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Biochemistry

2003

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Articles 1 - 17 of 17

Full-Text Articles in Molecular Biology

Inhibition Of Fructose-1,6-Bisphosphatase By A New Class Of Allosteric Effectors, Jun-Young Choe, Scott W. Nelson, Kristen L. Arienti, Frank U. Axe, Tassie L. Collins, Todd K. Jones, Rachel D.A. Kimmich, Michael J. Newman, Karl Norvell, William C. Ripka, Suzanne J. Romano, Kevin M. Short, Deborah H. Slee, Herbert J. Fromm, Richard B. Honzatko Dec 2003

Inhibition Of Fructose-1,6-Bisphosphatase By A New Class Of Allosteric Effectors, Jun-Young Choe, Scott W. Nelson, Kristen L. Arienti, Frank U. Axe, Tassie L. Collins, Todd K. Jones, Rachel D.A. Kimmich, Michael J. Newman, Karl Norvell, William C. Ripka, Suzanne J. Romano, Kevin M. Short, Deborah H. Slee, Herbert J. Fromm, Richard B. Honzatko

Biochemistry, Biophysics and Molecular Biology Publications

A highly constrained pseudo-tetrapeptide (OC252-324) further defines a new allosteric binding site located near the center of fructose-1,6-bisphosphatase. In a crystal structure, pairs of inhibitory molecules bind to opposite faces of the enzyme tetramer. Each ligand molecule is in contact with three of four subunits of the tetramer, hydrogen bonding with the side chain of Asp187 and the backbone carbonyl of residue 71, and electrostatically interacting with the backbone carbonyl of residue 51. The ligated complex adopts a quaternary structure between the canonical R- and T-states of fructose-1,6-bisphosphatase, and yet a dynamic loop essential for catalysis ...


A Comparative Femtosecond Coherence Study Of The Unligated Monomeric Hemeproteins Myoglobin And Leghemoglobin, Mintu Halder, K. Das, Pramit Kumar Chowdhury, S. Kundu, Mark S. Hargrove, Jacob W. Petrich Aug 2003

A Comparative Femtosecond Coherence Study Of The Unligated Monomeric Hemeproteins Myoglobin And Leghemoglobin, Mintu Halder, K. Das, Pramit Kumar Chowdhury, S. Kundu, Mark S. Hargrove, Jacob W. Petrich

Chemistry Publications

Impulsive optical excitation has been performed on wild type, unligated leghemoglobin for the first time to compare the induced vibrational coherence with that observed in myoglobin. Both proteins were excited at the Soret maxima and probed at red and blue edges of the Soret band. The resulting kinetic traces were modulated by low-frequency vibrations. Leghemoglobin shows a decrease in vibrational amplitude compared with myoglobin. The possible cause for the amplitude differences is discussed in terms of contributions from both ground- and excited-state vibrational coherences and ground-state heterogeneity.


Dual Recognition Of The Ribosome And The Signal Recognition Particle By The Srp Receptor During Protein Targeting To The Endoplasmic Reticulum, Elisabet C. Mandon, Ying Jiang, Reid Gilmore Aug 2003

Dual Recognition Of The Ribosome And The Signal Recognition Particle By The Srp Receptor During Protein Targeting To The Endoplasmic Reticulum, Elisabet C. Mandon, Ying Jiang, Reid Gilmore

Open Access Articles

We have analyzed the interactions between the signal recognition particle (SRP), the SRP receptor (SR), and the ribosome using GTPase assays, biosensor experiments, and ribosome binding assays. Possible mechanisms that could contribute to an enhanced affinity between the SR and the SRP-ribosome nascent chain complex to promote protein translocation under physiological ionic strength conditions have been explored. Ribosomes or 60S large ribosomal subunits activate the GTPase cycle of SRP54 and SRalpha by providing a platform for assembly of the SRP-SR complex. Biosensor experiments revealed high-affinity, saturable binding of ribosomes or large ribosomal subunits to the SR. Remarkably, the SR has ...


Effects Of Distal Pocket Mutations On The Geminate Recombination Of No With Leghemoglobin On The Picosecond Time Scale, Pramit Kumar Chowdhury, S. Kundu, Mintu Halder, K. Das, Mark S. Hargrove, Jacob W. Petrich Aug 2003

Effects Of Distal Pocket Mutations On The Geminate Recombination Of No With Leghemoglobin On The Picosecond Time Scale, Pramit Kumar Chowdhury, S. Kundu, Mintu Halder, K. Das, Mark S. Hargrove, Jacob W. Petrich

Chemistry Publications

The picosecond NO geminate rebinding kinetics of wild-type leghemoglobin, a monomeric plant hemoglobin with structural similarity to myoglobin, and six mutant proteins at the distal histidine (H61G, H61A, H61V, H61L, H61R, H61F) are investigated. All of the mutant proteins yield rebinding kinetics that are initially more rapid than that of the wild-type protein. At long times, the rebinding of H61F becomes slower than that of wild-type leghemoglobin. The H61V, H61L, and H61G mutant proteins give extraordinarily rapid and complete geminate rebinding. On a 40 ps time scale, distal effects are overwhelmingly evident for all of the mutants considered. That binding ...


Perilipin A Is Essential For The Translocation Of Hormone-Sensitive Lipase During Lipolytic Activation. J Cell Biol, John Tansey Jun 2003

Perilipin A Is Essential For The Translocation Of Hormone-Sensitive Lipase During Lipolytic Activation. J Cell Biol, John Tansey

Chemistry Faculty Scholarship

A key step in lipolytic activation of adipocytes is the translocation of hormone-sensitive lipase (HSL) from the cytosol to the surface of the lipid storage droplet. Adipocytes from perilipin -null animals have an elevated basal rate of lipolysis compared with adipocytes from wild-type mice, but fail to respond maximally to lipolytic stimuli. This defect is downstream of the -adrenergic receptor–adenylyl cyclase complex. Now, we show that HSL is basally associated with lipid droplet surfaces at a low level in perilipin nulls, but that stimulated translocation from the cytosol to lipid droplets is absent in adipocytes derived from embryonic fibroblasts ...


Photocross-Linking Of Nascent Chains To The Stt3 Subunit Of The Oligosaccharyltransferase Complex, Ingmarie Nilsson, Daniel J. Kelleher, Yiwei Miao, Yuanlong Shao, Gert Kreibich, Reid Gilmore, Gunnar Von Heijne, Arthur E. Johnson May 2003

Photocross-Linking Of Nascent Chains To The Stt3 Subunit Of The Oligosaccharyltransferase Complex, Ingmarie Nilsson, Daniel J. Kelleher, Yiwei Miao, Yuanlong Shao, Gert Kreibich, Reid Gilmore, Gunnar Von Heijne, Arthur E. Johnson

Biochemistry and Molecular Pharmacology Publications

In eukaryotic cells, polypeptides are N glycosylated after passing through the membrane of the ER into the ER lumen. This modification is effected cotranslationally by the multimeric oligosaccharyltransferase (OST) enzyme. Here, we report the first cross-linking of an OST subunit to a nascent chain that is undergoing translocation through, or integration into, the ER membrane. A photoreactive probe was incorporated into a nascent chain using a modified Lys-tRNA and was positioned in a cryptic glycosylation site (-Q-K-T- instead of -N-K-T-) in the nascent chain. When translocation intermediates with nascent chains of increasing length were irradiated, nascent chain photocross-linking to translocon ...


Interaction Of Tl+ With Product Complexes Of Fructose-1,6-Bisphosphatase, Jun-Yong Choe, Scott W. Nelson, Herbert J. Fromm, Richard B. Honzatko May 2003

Interaction Of Tl+ With Product Complexes Of Fructose-1,6-Bisphosphatase, Jun-Yong Choe, Scott W. Nelson, Herbert J. Fromm, Richard B. Honzatko

Biochemistry, Biophysics and Molecular Biology Publications

The dissociation equilibrium constant for heparin binding to antithrombin III (ATIII) is a measure of the cofactor's binding to and activation of the proteinase inhibitor, and its salt dependence indicates that ionic and non-ionic interactions contribute ∼40 and ∼60% of the binding free energy, respectively. We now report that phenylalanines 121 and 122 (Phe-121 and Phe-122) together contribute 43% of the total binding free energy and 77% of the energy of non-ionic binding interactions. The large contribution of these hydrophobic residues to the binding energy is mediated not by direct interactions with heparin, but indirectly, through contacts between their ...


Dependence Of Endoplasmic Reticulum-Associated Degradation On The Peptide Binding Domain And Concentration Of Bip, Mehdi Kabani, Stephanie Kelley, Michael Morrow, Diana Montgomery, Renuka Sivendran, Mark Rose, Lila Gierasch, Jeffrey Brodsky Mar 2003

Dependence Of Endoplasmic Reticulum-Associated Degradation On The Peptide Binding Domain And Concentration Of Bip, Mehdi Kabani, Stephanie Kelley, Michael Morrow, Diana Montgomery, Renuka Sivendran, Mark Rose, Lila Gierasch, Jeffrey Brodsky

Lila Gierasch

ER-associated degradation (ERAD) removes defective and mis-folded proteins from the eukaryotic secretory pathway, but mutations in the ER lumenal Hsp70, BiP/Kar2p, compromise ERAD efficiency in yeast. Because attenuation of ERAD activates the UPR, we screened for kar2 mutants in which the unfolded protein response (UPR) was induced in order to better define how BiP facilitates ERAD. Among the kar2 mutants isolated we identified the ERAD-specific kar2-1 allele (Brodsky et al. J. Biol. Chem. 274, 3453–3460). The kar2-1 mutation resides in the peptide-binding domain of BiP and decreases BiP's affinity for a peptide substrate. Peptide-stimulated ATPase activity was ...


Purified Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath) Is A Dimer With Both Mononuclear Copper And A Copper-Containing Cluster, Raquel L. Lieberman, Deepak B. Shrestha, Peter E. Doan, Brian M. Hoffman, Timothy L. Stemmler, Amy C. Rosenzweig Mar 2003

Purified Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath) Is A Dimer With Both Mononuclear Copper And A Copper-Containing Cluster, Raquel L. Lieberman, Deepak B. Shrestha, Peter E. Doan, Brian M. Hoffman, Timothy L. Stemmler, Amy C. Rosenzweig

Biochemistry and Molecular Biology Faculty Publications

Particulate methane monooxygenase (pMMO) is a membrane-bound enzyme that catalyzes the oxidation of methane to methanol in methanotropic bacteria. Understanding how this enzyme hydroxylates methane at ambient temperature and pressure is of fundamental chemical and potential commercial importance. Difficulties in solubilizing and purifying active pMMO have led to conflicting reports regarding its biochemical and biophysical properties, however. We have purified pMMO from Methylococcus capsulatus (Bath) and detected activity. The purified enzyme has a molecular mass of ~200 kDa, probably corresponding to an a2b2g2 polypeptide arrangement. Each 200 kDa pMMO complex contains 4.8 ± 0.8 copper ions and 1.5 ...


Androgen-Induced Recruitment Of Rna Polymerase Ii To A Nuclear Receptor–P160 Coactivator Complex, Maggie C. Louie, Hong Qiong Yang, Ai-Hong Ma, Wei Xu, June X. Zou, Hsing-Jien Kung, Hong-Wu Chen Mar 2003

Androgen-Induced Recruitment Of Rna Polymerase Ii To A Nuclear Receptor–P160 Coactivator Complex, Maggie C. Louie, Hong Qiong Yang, Ai-Hong Ma, Wei Xu, June X. Zou, Hsing-Jien Kung, Hong-Wu Chen

Collected Faculty and Staff Scholarship

The androgen receptor, like other nuclear receptors, activates target genes by binding to hormone-responsive enhancers. Here we demonstrate that androgen induces robust recruitment of androgen receptor, members of the p160 coactivator family, and CREB-binding protein/p300 specifically at the distant enhancer of prostate-specific antigen (PSA) gene. Unexpectedly, we found that RNA polymerase II (Pol II) is directly recruited to the enhancer in a hormone-dependent manner, independent of the proximal promoter, and that the isolated PSA enhancer can mediate efficient androgen induction of transcription. Inhibition of the Pol II carboxyl-terminal domain kinase activity with low concentrations of flavopiridol blocks Pol II ...


Multiple Transporters Associated With Malaria Parasite Responses To Chloroquine And Quinine, Jianbing Mu, Michael T. Ferdig, Xiaorong Feng, Deirdre A. Joy, Junhui Duan, Tetsuya Furuya, G. Subramanian, L. Aravind, Roland A. Cooper, John C. Wootton, Momia Xiong, Xin-Zhuan Su Jan 2003

Multiple Transporters Associated With Malaria Parasite Responses To Chloroquine And Quinine, Jianbing Mu, Michael T. Ferdig, Xiaorong Feng, Deirdre A. Joy, Junhui Duan, Tetsuya Furuya, G. Subramanian, L. Aravind, Roland A. Cooper, John C. Wootton, Momia Xiong, Xin-Zhuan Su

Biological Sciences Faculty Publications

Mutations and/or overexpression of various transporters are known to confer drug resistance in a variety of organisms. In the malaria parasite Plasmodium falciparum, a homologue of P-glycoprotein, PfMDR1, has been implicated in responses to chloroquine (CO), quinine (ON) and other drugs, and a putative transporter, PfCRT, was recently demonstrated to be the key molecule in CO resistance. However, other unknown molecules are probably involved, as different parasite clones carrying the same pfcrt and pfmdr1 alleles show a wide range of quantitative responses to CO and ON. Such molecules may contribute to increasing incidences of ON treatment failure, the molecular ...


Characterization Of Two Novel Spindle Matrix Proteins In Drosophila, Chromator And Megator , Dong Wang Jan 2003

Characterization Of Two Novel Spindle Matrix Proteins In Drosophila, Chromator And Megator , Dong Wang

Retrospective Theses and Dissertations

A spindle matrix has been proposed to help organize and stabilize microtubules during mitosis. This concept has gained new interest due to the identification of Skeletor as a potential component of the spindle matrix. Skeletor is associated with chromosomes during interphase but reorganizes into a spindle-like structure during early prophase before the nuclear envelope breaks down and microtubules enter the nucleus. The Skeletor spindle extends from pole to pole during metaphase coaligning with the microtubule spindle and persists even after nocodazole treatment dissembles the microtubules. These features make Skeletor an ideal candidate as a spindle matrix protein.;In this study ...


Rec12 (Spo11) Recominase Of Fission Yeast Promotes A Backup, Distributive Pathway For Chromosome Segregation In Meiosis I, Wallace D. Sharif, Mari K. Davidson, Wayne P. Wahls Jan 2003

Rec12 (Spo11) Recominase Of Fission Yeast Promotes A Backup, Distributive Pathway For Chromosome Segregation In Meiosis I, Wallace D. Sharif, Mari K. Davidson, Wayne P. Wahls

Journal of the Arkansas Academy of Science

We studied the relationship between recombination and segregation in the fission yeast Schizosaccharomyces pombe. In meiosis, chromosomes undergo two rounds of segregation to produce haploid meiotic products. Crossover meiotic ecombination (chiasmata) promotes chromosome segregation during meiosis I; achiasmatic chromosomes often suffer on disjunction in meiosis I. Recl2 protein is a topoisomerase IIortholog that introduces double-strand DNA breaks that nitiate recombination. The red2 null (deletion) and active site (Y98F) mutants lack recombination and crossovers, and onsequently suffer meiosis I nondisjunction. However, null mutants chromosomes segregate to opposite poles more frequently than predicted. Thus, fission yeast has a backup, "distributive segregation" pathway ...


Protein-Carbohydrate And Protein-Protein Interactions: Using Models To Better Understand And Predict Specific Molecular Recognition, Alain Teboho Laederach Jan 2003

Protein-Carbohydrate And Protein-Protein Interactions: Using Models To Better Understand And Predict Specific Molecular Recognition, Alain Teboho Laederach

Retrospective Theses and Dissertations

Any molecular recognition event results in a change in the free energy of the system. The extent of this change is related to the association constant, such that the more negative the free energy change is, the tighter the interaction between receptor and ligand. Protein-carbohydrate interactions play a critical role in signal transduction, innate immunity, and metabolism. Modeling these interactions is somewhat complicated by the inherent flexibility of carbohydrates as well as their relatively large number of functional groups. An empirical scoring function for docking carbohydrates to proteins, specifically tailored to predict both the correct binding orientation and free energy ...


Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen Jan 2003

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation ...


A Model For Ethylene Receptor Function And 1-Methylcyclopropene Action, Brad Binder, A. Bleecker Dec 2002

A Model For Ethylene Receptor Function And 1-Methylcyclopropene Action, Brad Binder, A. Bleecker

Brad M. Binder

This paper provides a comprehensive review of current understanding of ethylene receptors, signal transduction using Arabidopsis as the model plant. It discusses the current theory on the mechanism of ethylene binding and proposes a mechanism for the action of ethylene response inhibitors such as 1-MCP.


Actin-Depolymerizing Factor Mediates Rac/Rop Gtpase-Regulated Pollen Tube Growth, C, Y, Chen, Alice Cheung, H. M. Wu Dec 2002

Actin-Depolymerizing Factor Mediates Rac/Rop Gtpase-Regulated Pollen Tube Growth, C, Y, Chen, Alice Cheung, H. M. Wu

Alice Cheung

Pollen tube elongation is a rapid tip growth process that is driven by a dynamic actin cytoskeleton. A ubiquitous family of actin binding proteins, actin-depolymerizing factors (ADFs)/cofilins, bind to actin filaments, induce severing, enhance depolymerization from their slow-growing end, and are important for maintaining actin dynamics in vivo. ADFs/cofilins are regulated by multiple mechanisms, among which Rho small GTPase-activated phosphorylation at a terminal region Ser residue plays an important role in regulating their actin binding and depolymerizing activity, affecting actin reorganization. We have shown previously that a tobacco pollen-specific ADF, NtADF1, is important for maintaining normal pollen tube ...