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Articles 1 - 30 of 1485

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Induction Of Ethylene Inhibits Development Of Soybean Sudden Death Syndrome By Inducing Defense-Related Genes And Reducing Fusarium Virguliforme Growth, Noor A. Abdelsamad, Gustavo C. Macintosh, Leonor F.S. Leandro May 2019

Induction Of Ethylene Inhibits Development Of Soybean Sudden Death Syndrome By Inducing Defense-Related Genes And Reducing Fusarium Virguliforme Growth, Noor A. Abdelsamad, Gustavo C. Macintosh, Leonor F.S. Leandro

Biochemistry, Biophysics and Molecular Biology Publications

Ethylene is a gaseous hormone that regulates plant responses to biotic and abiotic stresses. To investigate the importance of ethylene in soybean resistance to Fusarium virguliforme (Fv), the causal agent of sudden death syndrome (SDS), soybean cultivars Williams 82 (SDS-susceptible) and MN1606 (SDS-resistant) were treated 24 h before and 24h after Fv inoculation with either ethephon (ethylene inducer), cobalt chloride (ethylene biosynthesis inhibitor), or 1-MCP (ethylene perception inhibitor). Inoculated plants were grown for 21 days at 24°C in the greenhouse and then evaluated for SDS severity and expression of soybean defense genes. In both cultivars, plants treated with ethephon ...


Aptamers For Diagnostics With Applications For Infectious Diseases, Muslum Ilgu, Rezzan Fazlioglu, Meric Ozturk, Yasemin Ozsurekci, Marit Nilsen-Hamilton Apr 2019

Aptamers For Diagnostics With Applications For Infectious Diseases, Muslum Ilgu, Rezzan Fazlioglu, Meric Ozturk, Yasemin Ozsurekci, Marit Nilsen-Hamilton

Biochemistry, Biophysics and Molecular Biology Publications

Aptamers are in vitro selected oligonucleotides (DNA, RNA, oligos with modified nucleotides) that can have high affinity and specificity for a broad range of potential targets with high affinity and specificity. Here we focus on their applications as biosensors in the diagnostic field, although they can also be used as therapeutic agents. A small number of peptide aptamers have also been identified. In analytical settings, aptamers have the potential to extend the limit of current techniques as they offer many advantages over antibodies and can be used for real-time biomarker detection, cancer clinical testing, and detection of infectious microorganisms and ...


Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo Mar 2019

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo

Chemistry Publications

Background

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

Results

In the present study, a MIL-based magnet-assisted dispersive liquid–liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal ...


Multiple Variables At The Leukocyte Cell Surface Impact Fc Γ Receptor-Dependent Mechanisms, Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb Feb 2019

Multiple Variables At The Leukocyte Cell Surface Impact Fc Γ Receptor-Dependent Mechanisms, Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

Fc γ receptors (FcγR) expressed on the surface of human leukocytes bind clusters of immunoglobulin G (IgG) to induce a variety of responses. Many therapeutic antibodies and vaccine-elicited antibodies prevent or treat infectious diseases, cancers and autoimmune disorders by binding FcγRs, thus there is a need to fully define the variables that impact antibody-induced mechanisms to properly evaluate candidate therapies and design new intervention strategies. A multitude of factors influence the IgG-FcγR interaction; one well-described factor is the differential affinity of the six distinct FcγRs for the four human IgG subclasses. However, there are several other recently described factors that ...


Altering The Substrate Specificity Of Acetyl-Coa Synthetase By Rational Mutagenesis Of The Carboxylate Binding Pocket, Naazneen Sofeo, Jason H. Hart, Brandon Butler, David J. Oliver, Marna D. Yandeau-Nelson, Basil J. Nikolau Jan 2019

Altering The Substrate Specificity Of Acetyl-Coa Synthetase By Rational Mutagenesis Of The Carboxylate Binding Pocket, Naazneen Sofeo, Jason H. Hart, Brandon Butler, David J. Oliver, Marna D. Yandeau-Nelson, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

Acetyl-CoA synthetase (ACS) is a member of a large superfamily of enzymes that display diverse substrate specificities, with a common mechanism of catalyzing the formation of a thioester bond between Coenzyme A and a carboxylic acid, while hydrolyzing ATP to AMP and pyrophosphate. As an activated form of acetate, acetyl-CoA is a key metabolic intermediate that links many metabolic processes, including the TCA cycle, amino acid metabolism, fatty acid metabolism and biosynthetic processes that generate many polyketides and some terpenes. We explored the structural basis of the specificity of ACS for only activating acetate, whereas other members of this superfamily ...


A Single-Cell Platform For Reconstituting And Characterizing Fatty Acid Elongase Component Enzymes, Alexis A. Campbell, Kenna E. Stenback, Kayla Flyckt, Trang Hoang, M. Ann Perera, Basil J. Nikolau Jan 2019

A Single-Cell Platform For Reconstituting And Characterizing Fatty Acid Elongase Component Enzymes, Alexis A. Campbell, Kenna E. Stenback, Kayla Flyckt, Trang Hoang, M. Ann Perera, Basil J. Nikolau

Biochemistry, Biophysics and Molecular Biology Publications

Fatty acids of more than 18-carbons, generally known as very long chain fatty acids (VLCFAs) are essential for eukaryotic cell viability, and uniquely in terrestrial plants they are the precursors of the cuticular lipids that form the organism’s outer barrier to the environment. VLCFAs are synthesized by fatty acid elongase (FAE), which is an integral membrane enzyme system with multiple components. The genetic complexity of the FAE system, and its membrane association has hampered the biochemical characterization of FAE. In this study we computationally identified Zea mays genetic sequences that encode the enzymatic components of FAE and developed a ...


Vitamin D Metabolites And Their Intestinal Responses, Carmen J. Reynolds Jan 2019

Vitamin D Metabolites And Their Intestinal Responses, Carmen J. Reynolds

Graduate Theses and Dissertations

Vitamin D metabolites regulate calcium absorption in the intestines through activation of the vitamin D receptor (VDR) and resulting in increased expression of calcium-associated proteins. Presently, it is thought that vitamin D metabolizes into a hormonal form, 1,25-dihydroxyvitamin D (1,25D), and the hormone then circulates via blood to the duodenum to stimulate calcium absorption. Recently, Koszewski et al. proposed that delivery of the hormone occurs via digestive passage rather than by the blood (Koszewski et al., 2012). Growing evidence has suggested, instead, that the hormonal precursor, 25-hydroxyvitamin D (25D), may have functional activity by either providing substrate for ...


Evidence For A Role Of Spindle Matrix Formation In Cell Cycle Progression By Antibody Perturbation, Changfu Yao, Chao Wang, Yeran Li, Michael Zavortink, Vincent Archambault, Jack Girton, Kristen M. Johansen, Jorgen Johansen Nov 2018

Evidence For A Role Of Spindle Matrix Formation In Cell Cycle Progression By Antibody Perturbation, Changfu Yao, Chao Wang, Yeran Li, Michael Zavortink, Vincent Archambault, Jack Girton, Kristen M. Johansen, Jorgen Johansen

Biochemistry, Biophysics and Molecular Biology Publications

In Drosophila it has recently been demonstrated that a spindle matrix in the form of a membrane-less macromolecular assembly embeds the microtubule-based spindle apparatus. In addition, two of its constituents, Megator and Chromator, were shown to function as spatial regulators of spindle checkpoint proteins. However, whether the spindle matrix plays a wider functional role in spatially regulating cell cycle progression factors was unknown. Here using a live imaging approach we provide evidence that a number of key cell cycle proteins such as Cyclin B, Polo, and Ran co-localize with the spindle matrix during mitosis. Furthermore, prevention of spindle matrix formation ...


A Third Class: Functional Gibberellin Biosynthetic Operon In Beta-Proteobacteria, Raimund Nagel, John E. Bieber, Mark G. Schmidt-Dannert, Ryan S. Nett, Reuben J. Peters Nov 2018

A Third Class: Functional Gibberellin Biosynthetic Operon In Beta-Proteobacteria, Raimund Nagel, John E. Bieber, Mark G. Schmidt-Dannert, Ryan S. Nett, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

The ability of plant-associated microbes to produce gibberellin A (GA) phytohormones was first described for the fungal rice pathogen Gibberella fujikuroi in the 1930s. Recently the capacity to produce GAs was shown for several bacteria, including symbiotic alpha-proteobacteria (α-rhizobia) and gamma-proteobacteria phytopathogens. All necessary enzymes for GA production are encoded by a conserved operon, which appears to have undergone horizontal transfer between and within these two phylogenetic classes of bacteria. Here the operon was shown to be present and functional in a third class, the beta-proteobacteria, where it is found in several symbionts (β-rhizobia). Conservation of function was examined by ...


Arginine In The Farm And Sarm: A Role In Chain-Length Determination For Arginine In The Aspartate-Rich Motifs Of Isoprenyl Diphosphate Synthases From Mycobacterium Tuberculosis, Raimund Nagel, Jill A. Thomas, Faith A. Adekunle, Francis M. Mann, Reuben J. Peters Oct 2018

Arginine In The Farm And Sarm: A Role In Chain-Length Determination For Arginine In The Aspartate-Rich Motifs Of Isoprenyl Diphosphate Synthases From Mycobacterium Tuberculosis, Raimund Nagel, Jill A. Thomas, Faith A. Adekunle, Francis M. Mann, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Isoprenyl chains are found in many important metabolites. These are derived from precursors of the appropriate length produced by isoprenyl diphosphate synthases (IDSs). The human pathogen Mycobacterium tuberculosis makes various isoprenoids/terpenoids, with important roles in their biosynthesis played by two closely related IDSs, encoded by grcC1 (Rv0562) and grcC2 (Rv0989c), with Rv0989c generating the 10-carbon precursor (E)-geranyl diphosphate (GPP), and Rv0562 the 20-carbon precursor (E,E,E)-geranylgeranyl diphosphate (GGPP). Intriguingly, while Rv0562 contains the prototypical trans-IDS first and second aspartate-rich (DDxxD) motifs (FARM and SARM, respectively), Rv0989c uniquely contains arginine in place of the second Asp in ...


Continuous Interdomain Orientation Distributions Reveal Components Of Binding Thermodynamics, Yang Qi, Jeffrey W. Martin, Adam W. Barb, Francois Thelot, Anthony Yan, Bruce R. Donald, Terrence G. Oas Sep 2018

Continuous Interdomain Orientation Distributions Reveal Components Of Binding Thermodynamics, Yang Qi, Jeffrey W. Martin, Adam W. Barb, Francois Thelot, Anthony Yan, Bruce R. Donald, Terrence G. Oas

Biochemistry, Biophysics and Molecular Biology Publications

The flexibility of biological macromolecules is an important structural determinant of function. Unfortunately, the correlations between different motional modes are poorly captured by discrete ensemble representations. Here, we present new ways to both represent and visualize correlated interdomain motions. Interdomain motions are determined directly from residual dipolar couplings, represented as a continuous conformational distribution, and visualized using the disk-on-sphere representation. Using the disk-on-sphere representation, features of interdomain motions, including correlations, are intuitively visualized. The representation works especially well for multidomain systems with broad conformational distributions.This analysis also can be extended to multiple probability density modes, using a Bingham mixture ...


A 2′Fy-Rna Motif Defines An Aptamer For Ebolavirus Secreted Protein, Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A. Dillard, Nicholas J. Lennemann, Teresa M. Przytycka, Wendy Maury, Marit Nilsen-Hamilton Aug 2018

A 2′Fy-Rna Motif Defines An Aptamer For Ebolavirus Secreted Protein, Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A. Dillard, Nicholas J. Lennemann, Teresa M. Przytycka, Wendy Maury, Marit Nilsen-Hamilton

Biochemistry, Biophysics and Molecular Biology Publications

With properties such as stability to long-term storage and amenability to repetitive use, nucleic acid aptamers are compatible with many sensing/transducing platforms intended for use in remote locations. Sensors with these properties are important for quickly identifying ebolavirus outbreaks, which frequently start in locations that lack sophisticated equipment. Soluble glycoprotein (sGP), an excellent biomarker for ebolaviruses, is produced from the same gene as the ebolavirus glycoprotein GP1,2 that decorates the surface of the viral particle and is secreted in abundance into the blood stream even during the early stages of infection. Here, we report the selection and properties ...


Direct Determination Of The Site Of Addition Of Glucosyl Units To Maltooligosaccharide Acceptors Catalyzed By Maize Starch Synthase I, Ying Xie, Adam W. Barb, Tracie A. Hennen-Bierwagen, Alan M. Myers Aug 2018

Direct Determination Of The Site Of Addition Of Glucosyl Units To Maltooligosaccharide Acceptors Catalyzed By Maize Starch Synthase I, Ying Xie, Adam W. Barb, Tracie A. Hennen-Bierwagen, Alan M. Myers

Biochemistry, Biophysics and Molecular Biology Publications

Starch synthase (SS) (ADP-glucose:1,4-α-D-glucan 4-α-D-glucosyltransferase) elongates α-(1→4)-linked linear glucans within plastids to generate the storage polymers that constitute starch granules. Multiple SS classes are conserved throughout the plant kingdom, indicating that each provides a unique function responsible for evolutionary selection. Evidence has been presented arguing for addition of glucosyl units from the ADPglucose donor to either the reducing end or the non-reducing end of the acceptor substrate, although until recently direct evidence addressing this question was not available. Characterization of newly incorporated glucosyl units determined that recombinant maize (Zea mays L.) SSIIa elongates its substrates ...


Protein Dynamic Communities From Elastic Network Models Align Closely To The Communities Defined By Molecular Dynamics, Sambit Kumar Mishra, Robert L. Jernigan Jun 2018

Protein Dynamic Communities From Elastic Network Models Align Closely To The Communities Defined By Molecular Dynamics, Sambit Kumar Mishra, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Dynamic communities in proteins comprise the cohesive structural units that individually exhibit rigid body motions. These can correspond to structural domains, but are usually smaller parts that move with respect to one another in a protein’s internal motions, key to its functional dynamics. Previous studies emphasized their importance to understand the nature of ligand-induced allosteric regulation. These studies reported that mutations to key community residues can hinder transmission of allosteric signals among the communities. Usually molecular dynamic (MD) simulations (~ 100 ns or longer) have been used to identify the communities—a demanding task for larger proteins. In the present ...


Probing The Specificity Of Cyp112 In Bacterial Gibberellin Biosynthesis, Raimund Nagel, Reuben J. Peters Jun 2018

Probing The Specificity Of Cyp112 In Bacterial Gibberellin Biosynthesis, Raimund Nagel, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Biosynthesis of the gibberellin A (GA) plant hormones evolved independently in plant-associated fungi and bacteria. While the relevant enzymes have distinct evolutionary origins, the pathways proceed via highly similar reactions. One particularly complex transformation involves combined demethylation and γ-lactone ring formation, catalyzed in bacteria by the cytochrome P450 CYP112 in three individual steps, which involves large structural changes in the transition from substrate to product, with further divergence in the recently demonstrated use of two separate mechanistic routes. Here the substrate specificity of the isozyme from Erwinia tracheiphila, EtCYP112, was probed via UV-Vis spectral binding studies and activity assays with ...


Direct Production Of Dihydroxylated Sesquiterpenoids By A Maize Terpene Synthase, Jin Liang, Jiang Liu, Reid Brown, Meirong Jia, Ke Zhou, Reuben J. Peters, Qiang Wang Jun 2018

Direct Production Of Dihydroxylated Sesquiterpenoids By A Maize Terpene Synthase, Jin Liang, Jiang Liu, Reid Brown, Meirong Jia, Ke Zhou, Reuben J. Peters, Qiang Wang

Biochemistry, Biophysics and Molecular Biology Publications

The astounding structural and biological diversity of the large class of terpenoid natural products are imparted by both their complex hydrocarbon backbones and further elaboration by the addition of multiple hydroxyl groups, which provide both solubility and specific binding properties. While the role of terpene synthases in generating hydrocarbons with complex backbones is well known, these also are known to generate (singly) hydroxylated products by the addition of water prior to terminating deprotonation. Here a maize sesquiterpene synthase was unexpectedly found to generate dually hydroxylated products directly from (E,E)-farnesyl diphosphate, primarily eudesmane-2,11-diol, along with two closely related ...


Characterizing Virus-Induced Gene Silencing At The Cellular Level With In Situ Multimodal Imaging, Sadie J. Burkhow, Nicole M. Stephens, Yu Mei, Maria Emilia Duenas, Daniel J. Freppon, Geng Ding, Shea C. Smith, Young-Jin Lee, Basil J. Nikolau, Steven A. Whitham, Emily A. Smith May 2018

Characterizing Virus-Induced Gene Silencing At The Cellular Level With In Situ Multimodal Imaging, Sadie J. Burkhow, Nicole M. Stephens, Yu Mei, Maria Emilia Duenas, Daniel J. Freppon, Geng Ding, Shea C. Smith, Young-Jin Lee, Basil J. Nikolau, Steven A. Whitham, Emily A. Smith

Chemistry Publications

Background: Reverse genetic strategies, such as virus-induced gene silencing, are powerful techniques to study gene function. Currently, there are few tools to study the spatial dependence of the consequences of gene silencing at the cellular level.

Results: We report the use of multimodal Raman and mass spectrometry imaging to study the cellular-level biochemical changes that occur from silencing the phytoene desaturase (pds) gene using a Foxtail mosaic virus (FoMV) vector in maize leaves. The multimodal imaging method allows the localized carotenoid distribution to be measured and reveals differences lost in the spatial average when analyzing a carotenoid extraction of the ...


A Dendritic Guidance Receptor Complex Brings Together Distinct Actin Regulators To Drive Efficient F-Actin Assembly And Branching, Wei Zhou, Xintong Dong, Timothy R. Broederdorf, Ao Shen, Daniel A. Kramer, Rebecca Shi, Xing Liang, David M. Miller Iii, Yang K. Xiang, Ryohei Yasuda, Baoyu Chen, Kang Shen May 2018

A Dendritic Guidance Receptor Complex Brings Together Distinct Actin Regulators To Drive Efficient F-Actin Assembly And Branching, Wei Zhou, Xintong Dong, Timothy R. Broederdorf, Ao Shen, Daniel A. Kramer, Rebecca Shi, Xing Liang, David M. Miller Iii, Yang K. Xiang, Ryohei Yasuda, Baoyu Chen, Kang Shen

Biochemistry, Biophysics and Molecular Biology Publications

Proper morphogenesis of dendrites plays a fundamental role in the establishment of neural circuits. The molecular mechanism by which dendrites grow highly complex branches is not well understood. Here, using the C. elegans PVD neuron, we demonstrate that high-order dendritic branching requires actin polymerization driven by coordinated interactions between two membrane proteins, DMA-1 and HPO-30, and with their cytoplasmic interactors, the RacGEF TIAM-1 and the actin nucleation promotion factor WAVE Regulatory Complex (WRC). The dendrite branching receptor DMA-1 directly binds to the PDZ domain of TIAM-1, while the claudin-like protein HPO-30 directly interacts with the WRC. On dendrites, DMA-1 and ...


Inferring Roles In Defense From Metabolic Allocation Of Rice Diterpenoids, Xuan Lu, Juan Zhang, Benjamin Brown, Riqing Li, Julio Rodríguez-Romero, Aileen Berasategui, Bo Liu, Meimei Xu, Dangping Luo, Zhiqiang Pan, Scott R. Baerson, Jonathan Gershenzon, Zhaohu Li, Ane Sesma, Bing Yang, Reuben J. Peters May 2018

Inferring Roles In Defense From Metabolic Allocation Of Rice Diterpenoids, Xuan Lu, Juan Zhang, Benjamin Brown, Riqing Li, Julio Rodríguez-Romero, Aileen Berasategui, Bo Liu, Meimei Xu, Dangping Luo, Zhiqiang Pan, Scott R. Baerson, Jonathan Gershenzon, Zhaohu Li, Ane Sesma, Bing Yang, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Among their responses to microbial infection, plants deploy an arsenal of natural antibiotic products. Historically these have been identified on the basis of their antibiotic activity in vitro, which leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syn-copalyl diphosphate (CPP) intermediates, which were isolated on the basis of their antibiotic activity against the fungal blast pathogen Magnaporthe oryzae. However, rice plants in which the gene for the syn-CPP synthase Os-CPS4 is ...


Transcytosis Of Junonia Coenia Densovirus Vp4 Across The Gut Epithelium Of Spodoptera Frugiperda (Lepidoptera: Noctuidae), Mariah Kemmerer, Bryony Bonning Apr 2018

Transcytosis Of Junonia Coenia Densovirus Vp4 Across The Gut Epithelium Of Spodoptera Frugiperda (Lepidoptera: Noctuidae), Mariah Kemmerer, Bryony Bonning

Entomology Publications

The Junonia coenia densovirus rapidly traverses the gut epithelium of the host lepidopteran without replicating in the gut cells. The ability of this virus to transcytose across the gut epithelium is of interest for the potential use of virus structural proteins as delivery vehicles for insecticidal peptides that act within the insect hemocoel, rather than in the gut. In this study, we used fall armyworm, Spodoptera frugiperda to examine the binding of the virus to brush border membrane vesicle proteins by two-dimensional ligand blot analysis. We also assessed the rate of flux of the primary viral structural protein, VP4 fused ...


Restricted Processing Of Cd16a/Fc Γ Receptor Iiia N-Glycans From Primary Human Nk Cells Impacts Structure And Function, Kashyap R. Patel, Jacob T. Roberts, Ganesh P. Subedi, Adam W. Barb Mar 2018

Restricted Processing Of Cd16a/Fc Γ Receptor Iiia N-Glycans From Primary Human Nk Cells Impacts Structure And Function, Kashyap R. Patel, Jacob T. Roberts, Ganesh P. Subedi, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

CD16a/Fc γ receptor IIIa is the most abundant antibody Fc receptor expressed on human natural killer (NK) cells and activates a protective cytotoxic response following engagement with antibody clustered on the surface of a pathogen or diseased tissue. Therapeutic monoclonal antibodies (mAbs) with greater Fc-mediated affinity for CD16a show superior therapeutic outcome; however, one significant factor that promotes antibody–CD16a interactions, the asparagine-linked carbohydrates (N-glycans), remains undefined. Here, we purified CD16a from the primary NK cells of three donors and identified a large proportion of hybrid (22%) and oligomannose N-glycans (23%). These proportions indicated restricted N-glycan ...


Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau Feb 2018

Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate’s acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of ...


Seqstruct : A New Amino Acid Similarity Matrix Based On Sequence Correlations And Structural Contacts Yields Sequence-Structure Congruence, Kejue Jia, Robert L. Jernigan Feb 2018

Seqstruct : A New Amino Acid Similarity Matrix Based On Sequence Correlations And Structural Contacts Yields Sequence-Structure Congruence, Kejue Jia, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Protein sequence matching does not properly account for some well-known features of protein structures: surface residues being more variable than core residues, the high packing densities in globular proteins, and does not yield good matches of sequences of many proteins known to be close structural relatives. There are now abundant protein sequences and structures to enable major improvements to sequence matching. Here, we utilize structural frameworks to mount the observed correlated sequences to identify the most important correlated parts. The rationale is that protein structures provide the important physical framework for improving sequence matching. Combining the sequence and structure data ...


The Oligomerization State Of Bacterial Enzyme I (Ei) Determines Ei's Allosteric Stimulation Or Competitive Inhibition By Α-Ketoglutarate, Trang T. Nguyen, Rodolfo Ghirlando, Vincenzo Venditti Feb 2018

The Oligomerization State Of Bacterial Enzyme I (Ei) Determines Ei's Allosteric Stimulation Or Competitive Inhibition By Α-Ketoglutarate, Trang T. Nguyen, Rodolfo Ghirlando, Vincenzo Venditti

Chemistry Publications

The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by phosphorylation of enzyme I (EI) by phosphoenolpyruvate (PEP). The EI phosphorylation state determines the phosphorylation states of all other PTS components and is thought to play a central role in the regulation of several metabolic pathways and to control the biology of bacterial cells at multiple levels, for example, affecting virulence and biofilm formation. Given the pivotal role of EI in bacterial metabolism, an improved understanding of the mechanisms controlling its activity could ...


Mouse Igg2c Fc Loop Residues Promote Greater Receptor-Binding Affinity Than Mouse Igg2b Or Human Igg1, Daniel J. Falconer, Adam W. Barb Feb 2018

Mouse Igg2c Fc Loop Residues Promote Greater Receptor-Binding Affinity Than Mouse Igg2b Or Human Igg1, Daniel J. Falconer, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

The structures of non-human antibodies are largely unstudied despite the potential for the identification of alternative structural motifs and physical properties that will benefit a basic understanding of protein and immune system evolution as well as highlight unexplored motifs to improve therapeutic monoclonal antibody. Here we probe the structure and receptor-binding properties of the mouse IgG2c crystallizable fragment (Fc) to compare to mouse IgG2b and human IgG1 Fcs. Models of mIgG2c Fc determined by x-ray crystallography with a complex-type biantennary (to 2.05 Å) or a truncated (1)GlcNAc asparagine-linked (N)-glycan attached (to 2.04 Å) show differences in ...


Comparisons Of Protein Dynamics From Experimental Structure Ensembles, Molecular Dynamics Ensembles, And Coarse-Grained Elastic Network Models, Kannan Sankar, Sambit K. Mishra, Robert L. Jernigan Jan 2018

Comparisons Of Protein Dynamics From Experimental Structure Ensembles, Molecular Dynamics Ensembles, And Coarse-Grained Elastic Network Models, Kannan Sankar, Sambit K. Mishra, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Predicting protein motions is important for bridging the gap between protein structure and function. With growing numbers of structures of the same, or closely related proteins becoming available, it is now possible to understand more about the intrinsic dynamics of a protein with principal component analysis (PCA) of the motions apparent within ensembles of experimental structures. In this paper, we compare the motions extracted from experimental ensembles of 50 different proteins with the modes of motion predicted by several types of coarse-grained elastic network models (ENMs) which additionally take into account more details of either the protein geometry or the ...


Automated Nmr Resonance Assignments And Structure Determination Using A Minimal Set Of 4d Spectra, Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes Jan 2018

Automated Nmr Resonance Assignments And Structure Determination Using A Minimal Set Of 4d Spectra, Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes

Chemistry Publications

Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6–10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate ...


Functions Of Maize Genes Encoding Pyruvate Phosphate Dikinase In Developing Endosperm, Ryan R. Lappe, John W. Baier, Susan K. Boehlein, Ryan Huffman, Qiaohui Lin, Fabrice Wattebled, A. Mark Settles, L. Curtis Hannah, Ljudmilla Borisjuk, Hardy Rolletschek, Jon D. Stewart, M. Paul Scott, Tracie A. Hennen-Bierwagen, Alan M. Myers Jan 2018

Functions Of Maize Genes Encoding Pyruvate Phosphate Dikinase In Developing Endosperm, Ryan R. Lappe, John W. Baier, Susan K. Boehlein, Ryan Huffman, Qiaohui Lin, Fabrice Wattebled, A. Mark Settles, L. Curtis Hannah, Ljudmilla Borisjuk, Hardy Rolletschek, Jon D. Stewart, M. Paul Scott, Tracie A. Hennen-Bierwagen, Alan M. Myers

Agronomy Publications

Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the ...


Molecular Mechanisms Governing Plant Parasitic Nematode Signaling And Host Parasitism, Stacey Nicola Barnes Jan 2018

Molecular Mechanisms Governing Plant Parasitic Nematode Signaling And Host Parasitism, Stacey Nicola Barnes

Graduate Theses and Dissertations

Pathogen infection of crops causes large-scale annual yield losses for farmers worldwide and hinders global efforts to provide adequate amounts of nutrition for the ever-growing human population. Plant-parasitic nematodes (PPN) are among some of the most devastating pathogens due to their ability to parasitize an expansive variety of agriculturally important crops. In order to identify ways to attenuate PPN infection and limit yield losses it is vital that we increase our understanding of host-PPN interactions. Here we investigate the molecular mechanisms that are occurring both within PPN and at the interface between PPN and their host plants.

Research into PPN-derived ...


Comparison And Evaluation Of Two Rapid Diagnostic Assays For The Identification Of Mycoplasma Species, Aric James Mcdaniel Jan 2018

Comparison And Evaluation Of Two Rapid Diagnostic Assays For The Identification Of Mycoplasma Species, Aric James Mcdaniel

Graduate Theses and Dissertations

Members of the class Mollicutes are unique among bacteria in that they are unable to synthesize a cell wall. These organisms are also difficult to culture and very slow-growing with some species requiring up to 40 days to culture. Many of these bacteria are also significant pathogens in humans and animals, so rapid identification of isolates is a necessary diagnostic step. Many different tests are used for identification of pathogenic Mollicutes (primarily Mycoplasma and Ureaplasma species), however most tests are not cost or time efficient. Two relatively recent diagnostic tools are matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and ...