Papers by Steven Van Doren
Journal of Back and Musculoskeletal Rehabilitation, Oct 26, 1999
Ostrinia furnacalis, a lepidopteran moth, is an invasive pest found in Asia, Australia, Africa, a... more Ostrinia furnacalis, a lepidopteran moth, is an invasive pest found in Asia, Australia, Africa, and parts of the United States. The O. furnacalis pheromone-binding protein2 (OfurPBP2), present in the male moth antenna, plays a role in the detection of female-secreted pheromone in a process that leads to mating. To understand the structural mechanism of pheromone binding and release in this pest, we have initiated characterization of OfurPBP2 by solution NMR. Here, we report the backbone resonance assignments and the secondary structural elements of OfurPBP2 at pH 6.5 using uniformly 13 C, 15 N-labeled protein with various triple resonance NMR experiments. The assignments are 97% completed for backbone and 88% completed for side-chain resonances. The secondary structure of OfurPBP2, based on backbone chemical shifts, consists of eight α-helices, including a well-structured C-terminal helix.
The FASEB Journal, Apr 1, 2012
Methods in Enzymology, 2018
The new TREND NMR software package makes significant new insights into enzymes and other molecule... more The new TREND NMR software package makes significant new insights into enzymes and other molecules easily accessible from collections of unassigned NMR spectra. TREND NMR uses unsupervised multivariate statistics to automate extraction of reaction courses for fitting, including binding isotherms from titrations detected by NMR spectra. The package also makes comparisons and groupings of NMR-detected enzyme states straightforward, by using principal component analysis (PCA). Such comparisons are illustrated for human protein tyrosine phosphatase 1B variants and inhibitor complexes. The "unfold" PCA-based comparisons of these protein phosphatase samples in one to three statistical dimensions are consistent with the recent structural characterizations of the samples, suggesting the relevance of quick assessment by PCA implemented semiautomatically in TREND NMR. The software is free for academic use. Step-by-step protocols are provided for measuring affinities and comparing molecular states using TREND NMR.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Feb 9, 2010
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Feb 9, 2011
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Apr 27, 2010
Biophysical Journal, Feb 1, 2018
Journal of Back and Musculoskeletal Rehabilitation, Sep 8, 2005
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Apr 4, 2012
Journal of Biological Chemistry, Aug 1, 1991
The ubiquinol:cytochrome c2 oxidoreductase (bc1 complex) of Rhodobacter sphaeroides consists of f... more The ubiquinol:cytochrome c2 oxidoreductase (bc1 complex) of Rhodobacter sphaeroides consists of four subunits. One of these subunits, cytochrome c1, is the site of interaction with cytochrome c2, a periplasmic protein. In addition, the sequences of the fbcC gene and of the cytochrome c1 subunit that it encodes suggest that the protein should be located on the periplasmic side of the cytoplasmic membrane and that it is anchored to the membrane by a single membrane-spanning alpha-helix located at the carboxyl-terminal end of the polypeptide. Site-directed mutagenesis of the fbcC gene was used to alter the codon for Gln228 to a stop codon. This results in the production of a truncated version of the cytochrome c1 subunit that lacks the membrane anchor at the carboxyl terminus. The bc1 complex fails to assemble properly as a result of this mutation, but the Rb. sphaeroides cells expressing the altered gene contain a water-soluble form of cytochrome c1 in the periplasm. The water-soluble cytochrome c1 was purified and characterized. The amino-terminal sequence is identical with that of the membrane-bound subunit, indicating the signal sequence is properly processed. High pressure liquid chromatography gel filtration chromatography indicates it is monomeric (28 kDa). The heme content and electrochemical properties are similar to those of the intact subunit within the complex. Flash-induced electron transfer kinetics measured using whole cells demonstrated that the water-soluble cytochrome c1 is competent as a reductant for cytochrome c2 within the periplasmic space. These data show that the isolated water-soluble cytochrome c1 retains many of the properties of the membrane-bound subunit of the bc1 complex and, therefore, will be useful for further structural and functional characterization.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Oct 5, 2011
The FASEB Journal, Apr 1, 2013
Human matrix metalloproteinase‐7 (MMP‐7 or matrilysin) and glycosaminolycans (GAGs) are two impor... more Human matrix metalloproteinase‐7 (MMP‐7 or matrilysin) and glycosaminolycans (GAGs) are two important players in extracellular matrix (ECM), participating in innate immunity, aging and cancer. MMP‐7 is over‐expressed in tumor cells and secreted into the ECM as a proenzyme (proMMP‐7). It has been found that MMP‐7 forms complexes with glycoproteins CD44 and heparin‐binding EGF via GAG carbohydrate chains. Recent in vitro studies showed that some GAGs regulate MMP‐7 activities by accelerating proMMP‐7 autolytic cleavage of the pro‐domain (Ra et al., 2009, JBC). We have found recombinant proMMP‐7 to be activated by homogeneous oligosaccharides from heparin in a saccharide length‐dependent manner. 6‐mer, 8‐mer, and 12‐mer heparin oligosaccharides accelerate proMMP‐7 activation at a similar rate while 16‐mer and 20‐mer oligosaccharides accelerate proMMP‐7 activation several‐fold more dramatically. ProMMP‐7 free or bound to the 6‐mer appear to be monomeric by atomic force microscopy. By contrast, proMMP‐7 and the 20‐mer formed large, elongated assemblies. Interface mapping by NMR spectroscopy suggests GAG binding sites in the catalytic and pro domains and potential modes of binding. Our results suggest GAGs regulate proMMP‐7 activation by drawing these protease molecules together. Supported by NIH grant R01GM57289.
Methods in molecular biology, 2017
Peripheral binding of proteins to lipid bilayers is critical not only in intracellular signaling ... more Peripheral binding of proteins to lipid bilayers is critical not only in intracellular signaling but also in metalloproteinase shedding of signaling proteins from cell surfaces. Assessment of how proteins recognize fluid bilayers peripherally using crystallography or structure-based predictions has been important but incomplete. Assay of dynamic protein-bilayer interactions in solution has become feasible and reliable using paramagnetic NMR and site-directed fluor labeling. Details of preparations and assay protocols for these spectroscopic measurements of bilayer proximity or contact, respectively, are described.
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Papers by Steven Van Doren