Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session C63: Quantum Phenomena, Instrumentation, and Techniques in Biology |
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Sponsoring Units: DBIO Chair: Jason Hafner, Rice University Room: BCEC 259A |
Monday, March 4, 2019 2:30PM - 2:42PM |
C63.00001: Ab-initio Electronic Structure Calculations of Entire Metalloproteins Carlos Romero-Muñiz, María Ortega, José G. Vilhena, Ismael Díez-Pérez, Juan Carlos Cuevas, Ruben Perez, Linda Angela Zotti In this work we present a theoretical approach to deal with entire metalloproteins at quantum level. In particular we focus on single-Cu azurins and cytochrome c, which contains a heme group with its typical Fe-center. In this approach we consider the complete structure of these proteins as a whole rather than limiting our analysis to relevant fragments of coordination complexes. This is accomplished by combining fully ab-initio calculations based on density functional theory with atomic-scale molecular dynamics simulations. Beyond the main features arising from the metallic ions, our study reveals that the role played by the peripheral parts of the proteins could be of remarkable importance. More precisely, we find that oxygen atoms belonging to carboxyl groups of acidic amino acids, distributed all over the protein contribute to electronic states near the HOMO in the case of azurins. The contribution of the outer regions to the electronic structure of metalloproteins had so far been overlooked. Our results stress the need to investigate them thoroughly; this is especially important in prospect of understanding complex processes like the electronic transport through metal-metalloprotein junctions. |
Monday, March 4, 2019 2:42PM - 2:54PM |
C63.00002: Quantum Mechanics of Proteins in Water: The role of Plasmon-like Solute-Solvent Interactions Martin Stoehr, Alexandre Tkatchenko van der Waals dispersion interactions form a major component of both intra-protein and protein-water interactions. As such, they play an essential role for the spontaneous folding of proteins in water. van der Waals forces arise from long-range electron correlation and are thus inherently quantum-mechanical and many-body in nature. Nevertheless, they are typically only treated in a phenomenological manner via pairwise potentials. Here, we employ an explicit quantum-mechanical framework based on the many-body dispersion formalism, which allows us to highlight the importance of the many-body character of dispersion interactions for protein energetics and protein-water interactions. As such, our study provides insights into the fundamental quantum-mechanics of proteins in water. Contrary to commonly used pairwise approaches, many-body quantum effects significantly affect relative stabilities during protein folding in the gas-phase. Embedding in an aqueous environment leads to a quenching of such effects and stabilizes native conformations. Remarkably, this arises from a high degree of delocalization and collectivity of protein-water dispersion interactions. Our findings are exemplified on several prototypical proteins, emphasizing their broad validity in the biomolecular context. |
Monday, March 4, 2019 2:54PM - 3:06PM |
C63.00003: Discrimination of bosonic loss: Applications to biological samples and photo-degradable materials Gaetana Spedalieri, Stefano Pirandola, Samuel Leon Braunstein We consider quantum discrimination of bosonic loss based on both symmetric and asymmetric hypothesis testing. In both approaches, an entangled resource is able to outperform any classical strategy based on coherent-state transmitters in the regime of low photon numbers. In the symmetric case, we then consider the low energy detection of bacterial growth in culture media. Assuming an exponential growth law for the bacterial concentration and the Beer-Lambert law for the optical transmissivity of the sample, we find that the use of entanglement allows one to achieve a much faster detection of growth with respect to the use of coherent states. This performance is also studied by assuming an exponential photo-degradable model, where the concentration is reduced by increasing the number of photons irradiated over the sample. This investigation is then extended to the readout of classical information from suitably-designed photo-degradable optical memories (quantum reading). |
Monday, March 4, 2019 3:06PM - 3:18PM |
C63.00004: Surface-Enhanced Raman Scattering as a Tool for Biomembrane Structure Jason Hafner Gold nanostructures focus light to the molecular length scale at their surface. The large optical intensity leads to surface-enhanced Raman scattering (SERS) from nearby molecules. SERS spectra contain information on molecular position and orientation relative to the surface but are difficult to interpret quantitatively. Here we describe a ratiometric analysis method that combines SERS and unenhanced Raman spectra with theoretical calculations of the optical field and molecular polarizability. The analysis was also applied to fluid phase phospholipid bilayers that contain tryptophan on the surface of gold nanorods. The lipid double bond was found to be oriented normal to the bilayer and 13 Å from the nitrogen atom. Tryptophan was found to sit near the glycerol headgroup region with its indole ring 43° from the bilayer normal. The potentiometric membrane probe di-4-ANEPPS has also been detected and its orientation characterized in the lipid bilayer. This new method can determine specific interfacial structure under ambient conditions, with microscopic quantities of material, and without molecular labels. |
Monday, March 4, 2019 3:18PM - 3:30PM |
C63.00005: Cellular response to far infrared radiation V.R. Gabriele, J. Shi, J. Eberhard, C.M. Gunathunge, Alexander Shvonski, M. Waegele, Keith Adam Nelson, Michael J Naughton, Krzysztof Kempa Previous studies have indicated selective biological cell damage due to local rapid thermalization [1] effects induced by laser irradiation. We have studied the effects of intense pulsed laser radiation on the prokaryote S. cerevisiae and eukaryote E. coli. These species are comparable to either cells found in the human body or pathogenic cells, respectively. We obtained the optical absorption spectra for the cells, and found frequency bands in the far-infrared (FIR/THz) range where notable spectral differences emerge. We report results of strong laser illumination at these selected bands. |
Monday, March 4, 2019 3:30PM - 3:42PM |
C63.00006: X-ray Photon Correlation Spectroscopy Measurements of Protein Diffusion in Concentrated Alpha Crystallin Suspensions Laurence Lurio, Preeti Vodnala, Vidanage Nuwan C Karunaratne, George Thurston, Michael Vega, Elizabeth Gaillard, Suresh Narayanan, Alec Russell Sandy, Qingteng Zhang, Eric Dufresne, Giuseppe Foffi, Pawel Grybos, Piotr Kmon, Piotr Maj, Robert Szczygiel The dynamics of concentrated suspensions of the crystallin eye-lens protein alpha crystallin was measured using x-ray photon correlation spectroscopy. For pure alpha crystallin suspensions the diffusive dynamics near the peak in the hard sphere structure are well described by a polydisperse hard sphere model. The intermediate scattering factor can be described by a stretched exponential function, and the concentration dependence of the relaxation time agrees with predictions from Langevin dynamics simulations. |
Monday, March 4, 2019 3:42PM - 3:54PM |
C63.00007: Dual Color MIET and FRET for Cell Nanoscopy of Stress Fibers and Focal Adhesions Anna M. Chizhik, Carina Wollnik, Daja Ruhlandt, Narein Karedla, Alexey I. Chizhik, Lara Hauke, Dirk Hähnel, Ingo Gregor, Jörg Enderlein, Florian Rehfeldt We report a novel method, dual color axial nanometric localization by Metal Induced Energy Transfer (dcMIET), and combine it with Förster Resonant Energy Transfer (FRET) for resolving structural details in cells on the molecular level. We demonstrate the capability of this method on cytoskeletal elements and adhesions in human mesenchymal stem cells (hMSCs). Our approach is based on Fluorescence-Lifetime-Imaging Microscopy (FLIM), and allows for precise determination of the 3D architecture of intracellular structures, here in particular, stress fibers anchoring at focal adhesions, thus yielding crucial information to understand cell-matrix mechanics. In addition to resolving nanometric structural details along the z-axis, we use FRET to gain precise information on the distance between actin and vinculin at focal adhesions. Here, we will present data where we use our method to follow the maturation of focal adhesions and acto-myosin fibers in hMSCs over time and show that actin fibers are nearly parallel to the substrate yielding an inclination angle of only 0.2°. |
Monday, March 4, 2019 3:54PM - 4:06PM |
C63.00008: Separation of Protein and Water Dynamical Transitions Using Terahertz Spectroscopy AKANSHA SHARMA, Deepu George, Andrea Markelz Terahertz Time Domain spectroscopy (THz TDS) has been used to characterize the protein dynamical transition [1, 2]. The dynamical transition has been considered a manifestation of the slaving of protein motions to thermally activated motions of the solvent, however recently is has been reported that sharp temperature increases in protein dynamics occur independent of the solvent [3]. Potentially terahertz spectroscopy can resolve both the protein and water dynamical transitions using the ~ 5 THz intermolecular water vibrational line and the broad ~ 1.0 THz absorption arising from the protein intramolecular motions. Here we use a combination of THz TDS and FTIR to examine this possibility and resolve the protein and water contributions using a combination of spectral decomposition and concentration dependent measurements. Concentration dependent measurements using hen egg white lysozyme (HEWL) confirm that the transition measured at 1 THz is dominated by the protein dynamics. |
Monday, March 4, 2019 4:06PM - 4:18PM |
C63.00009: Non-destructive prediction of transcriptomic profiles by Raman microscopy Koseki Kobayashi-Kirschvink, Yuichi Wakamoto Raman microscopy can report on whole single-cell molecular compositions in both comprehensive and non-destructive manners. However, molecular compositions of cells are diverse and compounds such as proteins have severe spectral overlaps, making them nearly intractable to interpret. Instead of pursuing the spectral decomposition, we show that transcriptomic profiles of Schizosaccharomces pombe and Escherichia coli can be computationally linked and be predicted from their single-cell Raman spectra. Our method employs the low-dimensional structure of transcriptomes, and learns a non-linear linkage between the transcriptomes and Raman spectra. Permutation tests show that the probability of accidentally finding the same prediction precision level is extremely low (p-value<0.0001), suggesting that the prediction is real. These results demonstrate that whole-cell Raman spectra could unravel cellular omics information in non-destructive manners, opening the possibility of conducting living-cell genomic analyses. |
Monday, March 4, 2019 4:18PM - 4:30PM |
C63.00010: Probing Mechanical Properties of Biomolecules using Nanopores Prasad Bandarkar, Robert Henley, Huan Yang, Meni Wanunu, Paul Whitford Nanopore translocation is a promising label-free single molecule technique to distinguish between bio-molecules. The confined nature of the nanopore restricts the allowed conformations of the molecules or necessitates a conformational change. These effects are reflected in the observed current traces and thus help us in measuring the flexibility of these biomolecules. Recently, we applied molecular dynamics simulations using a structure-based model to observe a correlation between the maximum RMSF of the protein and the width of the experimental current blockade distribution. This suggests that protein translocation can be utilized as a high-throughput method to distinguish between functional conformers in proteins. Applying this technique to translocation of tRNA offers an interesting challenge since the tRNA is expected to undergo a conformational change due to the constricted size of the nanopore. Using the same energy landscape techniques, we have calculated the mean first passage time (MFPT) for crossing the rate-limiting free-energy barrier for multiple tRNA species. We find agreement between the MFPT values and the experimental translocation times. Further, these calculations suggest that the experiments specifically observe transient partial unfolding of tRNA. |
Monday, March 4, 2019 4:30PM - 4:42PM |
C63.00011: Interferometric scattering for label-free electrokinetic trapping of single nanoparticles Abhijit A Lavania, Allison H. Squires, Peter D. Dahlberg, W E Moerner Anti-Brownian ELectrokinetic (ABEL) trapping is a technique to trap single particles in solution, enabling extended characterization of their properties. It utilizes photon-by-photon fluorescence to estimate a particle’s position, and fast electrophoretic and electroosmotic feedback forces to counteract Brownian motion and confine a particle to the center of a nanofluidic chamber. This enables the observation of photophysical properties, diffusion constants, and electrokinetic mobility. However, trapping is limited to particles that are either tagged with a fluorescent label, or have bright native fluorescence. Here we present the Interferometric Scattering Anti-Brownian ELectrokinetic trap (ISABEL trap), which uses interferometric scattering to enable fast detection and trapping of non-fluorescent particles. The weak scattered light from a nanoparticle is enhanced by interference with a strong reflection from a nearby interface. This enables direct and extended-duration study of single particles that do not fluoresce, or which exhibit intermittent fluorescence or photobleaching. |
Monday, March 4, 2019 4:42PM - 4:54PM |
C63.00012: Study of interaction of Bovine Serum Albumin with Gold Nanoparticles Kavindya Senanayake, Ashis Mukhopadhyay The protein-nanoparticle conjugates have potential applications in the fields of colloidal science and biophysics. We study the pH-dependent thickness of bovine serum albumin (BSA) layer on gold nanoparticles (AuNPs). pH-dependent conformations of BSA were determined between pH values 4 and 8. Comparison of pH-dependent hydrodynamic radii results of BSA-AuNp conjugates with Langmuir binding isotherm will be presented. |
Monday, March 4, 2019 4:54PM - 5:06PM |
C63.00013: Spatiotemporal dynamics of Pma1 in Saccharomyces cerevisiae using a reversibly interacting tag-probe system Susan Pratt, Michael Hinrichsen, Lynne Regan, Yongdeng Zhang, Joerg Bewersdorf, Benjamin P Bratton, Joshua Shaevitz, Simon G Mochrie When fluorescent proteins (FPs) are directly fused to a protein of interest, they can interfere with wild-type protein functionality. For example, when plasma membrane (PM) protein Pma1, in Saccharomyces cerevisiae, is directly fused to an FP, it is mislocalized to the cells’ vacuoles. To circumvent such problems, we are developing a versatile live-cell imaging strategy in which a fluorescently-labeled tetratricopeptide repeat affinity protein (TRAP) probe can reversibly bind to a conjugate 5 amino-acid peptide tag, which is bound to the target protein’s C-terminus. We demonstrate the utility of this reversibly binding tag-probe system, showing that it properly localizes Pma1 to the PM. To further characterize the behavior of Pma1, we present the results of fluorescence recovery after photobleaching (FRAP), and single-particle tracking photoactivated localization microscopy (sptPALM) measurements under total internal reflection fluorescence (TIRF) illumination. Remarkably, we find significant differences in the diffusional dynamics of Pma1 imaged using our novel labeling methodology, and Pma1 directly fused to FP. |
Monday, March 4, 2019 5:06PM - 5:18PM |
C63.00014: Real-time Electrophysiological Monitoring of Anti-histamine Drug Effects on Live Cells via Reusable Carbon Nanotube Sensor Jin-Young Jeong, Viet Anh Pham Ba, Dong-guk Cho, Haneul Yoo, Van-Thao Ta, Seunghun Hong Here, we developed a real-time electrophysiological method for monitoring the effects of drugs on live cells via a reusable carbon nanotube field-effect transistor (CNT-FET) sensor. The real-time electrophysiological responses of an individual HeLa cell could be measured repeatedly with the system. The sensor measured the electrical signal induced by the activity of histamine type 1 receptors on a HeLa cell regulated by histamine. Furthermore, the effects of drugs such as cetirizine and chlorophenamine on the HeLa cell were assessed. Remarkably, we exploited only a single sensor to record the activity of numerous HeLa cells to reduce the errors caused by device-to-device variations. Our method provides reliable and statistically-meaningful data to study the activity of live cells. We could expect our method using the reusable CNT-FET sensors to contribute to the pharmaceutical and biological research. |
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