Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session C16: Native and Non-Native Protein Structure and StabilityFocus Live
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Sponsoring Units: GSNP DBIO Chair: Robert Hoy, Univ of South Florida |
Monday, March 15, 2021 3:00PM - 3:36PM Live |
C16.00001: Atomistic Go Model to Predict the Structure of Protein Cores Invited Speaker: Alex Grigas
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Monday, March 15, 2021 3:36PM - 3:48PM Live |
C16.00002: Quasi-two-dimensional diffusion of interacting globular proteins Zihan Tan, Jan K. G. Dhont, Vania Calandrini, Gerhard Nägele Diffusion of proteins along lipid membranes plays a vital role in cell signaling processes. How the collective and self-diffusion of proteins are affected by direct and hydrodynamic interactions is relevant, e.g., for protein clustering and oligomerization of receptor protein subunits. Using mesoscale hydrodynamic simulations, the dynamic predictions by a minimalistic protein-membrane-cytosol model are explored. The model describes globular proteins as Brownian spheres, confined to lateral motion in a planar monolayer embedded in a three-dimensional viscous fluid. The proteins are assumed to interact pairwisely either via a hard-core potential or a soft potential consisting of competing short-range attractive and long-range repulsive parts. We analyze spatio-temporal correlations from short times where inertial motion is resolved up to long times where the solvent-mediated hydrodynamic interactions between proteins are fully developed. In this context, we investigate the short-time buildup of inter-protein hydrodynamic interactions by multiple scattering of sound and vorticity diffusion, and long-time anomalous enhancement of collective diffusion, in their dependence on protein concentration. |
Monday, March 15, 2021 3:48PM - 4:00PM Live |
C16.00003: Dual mechanism of ionic liquid-induced protein unfolding Peiyin Lee A combination of experiment and simulation is used to investigate the thermal unfolding of lysozyme in the presence of two imidazolium-based ILs ([EMIM][EtSO4] and [EMIM][Et2PO4]). Both ILs reduce lysozyme melting temperature (T_m), but more gradually than strong denaturants. |
Monday, March 15, 2021 4:00PM - 4:12PM Live |
C16.00004: Investigating 'False Positive' Protein Decoys Based on Core Packing Features Zhuoyi Liu, Alex Grigas, Corey O'Hern It is well-known that the hydrophobic cores of proteins contribute significantly to their stability. Further, the cores of high-quality experimental protein structures share several important physical features: 1) the cores are densely packed with packing fraction around 0.56, and 2) the interatomic overlap between non-bonded core residues is small. However, many computationally generated decoys do not recapitulate these key features of core packing. We developed a feed-forward neural network based on packing features of cores to predict how well computational models recapitulate real protein structures. While this method achieves high accuracy, there are a number of 'false positive' decoys whose physical features match those expected for experimental structures, but still show low similarity to the true crystal structure. These 'false positive' protein decoys also yield high scores for many other state-of-the-art decoy detection methods. After identifying these 'false positive' decoys, I improved the accuracy of the neural network by including additional features concerning backbone secondary structure. In future studies, we will use the 'false positive' decoys as inputs into molecular dynamics simulations to test their stability in current force fields. |
Monday, March 15, 2021 4:12PM - 4:24PM Live |
C16.00005: Binding of Proteins to Surface Plasmon Resonance Biochips Functionalized with Native and Size-Reduced Phytoglycogen Nanoparticles Nicholas van Heijst, Kathleen Charlesworth, Aidan Maxwell, Michael Grossutti, John Dutcher Phytoglycogen is a highly branched, compact, natural polymer of glucose produced by sweet corn. Its softness, porosity and mechanical integrity, as well as nontoxicity and biodegradability, make it ideal for applications involving the human body. Many of these applications rely on binding of bioactive molecules to phytoglycogen nanoparticles. We probe intermolecular binding affinities and kinetics using Surface Plasmon Resonance (SPR) imaging. We have successfully produced SPR biochips functionalized with both native and size-reduced phytoglycogen using a self-assembled monolayer of 4-mercaptophenylboronic acid as an intermediate linker between the gold substrate and phytoglycogen. This has allowed us to determine the association constant between concanavalin A (conA) and both native and size-reduced phytoglycogen by fitting the SPR data to the Langmuir adsorption model. We used infrared spectroscopy to monitor the amide bands of the bound conA molecules, confirming that conA maintained a significant portion of its native beta-sheet content and suggesting that binding of conA to phytoglycogen does not significantly reduce its bioactivity. |
Monday, March 15, 2021 4:24PM - 5:00PM Live |
C16.00006: Molecular dynamics simulations of folded proteins: determining the properties of protein cores Invited Speaker: Zhe Mei Proteins are highly dynamic molecules that undergo conformational fluctuations on temporal and spatial scales. Theseconformational changes, often intimately connected to the functional forms of the proteins. Molecular dynamics (MD)simulations have provided ways to estimate the hidden conformations and understand the correlation between confor-mation change and their functions. However, whether MD can accurately recapitulate protein dynamics still remainsunclear. In this paper, we show that three of the most commonly used MD force fields, CHARMM36M, Amber99SB-ILDN and Amber99NMR cannot accurately recapitulate the conformations of proteins solved by solution NMR. Eventhough the MD simulations are initiated with the experimental structures, they quickly diverge from the NMR bundle. |
Monday, March 15, 2021 5:00PM - 5:12PM Live |
C16.00007: Proteinaceous optical devices in squids: understanding the reflectin-lipid interaction Irem Altan, Dillion Fox, Alison Sweeney The self-assembly of reflectins, a family of proteins in cephalopods, gives rise to optical properties like iridescence. The resulting structure consists of thin layers of reflectins sandwiched between the cell membrane; the high refractive index contrast between assembled reflectin and the extracellular fluid allows strong interaction with light. Simulations suggest that reflectins are partially unfolded and form a potentially novel interaction with the lipid bilayer resulting in the interdigitation of the lipid tails between membrane leaflets. This interaction is correlated with a shift in the physicochemical properties of the membrane. SANS results show that reflectin-lipid interactions cause changes in the larger assembled structure at length scales much greater than that of a single protein. SAXS data suggest that lamellar membrane structures that disappear with increasing experimental temperature are present. The temperature above which the lamellae disappear is higher when reflectin is present in the system. Our data suggest that reflectins trigger structural changes in lipid bilayers that in turn influence the material properties and resulting geometric configurations of the plasma membrane in living cells. |
Monday, March 15, 2021 5:12PM - 5:24PM Live |
C16.00008: Time-retarded electronic friction and enhanced mass of classical nuclei innonadiabatic molecular dynamics due to self-consistent coupling to electronictime-dependent nonequilibrium Green function Priyanka Mondal, Branislav Nikolic The most conventional way to calculate current induced force (including steady state and friction force) on classical degree of freedom due to fast electron dynamics is to use Wigner representation of Keldysh Green function that assumes slow variation of central time and fast variation of relative time leading to an expression for Born-Oppenheimer force in adiabatic limit and friction as the first order adiabatic correction. Here we present a new scheme of ab-initio MD that self-consistently couples molecular dynamics (MD) to quantum description of electrondynamics where current induced force is calculated including all higher order terms using time-dependent nonequilibrium Green function (TDNEGF) which leads to memory effect and show that the effect of highly nonadiabatic inertia term which has not been considered in previous studies. We took example of single electronic energy level of Hydrogen like atom which is coupled to a classical degree of freedom and showed that our formalism, unlike the conventional approach, captures the effect of inertia term included in current induced force leading to a highly nontrivial change in damping dynamics in a classial-quantum system. |
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