Chemistry & Biochemistry
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Item A Pro-Drug Approach for Selective Modulation of AI-2-Mediated Bacterial Cell-to-Cell Communication(MDPI, 2012-03-21) Guo, Min; Gamby, Sonja; Nakayama, Shizuka; Smith, Jacqueline; Sintim, Herman O.The universal quorum sensing autoinducer, AI-2, is utilized by several bacteria. Analogs of AI-2 have the potential to modulate bacterial behavior. Selectively quenching the communication of a few bacteria, in the presence of several others in an ecosystem, using analogs of AI-2 is non-trivial due to the ubiquity of AI-2 processing receptors in many bacteria that co-exist. Herein, we demonstrate that when an AI-2 analog, isobutyl DPD (which has been previously shown to be a quorum sensing, QS, quencher in both Escherichia coli and Salmonella typhimurium) is modified with ester groups, which get hydrolyzed once inside the bacterial cells, only QS in E. coli, but not in S. typhimurium, is inhibited. The origin of this differential QS inhibition could be due to differences in analog permeation of the bacterial membranes or ester hydrolysis rates. Such differences could be utilized to selectively target QS in specific bacteria amongst a consortium of other species that also use AI-2 signaling.Item Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch(MDPI, 2012-11-09) Zhou, Jie; Sayre, David A.; Wang, Jingxin; Pahadi, Nirmal; Sintim, Herman O.C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.Item Small Molecule Inhibitors of AI-2 Signaling in Bacteria: State-of-the-Art and Future Perspectives for Anti-Quorum Sensing Agents(MDPI, 2013-08-29) Guo, Min; Gamby, Sonja; Zheng, Yue; Sintim, Herman O.Bacteria respond to different small molecules that are produced by other neighboring bacteria. These molecules, called autoinducers, are classified as intraspecies (i.e., molecules produced and perceived by the same bacterial species) or interspecies (molecules that are produced and sensed between different bacterial species). AI-2 has been proposed as an interspecies autoinducer and has been shown to regulate different bacterial physiology as well as affect virulence factor production and biofilm formation in some bacteria, including bacteria of clinical relevance. Several groups have embarked on the development of small molecules that could be used to perturb AI-2 signaling in bacteria, with the ultimate goal that these molecules could be used to inhibit bacterial virulence and biofilm formation. Additionally, these molecules have the potential to be used in synthetic biology applications whereby these small molecules are used as inputs to switch on and off AI-2 receptors. In this review, we highlight the state-of-the-art in the development of small molecules that perturb AI-2 signaling in bacteria and offer our perspective on the future development and applications of these classes of molecules.Item 3D DNA Crystals and Nanotechnology(MDPI, 2016-08-18) Paukstelis, Paul J.; Seeman, Nadrian C.DNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.Item Implementation of Glycan Remodeling to Plant-Made Therapeutic Antibodies(MDPI, 2018-01-31) Bennett, Lindsay D.; Yang, Qiang; Berquist, Brian R.; Giddens, John P.; Ren, Zhongjie; Kommineni, Vally; Murray, Ryan P.; White, Earl L.; Holtz, Barry R.; Wang, Lai-Xi; Marcel, SylvainN-glycosylation profoundly affects the biological stability and function of therapeutic proteins, which explains the recent interest in glycoengineering technologies as methods to develop biobetter therapeutics. In current manufacturing processes, N-glycosylation is host-specific and remains difficult to control in a production environment that changes with scale and production batches leading to glycosylation heterogeneity and inconsistency. On the other hand, in vitro chemoenzymatic glycan remodeling has been successful in producing homogeneous pre-defined protein glycoforms, but needs to be combined with a cost-effective and scalable production method. An efficient chemoenzymatic glycan remodeling technology using a plant expression system that combines in vivo deglycosylation with an in vitro chemoenzymatic glycosylation is described. Using the monoclonal antibody rituximab as a model therapeutic protein, a uniform Gal2GlcNAc2Man3GlcNAc2 (A2G2) glycoform without α-1,6-fucose, plant-specific α-1,3-fucose or β-1,2-xylose residues was produced. When compared with the innovator product Rituxan®, the plant-made remodeled afucosylated antibody showed similar binding affinity to the CD20 antigen but significantly enhanced cell cytotoxicity in vitro. Using a scalable plant expression system and reducing the in vitro deglycosylation burden creates the potential to eliminate glycan heterogeneity and provide affordable customization of therapeutics’ glycosylation for maximal and targeted biological activity. This feature can reduce cost and provide an affordable platform to manufacture biobetter antibodies.Item Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level(MDPI, 2019-02-22) Lin, Xingcheng; Kulkarni, Prakash; Bocci, Federico; Schafer, Nicholas P.; Roy, Susmita; Tsai, Min-Yeh; He, Yanan; Chen, Yihong; Rajagopalan, Krithika; Mooney, Steven M.; Zeng, Yu; Weninger, Keith; Grishaev, Alex; Onuchic, José N.; Levine, Herbert; Wolynes, Peter G.; Salgia, Ravi; Rangarajan, Govindan; Uversky, Vladimir; Orban, John; Jolly, Mohit KumarFolded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do exhibit some structural and dynamical ordering, but are less constrained in their motions than folded proteins. The larger structural plasticity of IDPs emphasizes the importance of entropically driven motions. Many IDPs undergo function-related disorder-to-order transitions driven by their interaction with specific binding partners. As experimental techniques become more sensitive and become better integrated with computational simulations, we are beginning to see how the modest structural ordering and large amplitude collective motions of IDPs endow them with an ability to mediate multiple interactions with different partners in the cell. To illustrate these points, here, we use Prostate-associated gene 4 (PAGE4), an IDP implicated in prostate cancer (PCa) as an example. We first review our previous efforts using molecular dynamics simulations based on atomistic AWSEM to study the conformational dynamics of PAGE4 and how its motions change in its different physiologically relevant phosphorylated forms. Our simulations quantitatively reproduced experimental observations and revealed how structural and dynamical ordering are encoded in the sequence of PAGE4 and can be modulated by different extents of phosphorylation by the kinases HIPK1 and CLK2. This ordering is reflected in changing populations of certain secondary structural elements as well as in the regularity of its collective motions. These ordered features are directly correlated with the functional interactions of WT-PAGE4, HIPK1-PAGE4 and CLK2-PAGE4 with the AP-1 signaling axis. These interactions give rise to repeated transitions between (high HIPK1-PAGE4, low CLK2-PAGE4) and (low HIPK1-PAGE4, high CLK2-PAGE4) cell phenotypes, which possess differing sensitivities to the standard PCa therapies, such as androgen deprivation therapy (ADT). We argue that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.Item Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy(MDPI, 2019-09-25) Becette, Owen; Olenginski, Lukasz T.; Dayie, Theodore K.RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.Item Experimental and Theoretical Characterization of Effective Interactions Near 132Sn(1987) Stone, Craig A.; Walters, William B.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)Experimental investigations have been undertaken to study the multiplet structure in six nuclei near 132Sn: 132,130Sb, 131,129,127Sb, and 132Te. Experiments were performed using ion beams of mass-separated fission products produced by the TRISTAN mass separator at Brookhaven National Laboratory. Extensive four-detector gamma-gamma coincidences, gamma-multiscaling and conversion-electron data have been collected. Ultralarge shell model calculations were performed using the VLADIMIR shell model code on the Cray/CDC 7600 supercomputer system at Lawrence Livermore National Laboratory. These calculations were designed to look at the performance of the Kallio-Kolltveit and Siemen's g-matiix potentials on the 1-3 quasiparticle nuclides in the gddsh model space. Results show that realistic potentials work well on nuclei near 132Sn but show problems with 129,130Sn and 131Sb which can not be accounted for by core-polarization corrections. Problems are shown to be due to the use of a potential derived with the Scott-Moszkowski separation metl1od. The separation distance was demonstrated to have a weak dependence on the principal quantum number but a strong dependence on the orbital angular momentum. This suggests the Kallio-Kolltveit potential is underestimating the strength of the h11/2 interactions in 129,130Sn and 131Sb.Item Spacial and Temporal Variations in 36CI Deposition in the Northern United States(1994) Hainsworth, Laura J.; Mignerey, Alice C.; Chemistry and Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)Chlorine-36, a cosmogenic radioisotope, has been developed for use as a tracer in hydrological systems. The deposition of atmospheric 36Cl, although of primary importance to hydrological applications, has not been well studied. To begin to address this problem, 36Cl has been measured in monthly, wet-only, precipitation samples collected from February, 1991, to January, 1993, at the Elms Environmental Education Center in St. Mary's County, Maryland. In addition, bulk deposition samples were collected over a 1 y period at seven sites across the Northern United States and analyzed for 36CI. The mean, wet-only 36Cl/Cl ratio for the 2 y sampling period is 68±19 (x10 -15), and the mean 36 CI concentration is 1.2±0. 1 (x10 6) atoms/L. The 36Cl wet deposition flux data reveal a distinct seasonal deposition pattern, with peaks occurring in March and April. This pattern is attributed to stratospheric/ tropospheric exchange. The mean 36Cl wet deposition flux is 38.2±5 atoms/m2s. Comparison between wet-only and bulk deposition samples indicates that the difference accounts for approximately 25% of the total 36Cl deposition flux at the Elms site. A new model, using 90Sr to predict the 36CI deposition pattern, is developed to predict 36Cl/Cl ratios across the United States. Chlorine-36/Cl ratios in bulk deposition samples collected across the northern United States agree well with the model predictions. A mean global 36Cl production rate of approximately 28 to 38 atoms/m2s is indicated by these samples. A comparison between 36Cl concentrations in the Aquia and Magothy aquifers is southern Maryland and bulk deposition samples collected at the Elms, MD, site indicated that modern precipitation can account for the 36Cl content in the youngest water in these aquifers. Surface water samples from the Susquehanna River basin reveal 36 Cl and stable chloride concentrations an order of magnitude higher than in bulk deposition samples collected at State College, PA. The source of excess 36Cl in the Susquehanna is not known. Possible explanations include 'bomb-pulse' 36Cl and in-situ 36CI production in surface rocks.Item A Matrix Universe as the Origin of Inertia and Momentum and Translocation as a Chemical Reaction(2003-03) Hansen, John NormanIt is proposed that there is a matrix structure of the universe that persists both in the presence and absence of physical objects, and that chemical reactions involve reorganization of electronic orbitals within this matrix structure. The mechanism by which objects translocate within this matrix is similar to the chemical reaction mechanism, and therefore requires moving objects to cross transition-state energy barriers. This involves an input of energy, which is the origin of inertia and momentum. The matrix concept is used to derive equations of motion that conform to Newton’s laws and include terms for inertia and momentum.