NMR - PubMed

J Chem Theory Comput. 2014 Apr 8;10(4):1781-7. doi: 10.1021/ct4010646.

ABSTRACT

A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.

PMID:26580385 | DOI:10.1021/ct4010646

J Magn Reson Imaging. 2014 Sep;40(3):682-90. doi: 10.1002/jmri.24397. Epub 2013 Oct 31.

ABSTRACT

PURPOSE: To compare DW-MRI between 1.5 and 3 Tesla (T) in terms of image quality, apparent diffusion coefficient (ADC), reproducibility, lesion-to-background contrast and signal-to-noise ratio (SNR), using a test object.

MATERIALS AND METHODS: A spherical diffusion phantom was used for qualitatively assessing image quality and performing quantitative measurements between the two field strengths.

RESULTS: Distortions and signal losses degraded image quality at 3T even when the protocols were optimized for minimum TE. The ADC, in the majority of the phantom compartments, was significantly different between 1.5T and 3T (P < 0.009), while the average coefficient of variation, excluding the phantom compartments affected by artifacts, was <1.3% at both field strengths. The lesion-to-background contrast was improved at 1.5T for images acquired with b = 1000 s/mm(2) and comparable contrast was achieved at 3T with higher b-values. The SNR gain at 3T could, in theory, be balanced by the increased number of signal excitations one can accommodate at 1.5T to perform DW-MRI within the same acquisition time and possibly improved image quality, when 3T systems with no parallel transmission are used.

CONCLUSION: Further phantom and in vivo studies are required to investigate the utility of DW-MRI at 3T, if image quality and acquisition times comparable to the ones from 1.5T are assumed.

PMID:24925470 | DOI:10.1002/jmri.24397

Phytochemistry. 2011 Jun;72(9):875-81. doi: 10.1016/j.phytochem.2011.03.010. Epub 2011 Apr 7.

ABSTRACT

An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose formation was induced by lactofen (1), a soybean (Glycine max L.) disease resistance-inducing herbicide. First, LC-MS analyses of control and lactofen (1)-induced soybean extracts were performed. The LC-MS raw data were then processed by a custom designed bioinformatics program to detect the induced metabolites so formed. Finally, structures of unknown induced metabolites were determined on the basis of their 1D and 2D NMR spectroscopic data. Structure of two previously unreported compounds, 7,8-dihydroxy-4'-methoxy-3'-prenylisoflavone (2) and 7-hydroxy-4',8-dimethoxy-3'-prenylisoflavone (3) were elucidated together with four known prenylated compounds, 3'-prenyldaidzein (4), 8-prenyldaidzein (5), 3'-prenylgenistein (6), and 4-prenylcoumestrol (7). Compounds (2-6) are reported for the first time in soybean, as are the (13)C chemical shift assignments for compound (7). Formation of these six prenylated compounds was also induced by the primary defense glucan elicitor from the cell wall of the pathogen Phytophthora sojae (Kauf. and Gerde.), further suggesting a potential role in soybean defense. These results highlight the metabolic flexibility within soybean secondary product pathways and suggest that prenylation may be associated with defense responses. Moreover, this study demonstrates a promising future approach using metabolomics on elicitor-induced plants for discovery of unknown compounds even in relatively well studied plants.

PMID:21477824 | DOI:10.1016/j.phytochem.2011.03.010

Biochemistry. 2004 Sep 28;43(38):12152-61. doi: 10.1021/bi049116o.

ABSTRACT

Human gankyrin (226 residues, 24.4 kDa) is a liver oncoprotein that plays an important role in the development of human hepatocellular carcinomas. In this paper, its solution structure is reported, which is the largest ankyrin protein ever determined by NMR. The highly degenerate primary sequences of the seven ankyrin repeats presented a major challenge, which was overcome by combined use of TROSY experiments, perdeuterated samples, isotope-filtered NMR experiments, and residual dipolar couplings. The final structure was of high quality, with atomic rmsds for the backbone (N, C', and C(alpha)) and all heavy atoms (residues 4-224) of 0.69 +/- 0.09 and 1.04 +/- 0.09 A, respectively. Detailed analyses of NMR data suggested that the conserved TPLH motifs play important structural roles in stabilizing the repeating ankyrin scaffold. Gankyrin is conformationally more stable than the tumor suppressor p16(INK4A), possibly due to the structural roles of conserved residues evidenced by slowly exchanging backbone amides as well as hydrogen bonding networks involving labile side chain protons. Structural comparison with p16(INK4A) identified several residues of gankyrin that are potentially important for CDK4 binding, whereas observation of the thiol proton of C180 indicated a well-structured Rb-binding site in the helical region of the sixth ankyrin repeat. Interestingly, the CDK4-binding site and Rb-binding site located in N- and C-terminal regions, respectively, are separated by comparatively more stable ankyrin repeats and highly condensed positive surface charge. These results and analyses will shed light on the structural basis of the function of human gankyrin.

PMID:15379554 | DOI:10.1021/bi049116o

J Mol Biol. 2004 Jan 2;335(1):371-81. doi: 10.1016/j.jmb.2003.10.032.

ABSTRACT

Recent studies by use of short phosphopeptides showed that forkhead-associated (FHA) domains recognize pTXX(D/I/L) motifs. Solution structures and crystal structures of several different FHA domains and their complexes with short phosphopeptides have been reported by several groups. We now report the solution structure of the FHA domain of human Ki67, a large nuclear protein associated with the cell-cycle. Using fragments of its binding partner hNIFK, we show that Ki67-hNIFK binding involves ca 44 residues without a pTXX(D/I/L) motif. The pThr site of hNIFK recognized by Ki67 FHA is pThr234-Pro235, a motif also recognized by the proline isomerase Pin1. Heteronuclear single quantum coherence (HSQC) NMR was then used to map out the binding surface, and structural analyses were used to identify key binding residues of Ki67 FHA. The results represent the first structural characterization of the complex of an FHA domain with a biologically relevant target protein fragment. Detailed analyses of the results led us to propose that three major factors control the interaction of FHA with its target protein: the pT residue, +1 to +3 residues, and an extended binding surface, and that variation in the three factors is the likely cause of the great diversity in the function and specificity of FHA domains from different sources.

PMID:14659764 | DOI:10.1016/j.jmb.2003.10.032