Mechanical and Systems Biology of Cancer

Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control basic mechanical properties, such as cell tension, stiffness, and engagement with the extracellular environment, which can lead to extracellular matrix remodeling. Intracellular mechanics can alter signaling and transcription factors, impacting cell decision making. Additionally, signaling from soluble and mechanical factors in the extracellular environment, such as substrate stiffness and ligand density, can modulate cytoskeletal dynamics. Computational models closely integrated with experimental support, incorporating cancer-specific parameters, can provide quantitative assessments and serve as predictive tools toward dissecting the feedback between signaling and mechanics and across multiple scales and domains in tumor progression.Comment: 18 pages, 3 figure

Differential Hydrogen Bonding in Human CYP17 Dictates Hydroxylation versus Lyase Chemistry

Consequences of alternative H-bonding: Raman spectra of oxygenated intermediates of Nanodisc-incorporated human CYP17 in the presence of natural substrates (pregnenolone and progesterone) directly confirm that substrate structure effectively alters hydrogen-bonding interactions with the critical Fe–O–O fragment and dictates its predisposition for one of two alternative reaction pathways. Such substrate control has profound physiological implications

Resonance Raman Spectroscopy Reveals that Substrate Structure Selectively Impacts the Heme-Bound Diatomic Ligands of CYP17

An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by the well-known Compound I intermediate, the lyase reaction is believed to involve nucleophilic attack of the earlier peroxo- intermediate on the C20-carbonyl. Herein, resonance Raman (rR) spectroscopy reveals that substrate structure does not impact heme structure for this set of physiologically important substrates. On the other hand, rR spectra obtained here for the ferrous CO adducts with these four substrates show that substrates do interact differently with the Fe-C-O fragment, with large differences between the spectra obtained for the samples containing 17-OH PROG and 17-OH PREG, the latter providing evidence for the presence of two Fe-C-O conformers. Collectively, these results demonstrate that individual substrates can differentially impact the disposition of a heme-bound ligand, including dioxygen, altering the reactivity patterns in such a way as to promote preferred chemical conversions, thereby avoiding the profound functional consequences of unwanted side reactions

Effects of 3D Geometries on Cellular Gradient Sensing and Polarization

During cell migration, cells become polarized, change their shape, and move in response to various internal and external cues. Cell polarization is defined through the spatio-temporal organization of molecules such as PI3K or small GTPases, and is determined by intracellular signaling networks. It results in directional forces through actin polymerization and myosin contractions. Many existing mathematical models of cell polarization are formulated in terms of reaction-diffusion systems of interacting molecules, and are often defined in one or two spatial dimensions. In this paper, we introduce a 3D reaction-diffusion model of interacting molecules in a single cell, and find that cell geometry has an important role affecting the capability of a cell to polarize, or change polarization when an external signal changes direction. Our results suggest a geometrical argument why more roundish cells can repolarize more effectively than cells which are elongated along the direction of the original stimulus, and thus enable roundish cells to turn faster, as has been observed in experiments. On the other hand, elongated cells preferentially polarize along their main axis even when a gradient stimulus appears from another direction. Furthermore, our 3D model can accurately capture the effect of binding and unbinding of important regulators of cell polarization to and from the cell membrane. This spatial separation of membrane and cytosol, not possible to capture in 1D or 2D models, leads to marked differences of our model from comparable lower-dimensional models.Comment: 31 pages, 7 figure

Compensation for Coal Seam Gas Occupation: Assessing the Harms

Coal seam gas (CSG) extraction is expanding in eastern Australia. However, while the body of knowledge relating to compensation for partial taking is well established, the theory concerning the valuation of landholder compensation for occupation by CSG infrastructure is in an embryonic stage. In order to further the development of theory in this important area, this research investigates the harms that are inflicted upon landholders and their property by CSG occupation. As indicated in the Queensland mining case of Peabody West Burton Pty Ltd & Ors v Mason & Ors [2012] QLC 23, the assessment of compensation begins by enquiring as to the acts or events that occasion loss. In order to identify and assess the relevance of harms that may be inflicted upon landholders, this introductory research analyses key judgments relating to compensation for CSG and mining projects and takes advantage of the material created by the 2011, NSW and Australian Senate inquiries into matters related to CSG. Some aspects of CSG occupation are unusual. In land affected by CSG works, the property occupied is handed back to the landholder at the cessation of extraction: moreover, the actual term of occupation is difficult to determine at the outset of occupation. The research concludes that the harms inflicted by CSG occupation depend upon the interaction of the CSG project with the property occupied, its uses and its topography. Importantly, the “harms” caused by the occupation by part of land can extend outside the land occupied by the CSG work. The potential loss in value to “balance lands”, disturbance costs and potential for longer term blight are issues that need close consideration in assessing compensation

Coal Seam Gas Extraction: Does Landholder Compensation Match the Mischief?

Coal seam gas (CSG) extraction is set for expansion in New South Wales. However, controversy accompanies its introduction in that the present law grants miners access to private lands for the purposes of exploration and production. The NSW Petroleum (Onshore) Act 1991 regulates compensation for land access, and a number of questions have been raised about the adequacy of its compensation provisions. Additionally, compensation for coal seam gas poses a challenge for the valuation profession in that valuation theory has yet to be developed in this emerging sphere of practice. This paper compares the legal and physical impacts of coal seam gas infrastructure on private lands with the current provisions of the NSW Petroleum (Onshore) Act 1991 and questions if the present compensation provisions match the injury inflicted upon the holders of private land by coal seam gas occupation. The paper reviews the NSW legislation and case law relating to coal seam gas acquisition to identify the legal affects, whilst field observation and remote sensing techniques identify physical effects. The physical effects are then categorised according to the heads of compensation that apply to the compulsory taking of parts of property in Australia. A comparative analysis determines if all of the various “harms” that result from coal seam gas occupation are compensable under the current law. The research indicates that “severance” and “injurious affection” are key issues for landholder compensation where CSG plant occupies parts of land; however, the right to claim for “injurious affection” is unclear in the present legislation

Human P450 CYP17A1: Control of Substrate Preference by Asparagine 202

CYP17A1 is a key steroidogenic enzyme known to conduct several distinct chemical transformations on multiple substrates. In its hydroxylase activity, this enzyme adds a hydroxyl group at the 17α position of both pregnenolone and progesterone at approximately equal rates. However, the subsequent 17,20 carbon–carbon scission reaction displays variable substrate specificity in the numerous CYP17A1 isozymes operating in vertebrates, manifesting as different Kd and kcat values when presented with 17α-hydroxypregnenlone (OHPREG) versus 17α-hydroxyprogesterone (OHPROG). Here we show that the identity of the residue at position 202 in human CYP17A1, thought to form a hydrogen bond with the A-ring alcohol substituent on the pregnene- nucleus, is a key driver of this enzyme’s native preference for OHPREG. Replacement of asparagine 202 with serine completely reverses the preference of CYP17A1, more than doubling the rate of turnover of the OHPROG to androstenedione reaction and substantially decreasing the rate of formation of dehydroepiandrosterone from OHPREG. In a series of resonance Raman experiments, it was observed that, in contrast with the case for the wild-type protein, in the mutant the 17α alcohol of OHPROG tends to form a H-bond with the proximal rather than terminal oxygen of the oxy–ferrous complex. When OHPREG was a substrate, the mutant enzyme was found to have a H-bonding interaction with the proximal oxygen that is substantially weaker than that of the wild type. These results demonstrate that a single-point mutation in the active site pocket of CYP17A1, even when far from the heme, has profound effects on steroidogenic selectivity in androgen biosynthesis

Unveiling the Crucial Intermediates in Androgen Production

Significance: The human enzyme cytochrome P450 17A1 (CYP17A1) catalyzes the critical step in the biosynthesis of the male sex hormones, and, as such, it is a key target for the inhibition of testosterone production that is necessary for the progression of certain cancers. CYP17A1 catalyzes two distinct types of chemical transformations. The first is the hydroxylation of the steroid precursors pregnenolone and progesterone. The second is a different reaction involving carbon–carbon (C-C) bond cleavage, the mechanism of which has been actively debated in the literature. Using a combination of chemical and biophysical methods, we have been able to trap and characterize the active intermediate in this C-C lyase reaction, an important step in the potential design of mechanism-based inhibitors for the treatment of prostate cancers. Abstract: Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17–C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon–carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences

Supercontinuum generation in the vacuum ultraviolet through dispersive-wave and soliton-plasma interaction in noble-gas-filled hollow-core photonic crystal fiber

We report on the generation of a three-octave-wide supercontinuum extending from the vacuum ultraviolet (VUV) to the near-infrared, spanning at least 113 to 1000 nm (i.e., 11 to 1.2 eV), in He-filled hollow-core kagome-style photonic crystal fiber. Numerical simulations confirm that the main mechanism is a novel and previously undiscovered interaction between dispersive-wave emission and plasma-induced blueshifted soliton recompression around the fiber zero dispersion frequency. The VUV part of the supercontinuum, which modeling shows to be coherent and possess a simple phase structure, has sufficient bandwidth to support single-cycle pulses of 500 attosecond duration. We also demonstrate, in the same system, the generation of narrower-band VUV pulses, through dispersive-wave emission, tunable from 120 to 200 nm with efficiencies exceeding 1% and VUV pulse energies in excess of 50 nJ.Comment: 7 pages, 5 figure