptor complex detected by asymmetric reverse-protonation and two-dimensional NOESY. Biochemistry. 2010;49:5117-33 pubmed publisher..In addition, the new model strongly supports the recently proposed allosteric changes in IFNalpha2 upon binding of IFNAR1-EC to the binary IFNalpha2-IFNAR2-EC complex. ..
- Merrouche R, Bouras N, Coppel Y, Mathieu F, Monje M, Sabaou N, et al. Dithiolopyrrolone antibiotic formation induced by adding valeric acid to the culture broth of Saccharothrix algeriensis. J Nat Prod. 2010;73:1164-6 pubmed publisher..The production of the dithiolopyrrolone derivatives was induced by adding valeric acid to the culture medium. The compounds exhibited moderate antimicrobial activity in vitro. ..
- Knox R, Lu G, Opella S, Nevzorov A. A resonance assignment method for oriented-sample solid-state NMR of proteins. J Am Chem Soc. 2010;132:8255-7 pubmed publisher..This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination...
- Fang S, Liu J, Li B. A novel 1,10-seco withanolide from Physalis peruviana. J Asian Nat Prod Res. 2010;12:618-22 pubmed publisher..The structures of compounds 1-5 were determined on the basis of spectroscopic methods including extensive 1D and 2D NMR analysis. In addition, the possible biogenetic relationships among these five withanolides are discussed. ..
- Watanabe R, Suzuki T, Oshima Y. Development of quantitative NMR method with internal standard for the standard solutions of paralytic shellfish toxins and characterisation of gonyautoxin-5 and gonyautoxin-6. Toxicon. 2010;56:589-95 pubmed publisher..micromol), respectively. These results are useful to convert the amount of GTX5 and GTX6 into the mouse toxicity, especially in the areas where the dinoflagellate Gymnodinium catenatum predominantly produces both toxins. ..
- Doucet N, Jayasundera T, Simonovic M, Loria J. The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding. Proteins. 2010;78:2459-68 pubmed publisher..Accumulating evidence suggests that very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in this enzyme. ..
- Tan S, Low Y, Choo Y, Abdullah Z, Etoh T, Hayashi M, et al. Strychnan and secoangustilobine A type alkaloids from Alstonia spatulata. Revision of the C-20 configuration of scholaricine. J Nat Prod. 2010;73:1891-7 pubmed publisher..Alkaloids 1, 2, 6, 7, 9, 10, and 13 reversed multidrug resistance in vincristine-resistant KB cells. ..
- Robertson P, Chagot B, Chazin W, Eichman B. Solution NMR structure of the C-terminal DNA binding domain of Mcm10 reveals a conserved MCM motif. J Biol Chem. 2010;285:22942-9 pubmed publisher..Our results provide insight in the action of Mcm10 in the replisome and support a model in which it serves as a central scaffold through coupling of interactions with partner proteins and the DNA...
- Xu M, Zhang Y, Li X, Jacob M, Yang C. Steroidal saponins from fresh stems of Dracaena angustifolia. J Nat Prod. 2010;73:1524-8 pubmed publisher..Antifungal testing of all compounds showed that 6 and 7 were active against Cryptococcus neoformans with IC(50)s of 9.5 and 20.0 ?g/mL, respectively...
- Damo S, Phillips A, Young A, Li S, Woods V, Wemmer D. Probing the conformation of a prion protein fibril with hydrogen exchange. J Biol Chem. 2010;285:32303-11 pubmed publisher..We discuss our data with respect to several structural models proposed for infectious PrP aggregates and highlight HXMS as one of the few techniques well suited to studying natural prions. ..
- Castro A, Moco S, Coll J, Vervoort J. LC-MS-SPE-NMR for the isolation and characterization of neo-clerodane diterpenoids from Teucrium luteum subsp. flavovirens (perpendicular). J Nat Prod. 2010;73:962-5 pubmed publisher..flavovirens, harvested from two different locations. ..
- Rieping W, Vranken W. Validation of archived chemical shifts through atomic coordinates. Proteins. 2010;78:2482-9 pubmed publisher..ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. ..