An investigation into the role of protein-ligand interactions on obligate and transient protein-protein interactions

Protein-ligand and protein-protein interactions are critical to cellular function. Most cellular metabolic and signal tranduction pathways are influenced by these interactions, consequently molecular level understanding of these associations is an important area of biochemical research. We have examined the thermodynamics of several protein-protein associations and the protein-ligand interactions that mediate them. Using Fluorescence Correlation Spectroscopy, we have examined the putative interaction between pig heart malate dehydrogenase (MDH) and citrate synthase (CTS). We demonstrate a specific, low-affinity interaction between these enzymes. The association is highly polyethylene glycol (PEG)-dependent, and at high concentrations of NaCl or PEG, non-specific aggregates are formed. We demonstrate that oxaloacetate, the intermediate common to both CTS and MDH, induces the association at concentrations below the Km of CTS, suggesting that the open conformation of CTS is involved in the association. Using several biophysical techniques, we have examined the subunit associations of B. stearothermophilus phosphofructokinase (PFK). We demonstrate that the inhibitor bound conformation of the enzyme has reduced subunit affinity. The kinetics and thermodynamics of the phosphoenolpyrvuate (PEP)-induced dissociation of PFK have been quantified. Binding substrate, fructose-6-phosphate (F6P), stabilizes the enzyme to inhibitor-induced dissociation by 132-fold. These data suggest that subunit associations may play a role in the allosteric inhibition of PFK by PEP. The thermodynamics of the protein-ligand associations and allosteric inhibition of E. coli phosphofructokinase have been examined using intrinsic fluorescence and hydrostatic pressure. Both ligand-binding affinity and PEP inhibition are diminished by pressure, whereas substrate-binding affinity for inhibitor-bound enzyme is pressure-insensitive. Larger entropic than enthalpic changes with pressure lead to the overall reduction in free energies. Using a fluorescence-based assay, we have developed a series of baroresistant buffer mixtures. By combining a buffer with acid dissociation of negative volume with a buffer of positive volume, a pressure-resistant mixture is produced. Alteration of the molar ratio of the two component buffers yields mixtures that are pressure-insensitive at pH values around neutrality

Multi-Contrast Photoacoustic Computed Tomography

Imaging of small animals has played an indispensable role in preclinical research by providing high dimensional physiological, pathological, and phenotypic insights with clinical relevance. Yet pure optical imaging suffers from either shallow penetration (up to ~1–2 mm) or a poor depth-to-resolution ratio (~3), and non-optical techniques for whole-body imaging of small animals lack either spatiotemporal resolution or functional contrast. A stand-alone single-impulse photoacoustic computed tomography (PACT) system has been built, which successfully mitigates these limitations by integrating high spatiotemporal resolution, deep penetration, and full-view fidelity, as well as anatomical, dynamical, and functional contrasts. Based on hemoglobin absorption contrast, the whole-body dynamics and large scale brain functions of rodents have been imaged in real time. The absorption contrast between cytochrome and lipid has enabled PACT to resolve MRI-like whole brain structures. Taking advantage of the distinct absorption signature of melanin, unlabeled circulating melanoma cells have been tracked in real time in vivo. Assisted by near-infrared dyes, the perfusion processes have been visualized in rodents. By localizing single-dyed droplets, the spatial resolution of PACT has been improved by six-fold in vivo. The migration of metallic-based microrobots toward the targeted regions in the intestines has been monitored in real time. Genetically encoded photochromic proteins benefit PACT in detection sensitivity and specificity. The unique photoswitching characteristics of different photochromic proteins allow quantitative multi-contrast imaging at depths. A split version of the photochromic protein has permitted PA detection of protein-protein interactions in deep-seated tumors. The photochromic behaviors have also been utilized to guide photons to form an optical focus inside live tissue. As a rapidly evolving imaging technique, PACT promises pre-clinical applications and clinical translation.</p

Periodontal medicine : oral inflammatory conditions with special emphasis on immunological aspects

Systemic effects of periodontal disease have been a subject of interest for the past century, with intense focus converging since the past decade. Both rheumatoid arthritis (RA) and periodontal disease (PD) are immuno-inflammatory diseases with osteolysis as its hallmark feature. Activated T cells are known to modulate osteoclastogenesis. This thesis aimed to analyze the influence of PD on systemic inflammatory and immunological markers in both PD and RA subjects. Periodontal parameters, clinical (PI, BOP, PPD 3-<5mm and PPD ≥5mm) and radiographic (marginal bone loss or MBL) were investigated in four groups: RA with PD, RA without PD, PD and healthy groups. Immunosuppression of T cell activation via targeted surface protein was also studied. AIMS Study I aimed to investigate the expression and functional importance of low-density lipoprotein receptor-related protein1 (LRP1) in T cells. Study II aimed to investigate serum cytokines, chemokines, growth factors, enzymes and costimulatory proteins in association with periodontal conditions in PD and RA subjects. Study III aimed to investigate the serum markers osteopontin (OPN), tumor necrosis factor receptors 1 (TNFR1) and 2 (TNFR2) receptor activator of nuclear factor‐kappa B ligand (RANKL) and RANKL/ osteoprotegerin (OPG) ratio and compare them in PD and RA groups. Study IV aimed to investigate the severity of both PD and RA and investigate a correlation between glycemia and periodontal disease parameters using ΣPPD Total and ΣPPD Disease index. RESULTS Study I showed that T cells shed LRP1, which probably explains the low LRP1 expression in T cells. Shedding of LRP1 antagonizes T cell adhesion to integrin ligands and TCR-induced activation. Integrin ligands and CXCL12 antagonize shedding through a TSP-1-dependent pathway, whereas ligation of CD28 antagonizes shedding independent of TSP-1. The disappearance of LRP1 from the cell surface may provide basic immunosuppression at the T-cell level. Study II showed significant positive correlations for ST1A1, FGF-19 and NT-3 whereas EN-RAGE, DNER, CX3CL1 and TWEAK associated inversely with BOP, PPD≥ 5mm and MBL but positively with number of teeth. CD markers (CD244, CD40, CDCP1, LIF-R, IL-10RA, CD5 and CD6) were found to be associated with BOP, shallow and deep pockets, MBL and number of teeth, either directly or inversely. CCL8, CX3CL1, CXCL10, CXCL11, CCL11, CCL4, CCL20, CXCL5, CXCL6, and CCL23 were positively associated with number of teeth. Other growth factors were directly associated with MBL (HGF) and number of teeth (VEGF-A, LAP TGFbeta-1). Study III showed OPN, TNFR1, TNFR2 and RANKL serum levels were the highest in the RA group with PD, while the RA group without PD were comparable to PD subjects only. The RANKL/OPG ratios were comparable between PD group and both RA groups with and without PD. Serum RANKL levels were associated with and PPD ≥ 5mm. Study IV showed that the indices correlated strongly with number of deep pockets. DAS28 score correlated positively with RF in RA subjects with and without PD. Serum levels of HbA1c were higher in PD, RA with PD and without PD subjects as compared to the healthy group. HbA1c levels associated positively with PPD Total, PPD Disease, and MBL. Tooth adjusted PPD Total correlated with all periodontal parameters except for shallow pockets. CONCLUSIONS This thesis shows that periodontal disease is mirrored by a range of systemic immune markers, particularly those involved in inflammation. Furthermore, peripheral osteoclastogenesis is a feature of PD, comparable to RA. Overall, this thesis signifies the peripheral involvement of host immune system in combating PD essentially as an osteolytic disease and the need to approach PD measurement via a novel continuous index. The thesis also shows evidence that LRP1 controls motility, adhesion and activation in T cells

From Synthesis to Utilization: The Ins and Outs of Mitochondrial Heme

Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria

LONG-RANGE SIGNALING AT THE INTESTINAL-NEURAL AXIS PROMOTES ORGANISMAL HEME HOMEOSTASIS IN C. ELEGANS

Metazoans synthesize and regulate intracellular heme in a cell autonomous manner although genetic evidence in vertebrates suggests that cell non-autonomous mechanisms may exist at the organismal level. In C. elegans, a heme auxotroph, extraintestinal tissues are intrinsically dependent on the intestine, which acquires dietary heme for sustenance, supporting the concept that intestinal heme status must be coordinated at the systemic level to regulate whole-organism heme homeostasis. Here we show, by conducting a functional genome-wide RNAi screen in an intestinal-restricted heme sensor worm, that an interorgan heme signaling pathway exists and that >30% of the genes identified from the RNAi screen altered heme homeostasis in the intestine even though these genes are not expressed in the intestine. The biological basis for this signaling is underscored by HRG-7, a cathepsin protease-like protein secreted by the intestine and internalized by distally-located neurons. HRG-7 is specifically secreted from the intestine during heme limitation and hrg-7 depletion causes embryonic lethality concomitant with a heme deficiency response. Reciprocally, neuron-to-intestine heme signaling is mediated by the bone morphogenic protein homolog DBL-1, which recapitulates hrg-7 deficiency when depleted. Remarkably, depletion of both genes simultaneously results in markedly enhanced growth and heme deficiency phenotypes, suggesting that bidirectional signaling between the intestine and neurons mediates systemic heme homeostasis. Our results have uncovered an unexpected role for a protease family member in long-range communication between organs at the intestinal-neural axis to regulate systemic heme homeostasis in metazoa. As humans have over thirty cathepsin and cathepsin-like proteases, several of which are secreted, we anticipate that these proteins may play analogous roles in mammalian biology

44th Rocky Mountain Conference on Analytical Chemistry

Final program, abstracts, and information about the 44th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Denver, Colorado, July 28 - August 1, 2002

Detection and quantification of nitric oxide–derived oxidants in biological systems

The free radical nitric oxide (NO) exerts biological effects through the direct and reversible interaction with specific targets (e.g. soluble guanylate cyclase) or through the generation of secondary species, many of which can oxidize, nitrosate or nitrate biomolecules. The NO -derived reactive species are typically short-lived, and their preferential fates depend on kinetic and compartmentalization aspects. Their detection and quantification are technically challenging. In general, the strategies employed are based either on the detection of relatively stable end products or on the use of synthetic probes, and they are not always selective for a particular species. In this study, we describe the biologically relevant characteristics of the reactive species formed downstream from NO , and we discuss the approaches currently available for the analysis of NO , nitrogen dioxide (NO2 ), dinitrogen trioxide (N2O3), nitroxyl (HNO), and peroxynitrite (ONOO /ONOOH), as well as peroxynitrite-derived hydroxyl (HO) and carbonate anion (CO3) radicals. We also discuss the biological origins of and analytical tools for detecting nitrite (NO2), nitrate (NO3), nitrosyl–metal complexes, S-nitrosothiols, and 3-nitrotyrosine. Moreover, we highlight state– of–the–art methods, alert readers to caveats of widely used techniques, and encourage retirement of approaches that have been supplanted by more reliable and selective tools for detecting and measuring NO -derived oxidants. We emphasize that the use of appropriate analytical methods needs to be strongly grounded in a chemical and biochemical understanding of the species and mechanistic pathways involveAgencia Nacional de Investigación e Innovación FCE_1_2017_1_136043Comisión Sectorial de Investigación Científica (CSIC)Universidad de la República. Espacio Interdisciplinari

Resolvin E1 actions on polymorphonuclear neutrophils in diabetes

Dissertation (DScD) -- Boston University, Henry M. Goldman School of Dental Medicine, 2010 (Department of Periodontology and Oral Biology).Diabetes and periodontal disease exhibit a bidirectional relationship centered on an enhanced inflammatory response manifested both locally and systemically. The observation that hyperglycemia by itself, in the absence of additional inflammatory signals, promotes a proinflammatory environment indicates that diabetes is an independent risk factor for periodontal disease. Leukocyte pre-activation or priming in diabetes has been demonstrated. Excessive ROS release by leukocytes, upregulation of pro-inflammatory mediators and adhesion molecules are characteristic to T2DM-associated low-grade inflammation. However, the mechanisms by which chronic hyperglycemia leads to leukocyte activation are not fully understood. [TRUNCATED

Bioinorganic Chemistry

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry