Bulletin of the American Physical Society
2018 Joint Fall Meeting of the Texas Sections of APS, AAPT and Zone 13 of the SPS
Volume 63, Number 18
Friday–Saturday, October 19–20, 2018; University of Houston, Houston, Texas
Session P04: Biophysics and Soft Matter III |
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Chair: Lloyd Lumata, University of Texas, Dallas Room: Science and Engineering Classroom (SEC) 102 |
Saturday, October 20, 2018 2:10PM - 2:22PM |
P04.00001: Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma Fengdan Ye, Dongya Jia, Mingyang Lu, Herbert Levine, Michael Deem Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation for energy production and biomass synthesis. In this work, we analyzed the expression patterns of metabolism genes in terms of modularity for 371 hepatocellular carcinoma (HCC) samples from the Cancer Genome Atlas (TCGA). We found that higher modularity significantly correlated with glycolytic phenotype, later tumor stages, higher metastatic potential, and cancer recurrence, all of which contributed to poorer prognosis. Furthermore, we developed metrics to calculate individual modularity, which was shown to be predictive of cancer recurrence and patients’ survival and therefore may serve as a prognostic biomarker. Our overall conclusion is that more aggressive HCC tumors, as judged by decreased host survival probability, had more modular expression patterns of metabolic genes. |
Saturday, October 20, 2018 2:22PM - 2:34PM |
P04.00002: NMR Spectroscopic Investigation of Aberrant Cancer Metabolism and Factors that Affect Nuclear Relaxation Joseph Griesbauer The accelerated glycolysis in glioblastoma was analyzed using nuclear magnetic resonance spectroscopy. The rate of glucose metabolism and production of metabolites is increased to enhance cell proliferation in glioblastoma making it a useful biomarker in tracking carcinogenesis and cancer treatments with dynamic nuclear polarization. We utilize nuclear magnetic resonance to determine characteristics about the physical and biochemical environment of specific molecules containing isotopes with magnetic spin. The effect of certain properties in the environment specifically viscosity, tumbling rate, and the presence of free electrons were reexamined. We will present on how Ho-DOTA and 4-oxo-Tempo have ideal relaxivity for DNP enhancement and how we tracked aberrant glycolysis in brain cancer cells.
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Saturday, October 20, 2018 2:34PM - 2:46PM |
P04.00003: Nuclear Spin Diffusion Effects in Hyperpolarized [1-13C] Pyruvic Acid Christopher Parish, Qing Wang, Joseph Griesbauer, Fatemeh Khashami, Lloyd Lumata Increasing the concentration of 13C nuclei in a sample is frequently used in dynamic nuclear polarization (DNP) to raise the resulting nuclear magnetic resonance (NMR) signal. However, the exact relation between polarization and concentration does not seem to be currently known. In order to make some progress in this area, this study looked at the effect of altering the 13C concentration upon the 13C hyperpolarization and spin-lattice relaxation time of [1-13C] pyruvic acid, doped with 15 mM trityl OX063, at 3.35 T and 1.2 K. It was determined that both the 13C polarization and the 13C spin-lattice relaxation time roughly obeyed an inverse exponential equation: both increased asymptotically for sufficiently low concentrations of 13C nuclei. These two observations were discussed in light of spin diffusion and dipole-dipole interactions. |
Saturday, October 20, 2018 2:46PM - 2:58PM |
P04.00004: The role of actin filament brancher Arp2/3 in the dynamics and structures of actomyosin networks James Liman, Carlos A. Bueno, Yossi Eliaz, Peter G. Wolynes, Herbert Levine, Margaret S. Cheung Actomyosin network contractility underlies the motility and division of a cell, involving contraction and expansion that are driven by active protein motors and actin treadmilling. In this work, we present novel computational and theoretical approaches to model contractility and growth in actomyosin networks and evaluate the spatiotemporal patterns of actin reorganization. We consider two different actomyosin network morphologies, unbranched and branched. For the unbranched case, the system includes motor proteins (non-muscle myosin IIA (NMIIA)) and cross-linker proteins (α-actinin). For the branched case, the system includes a third component—Arp2/3 complexes—that allows us to investigate the role of branching in actomyosin contractility. We observe that linkers modulate contraction in the unbranched and the branched actomyosin networks. The branched actomyosin networks relax more slowly than their unbranched counterparts. However, the branched networks show pronounced convulsive contractions. We expect our results to give an insight into the importance of the branched morphological formation in enhancing contractility of the actomyosin networks. |
Saturday, October 20, 2018 2:58PM - 3:10PM |
P04.00005: Size and topology modulate the effects of frustration in protein folding Timothy A. Burt, Alex Kluber, Cecilia Clementi The presence of conflicting interactions, or frustration, determines how fast biomolecules can explore their configurational landscapes. Recent experiments have provided cases of systems with slow reconfiguration dynamics, perhaps arising from frustration. While it is well known that protein folding speed and mechanism are strongly affected by the protein native structure, it is still unknown how the response to frustration is modulated by the protein topology. We explore the effects of non-native interactions in the reconfigurational and folding dynamics of proteins with different sizes and topologies. We find that structural correlations related to the folded state size and topology play an important role in determining the folding kinetics of proteins that otherwise have the same amount of non-native interactions. In particular, we find that the reconfiguration dynamics of α-helical proteins are more susceptible to frustration than β-sheet proteins of the same size. Our results may explain recent experimental findings and suggest that attempts to measure the degree of frustration due to non-native interactions might be more successful with α-helical proteins. |
Saturday, October 20, 2018 3:10PM - 3:22PM |
P04.00006: Opposing Intermolecular Tuning of Ca2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides Pengzhi Zhang, Hoa Trinh, Swarnendu Tripathi, Margaret S Cheung We investigated the impact of bound calmodulin (CaM)-target structure on the affinity of calcium (Ca²⁺) by integrating coarse-grained and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca²⁺/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca²⁺ signaling pathways in neurons. It was shown experimentally that Ca²⁺/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca²⁺-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca²⁺ affinity for CaM. In contrast, Ng peptide binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. We discovered the molecular underpinnings of altered affinity of Ca²⁺ for CaM in the presence of Ng or CaMKII from the the distinctive structural difference in the complexes of apoCaM-Ng and holoCaM-CaMKII, which we speculate delineates the importance of CaM’s progressive mechanism of target binding on its Ca²⁺ binding affinities. |
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