Bulletin of the American Physical Society
APS March Meeting 2016
Volume 61, Number 2
Monday–Friday, March 14–18, 2016; Baltimore, Maryland
Session A39: Physics of Proteins: Bio Meets QuantumFocus
|
Hide Abstracts |
Sponsoring Units: DBIO DPOLY DCOMP Chair: Mark Tuominen, University of Massachusetts Amherst Room: 342 |
Monday, March 14, 2016 8:00AM - 8:12AM |
A39.00001: Hidden Linear Quantum States in Proteins: Did Davydov Get the Sign Wrong? Robert Austin, Aihua Xie, Britta Redlich, Lex van der Meer A fair amount of time has been spent hunting down one prospective quantum mechanical model, namely the Davydov solition along the $\alpha$-helix backbone of the protein. These experiments were challenging, we used a tunable ps mid-IR Free Electron Laser to try and observe the long-term (microsecond or greater) trapping of coherent excitation in proteins which had been proposed by a several theorists. These experiments were successful in the sense that we directly observed vibrational excited state population relaxation on the picsecond time scale, and transfer of coherent excitation into the incoherent themal bath: but we we did not see the trapping on the microsecond time scale of short (ps) coherent light pulses in the amide I band of a generic alpha-helix rich protein, myoglobin. However, we would like to revisit that experiment one more time in this paper to analyze and try to understand something puzzling that we did observe, in the context a possible unusual ``hidden'' quantum phenomena in proteins which probably is of no biological consequences, but bears re-examination. [Preview Abstract] |
Monday, March 14, 2016 8:12AM - 8:24AM |
A39.00002: Single-Molecule Electronic Measurements of the Dynamic Flexibility of Histone Deacetylases James Froberg, Seungyong You, Junru Yu, Manas Haldar, Abbas Sedigh, Sanku Mallik, D.K. Srivastava, Yongki Choi Due to their involvement in epigenetic regulation, histone deacetylases (HDACs) have gained considerable interest in designing drugs for treatment of a variety of human diseases including cancers. Recently, we applied a label-free, electronic single-molecule nano-circuit technique to gain insight into the contribution of the dynamic flexibility in HDACs structure during the course of substrates/ ligands binding and catalysis. We observed that HDAC8 has two major (dynamically interconvertible) conformational states, ``ground (catalytically unfavorable)'' and ``transition (catalytically favorable)''. In addition, we found that its cognate substrates/ligands reciprocally catalyze the transition of the ground to the transition state conformation of HDAC8. Thus, we propose that both enzymes and their substrates/ligands serve as ``catalysts'' in facilitating the structural changes of each other and promoting the overall chemical transformation reaction. Such new information provides the potential for designing a new class of mechanism-based inhibitors and activators of HDAC8 for treating human diseases. [Preview Abstract] |
Monday, March 14, 2016 8:24AM - 8:36AM |
A39.00003: Single-Molecule Electronic Monitoring of DNA Polymerase Activity Denys O. Marushchak, Kaitlin M. Pugliese, Mackenzie W. Turvey, Yongki Choi, O. Tolga Gul, Tivoli J. Olsen, Arith J. Rajapakse, Gregory A. Weiss, Philip G. Collins Single-molecule techniques can reveal new spatial and kinetic details of the conformational changes occurring during enzymatic catalysis. Here, we investigate the activity of DNA polymerases using an electronic single-molecule technique based on carbon nanotube transistors. Single molecules of the Klenow fragment (KF) of polymerase I were conjugated to the transistors and then monitored via fluctuations in electrical conductance. Continuous, long-term monitoring recorded single KF molecules incorporating up to 10,000 new bases into single-stranded DNA templates. The duration of individual incorporation events was invariant across all analog and native nucleotides, indicating that the precise structure of different base pairs has no impact on the timing of incorporation. Despite similar timings, however, the signal magnitudes generated by certain analogs reveal alternate conformational states that do not occur with native nucleotides. The differences induced by these analogs suggest that the electronic technique is sensing KF's O-helix as it tests the stability of nascent base pairs [1]. [1] K.M. Pugliese, et. al., "Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits." JACS 137, 9587 (2015). [Preview Abstract] |
Monday, March 14, 2016 8:36AM - 8:48AM |
A39.00004: Observation of an electrical signal from a single molecule arooj Aslan, Noor Shaheen, Kyle Dobiszewski, Alokik Kanwal, Reginald Farrow, Gordon Thomas We have attached a folded protein molecule to the tip of a carbon nanotube using electrophoresis. We have then measured the electrons produced when the protein catalyzes a series of reactions. As an initial example of the reactions, we have used the catalysis by glucose-oxidase of glucose. We can show that the characteristic dynamic signals from the molecule scale with the glucose concentration. The molecule on the carbon nanotube tip is stable with respect to time under controlled conditions. The signals also indicate the glucose diffusion as its concentration is locally depleted at the nanotube by the catalysis. We use a second carbon nanotube with a laccase molecule on its tip to complete the circuit with an oxygen reaction. In a previous stage of this process, the other end of the nanotube is attached with a low-impedance electrical connection to a Ti thin film and the measuring circuitry. This work is an early step toward investigating the feasibility of an implantable glucose monitor to help treat diabetes. [Preview Abstract] |
Monday, March 14, 2016 8:48AM - 9:00AM |
A39.00005: Relevance of Aromatic Amino Acids for Electron Conduction along \textit{Geobacter} Pili Protein. Ramesh Adhikari, Nikhil Malvankar, Mark Tuominen, Derek Lovley It has been proposed that the charge transport though \textit{Geobacter sulfurreducens} pili protein occurs through the aromatic amino acids forming helical conducting chain within pili.[1] X-ray studies of pili show that the aromatic amino acids are packed close enough (3-4 {\AA}) for pi-stacking to occur. Conductivity of the pili network increases with lowering temperature indicating metallic-like transport mechanism. [2] However due to the complexity of charge percolation path in 3D network, the intrinsic conductivity of an individual pili was not known. Here, we report transport measurements of individual pili of \textit{G. sulfurreducens.} The conductivity, similar to that of organic polymers, shows that the pili may have implications in materials research. In addition, the conductivity value is sufficient to explain the respiration rate of the \textit{G. sulfurreducens}. Further studies of pili from different natural and genetically modified species with varying amount of aromatic amino acid density demonstrate that it can play a decisive role on the magnitude of the conductivity. [1] Malvankar, N. S. et al. mBio 6, e00084-00015 (2015). [2] Malvankar, N. et al. Nature Nano. 6, 573-579 (2011). [Preview Abstract] |
(Author Not Attending)
|
A39.00006: Finite Difference Frequency Domain (FDFD) Band Structure Calculations of Diatom Frustules Jonathan Mishler, Stephen Bauman, Salvador Barraza-Lopez, Andrew Alverson, Joseph Herzog Diatoms are single-celled photosynthetic algae commonly known for their siliceous cell walls, called frustules. Over the last decade, the uncanny resemblance of their frustules to manufactured photonic crystals has led researchers to study their photonic properties with the hope of using them as self-constructing photonic crystals or biomimetic templates for artificial photonic crystals. The 2D photonic band structures of the foramen, areolae, and cribrum of the diatom species~\textit{Coscinodiscus}~sp. were calculated using the finite difference frequency domain (FDFD) method in both water and air. These calculations revealed the effects of all three layers on a frustule's photonic properties, both in and out of their natural environment. [Preview Abstract] |
Monday, March 14, 2016 9:12AM - 9:24AM |
A39.00007: Protein separation using an electrically tunable membrane Ining Jou, Dmitriy Melnikov, Maria Gracheva Separation of small proteins by charge with a solid-state porous membrane requires control over the protein's movement. Semiconductor membrane has this ability due to the electrically tunable electric potential profile inside the nanopore. In this work we investigate the possibility to separate the solution of two similar sized proteins by charge. As an example, we consider two small globular proteins abundant in humans: insulin (negatively charged) and ubiquitin (neutral). We find that the localized electric field inside the pore either attracts or repels the charged protein to or from the pore wall which affects the delay time before a successful translocation of the protein through the nanopore. However, the motion of the uncharged ubiquitin is unaffected. The difference in the delay time (and hence the separation) can be further increased by the application of the electrolyte bias which induces an electroosmotic flow in the pore. [Preview Abstract] |
Monday, March 14, 2016 9:24AM - 9:36AM |
A39.00008: Investigating the Binding of Peptides to Graphene Surfaces for Biosensing Applications Amanda Garley, Nabanita Saikia, Stephen Barr, Gary Leuty, Rajiv Berry, Hendrik Heinz The Air Force Research Lab is focused on developing highly selective and sensitive graphene-based sensors functionalized with peptides for biomolecule detection. To achieve this there is a need to model interfacial binding interactions between the organic and inorganic components to complement ongoing experimental investigations. It is important to characterize the binding behavior of individual amino acids, with the goal of predicting binding of large peptides. Since polarization is important in graphene systems, a new force field which includes polarizability is used. This allows for an in depth exploration of pi-pi interactions, electrostatics and van der Waals forces involved with binding. The binding strength is determined via enthalpy and free energy calculations. Additionally, structural quantities are computed, such as how aromatic rings align with the graphene surface and the arrangement of various residue substituents in relation to the surface and water layers. Computational results are useful in guiding experimental methods focused on rapidly screening optimal peptide sequence for binding. [Preview Abstract] |
Monday, March 14, 2016 9:36AM - 9:48AM |
A39.00009: The formation of bio-corona on graphene and boron nitride Achyut Raghavendra, Bishwambhar Sengupta, Jingyi Zhu, Apparao Rao, Ramakrishna Podila The increase in applications of engineered two-dimensional (2D) materials has raised concerns over their discharge into the environment. The inadvertent fouling of 2D-materials with natural organic matter (NOM) results in the formation of biocorona, which in turn determines the transport and fate of 2D-materials. Our experiments showed that the physicochemical characteristics of 2D-materials play an important role in biocorna formation. In particular, the formation of biocorona is determined by: i) the amount of aromatic content in NOM, and ii) the distribution of pi-electrons in 2D-materials such as graphene and BN. More importantly, we found that the delocalized pi-electron cloud in NOM results in significant charge transfer while while the charge transfer does not occur for the case of BN wherein the electron cloud is centered near N atoms. A detailed analysis of 2D-material biocorona formation and the impacts on 2D-material transport and fate will be presented. [Preview Abstract] |
Monday, March 14, 2016 9:48AM - 10:00AM |
A39.00010: First principles simulations of nano-peptides on copper surfaces. Duy Le, Talat S. Rahman Protein folding is the process in which a protein structure finds its stable conformation or functional shape. It is considered as a robust way for self-assembling proteins into conformations with desired functionalities. In this work, to obtain a microscopic understanding of the protein folding phenomenon, as influenced by a metallic environment, we perform density functional theory based simulations of the folding of a 9-amino-acid nano-peptide on various copper surfaces. We show that the considered nano-peptides fold into stable monomers or dimers with different conformations depending on the crystallographic orientation of the surface. Comparison of our simulated Scanning Tunneling Microscopy (STM) image with available experimental results [1] provides insights into the microscopic forces responsible for dimerization on Cu(100). [1] S. Rauschenbach et al., to be published [Preview Abstract] |
Monday, March 14, 2016 10:00AM - 10:12AM |
A39.00011: ``Cold Denaturation'' induces inversion of dipole and spin transfer in chiral peptide monolayers Soumyajit Sarkar, Meital Eckshtain-Levi, Eyal Capua, Sivan Refaely-Abramson, Yulian Gavrilov, Shinto Mathew, Yossi Paltiel, Yaakov Levy, Leeor Kronik, Ron Naaman Using a combination of several experimental and computational techniques, we show that the $\alpha $-helix structure of oligopeptides based on alanine and aminoisobutyric acid is transformed to a more linear conformation upon cooling, due to interaction with neighboring molecules in a self-assembled monolayer (SAM) structure. This process is similar to the known ``cold denaturation'' in peptides, but here the SAM plays the role of the solvent. Our DFT-based first principles calculations show that the structural change results in a flip in the direction of the electrical dipole moment of the adsorbed molecules. The dipole flip is accompanied by an associated change in the spin channel that is preferred in electron transfer through the molecules. This is also experimentally observed via a new solid state hybrid organic-inorganic device that is based on the Hall effect, but operates with no external magnetic field or magnetic material. [Preview Abstract] |
Monday, March 14, 2016 10:12AM - 10:24AM |
A39.00012: A New Apparatus for Studies of Low Energy Electron Collisions with Nucleotide Molecules Jessica Duron, Leigh Hargreaves Low-energy electrons, the most copiously produced by-product of radiation cancer therapy, have been shown to be a strong driver of DNA damage in living cells [1]. Quantitative data describing these collisions are presently rare due to technological challenges in performing electron scattering measurements from the nucleobases, e.g. uracil, thymine, guanine, etc. These challenges include the low-vapor pressure of commercial samples (which are powders at room temperature), and the difficulty in making accurate flow measurements from heated gas sources, required to establish the absolute scale of the measured data. Based on techniques pioneered in positron collision physics [2], a new apparatus is presently undergoing commissioning at the California State University Fullerton, which aims to address these issues. We will make the first cross-section measurements for slow (E0 < 30eV) electron collisions with nucleotides. We will report design parameters and ongoing progress in the commissioning of this new experiment. [Preview Abstract] |
Monday, March 14, 2016 10:24AM - 10:36AM |
A39.00013: Resonant soft X-ray scattering on protein solutions Dan Ye, Thinh Le, Cheng Wang, Peter Zwart, Esther Gomez, Enrique Gomez Protein structure is crucial for biological function, such that characterizing protein folding and packing is important for the design of therapeutics and enzymes. We propose resonant soft X-ray scattering (RSOXS) as an approach to study proteins and other biological assemblies in solution. Calculations of the scattering contrast suggest that soft X-ray scattering is more sensitive than hard X-ray scattering, because of contrast generated at the absorption edges of constituent elements such as carbon, nitrogen and oxygen. We have examined the structure of bovine serum albumin (BSA) in solution by RSOXS. We find that by varying incident X-ray energies, we are able to achieve higher scattering contrast near the absorption edge. From our RSOXS scattering result we are able to reconstruct the structure of BSA in 3D. These RSOXS results also agree with hard X-ray experiments, including crystallographic data. Our study demonstrates the potential of RSOXS for studying protein structure in solution. [Preview Abstract] |
Monday, March 14, 2016 10:36AM - 10:48AM |
A39.00014: Strontium and Barium in aqueous solution and an ion channel blocking site. Mangesh Chaudhari, Susan Rempe Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K$+)$ ion channels, and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2$+$, the most potent blocker of K$+$ channels among the simple metal ions. Here, we use a similar method of combining ab-initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2$+$, which does not block bacterial K$+$ channels. The radial distribution of water around Sr2$+$ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2$+$. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental results of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2$+$. When placed in an innermost K$+$ channel blocking site, the solvation free energies and lowest energy structures for both Sr2$+$ and Ba2$+$ are nearly unchanged compared with their respective hydration properties. That result suggests that difference in blocking behavior may arise due to kinetic properties associated with exchange of water ligands for channel ligands instead of equilibrium thermodynamic properties. [Preview Abstract] |
Monday, March 14, 2016 10:48AM - 11:00AM |
A39.00015: An Efficient Single-Molecule Resolution Method for Simulating Spatio-Temporal Dynamics of Protein Interaction Networks that Involve the Cell Membranes Osman N. Yogurtcu, Margaret E. Johnson A significant number of the cellular protein interaction networks, such as the receptor mediated signaling and vesicle trafficking pathways, includes membranes as a molecular assembly platform. Computer simulations can provide insight into the dynamics of complex formation and help identify the principles that govern recruitment and assembly on the membranes. Here, we introduce the Free-Propagator Re-weighting (FPR) algorithm, a recently developed method that efficiently simulates the spatio-temporal dynamics of multiprotein complex formation both in the solution and on the membranes. In the FPR, the position of each protein is propagated using the Brownian motion and the reactions between pairs of proteins can occur upon collisions. Depending on the dimensionality of the interaction, the association probabilities are determined by solving the Smoluchowski diffusion equations in 2D or 3D and trajectory reweighting allows us to obtain the exact association rates for all the reactive pairs. Using the FPR, in this presentation, we investigate the interaction dynamics of the receptor mediated endocytic network as a case study and discuss the possible effects of membrane binding and molecular crowding on the formation of complexes. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700