Bulletin of the American Physical Society
Mid-Atlantic Section Fall Meeting 2020
Volume 65, Number 20
Friday–Sunday, December 4–6, 2020; Virtual
Session K01: Protein and Lipid Dynamics |
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Chair: Aurelia Smith |
Sunday, December 6, 2020 11:30AM - 12:06PM |
K01.00001: Characterization of Phosphatidylinositol Phosphates Binding in Lipid Bilayers by Solid-state NMR Invited Speaker: Andrew Nieuwkoop Phosphatidylinositol phosphates (PIPs) are a class of membrane lipid that regulate diverse cell processes in eukaryotic organisms. As a major regulator of cellular growth, metabolism, immunity, and development, misregulation of PIP levels has enormous impacts on human health, factoring in diseases such as diabetes, cancer, obesity, and immune disorders amongst many others. Despite decades of effort, there remains no direct method to confirm PIP binding by a protein in a lipid bilayer. The Nieuwkoop lab is working use solid-state NMR and molecular dynamics simulations to understanding the properties of PIP containing lipid bilayers, map the PIP binding sites of PIP binding domains, and characterize the effects of PIP binding on the structure and dynamics of PIP binding proteins. We utilize $^{\mathrm{13}}$C, $^{\mathrm{31}}$P and $^{\mathrm{1}}$H detected solid-state NMR to assign the chemical shifts and probe the structure and phase transitions of lipid headgroups. We use $^{\mathrm{13}}$C, $^{\mathrm{15}}$N and $^{\mathrm{1}}$H detected spectra at 13, 40 and 100$+$ kHz MAS to assign the chemical shifts of the PIP binding domains and to look for binding at to nitrogen containing side chains. We use molecular dynamic simulations to probe the PIP binding sites and determine the effects of PIP binding on domain structure and orientation. The overall goal is to develop a set of tools to directly detect PIP binding in lipid membranes by solid-state NMR. [Preview Abstract] |
Sunday, December 6, 2020 12:06PM - 12:18PM |
K01.00002: Characterization of Silk/Cellulose Biocomposites Infused with rGO Abneris Morales, Bailey Blessing, Karleena Rybacki, Stacy Love, Sean O'Malley, Xiao Hu, David Salas-de la Cruz In the recent years, biomaterials from renewable sources have shown potential in medicine and materials science alike. Biomaterials are a class of materials and have been of interest in the recent decades due to their abundance, low cost, biocompatibility, and tunable morphological and physicochemical properties. Cellulose is appealing to the industry due to its crystalline and amorphous regions; while silk is made up of flexible protein fibers, is attractive due to its tunable biodegradation and biocompatibility. When the two natural polymers are mixed together, their properties can be tuned by changing material composition and fabrication method. Reduced graphene oxide (rGO) is ideal to increase molecular interactions and stabilization of these two components due to its strong oxidizing properties. We explore how rGO affects the carbohydrate crystallinity and protein secondary structure formation as well as their physicochemical properties including ionic conductivity. The biocomposites with rGO were investigated using FTIR, SEM, X-Ray Scattering, DSC, TGA, and DRS. The results showed that rGO stabilizes the morphology and thermal properties of the biocomposites. Additionally, they demonstrate that the cellulose crystallinity and the silk beta sheet content influence the ionic conductivity of the materials. With the DRS data collected as well as the Fulcher VFT Model and Arrhenius expression, the activation energy of the biocomposites were calculated. [Preview Abstract] |
Sunday, December 6, 2020 12:18PM - 12:54PM |
K01.00003: Conformational Dynamics of Short Peptides in Aqueous Solutions: Assessment of Molecular Dynamics Force Fields Invited Speaker: Brigita Urbanc Molecular dynamics (MD) offers deep insights into structure and dynamics of protein folding and assembly. MD predictions, however, strongly depend on the accuracy of MD force fields. In the past decade, a large number of MD force field modifications have been proposed, in particular to address the need to capture conformational dynamics of intrinsically disordered peptides and proteins. I will present our recent work elucidating three commonly used MD force fields with respect to their capacity to reproduce conformational ensembles of short unfolded cationic peptides in aqueous solutions in a way that is consistent with available spectroscopic data. [Preview Abstract] |
Sunday, December 6, 2020 12:54PM - 1:06PM |
K01.00004: An Experiment-Driven Molecular Dynamics Study of GAG in Water/Ethanol Mixtures Shuting Zhang, Brian Andrews, Reinhard Schweitzer-Stenner, Brigita Urbanc Cationic glycylalanylglycine (GAG) is reported to form a hydrogel in binary mixtures of water and ethanol in vitro. Alanine residue in GAG adopts high polyproline II (pPII) content in water. Spectroscopic data, including three J coupling constants and amide I' profiles, indicate that if the ethanol fraction in the aqueous solution exceeds 42\%, the pPII content of alanine residue in GAG is significantly reduced. Here, the experiment-based Gaussian model of Ramachandran distributions and three molecular dynamics (MD) force fields (Amber ff14SB, OPLS-AA/M, and CHARMM36m), are evaluated according to their ability to capture the ethanol-induced conformational changes observed in the experiments. MD simulations on monomeric GAG in eight water/ethanol mixtures reveal that only Amber ff14SB partially reproduces the conformational change in experiments due to ethanol. Further simulations of 200 mM GAG in the aqueous solution with 42\% ethanol and pure water reveal the capacity of CHARMM36m to capture the ethanol-induced pPII content change of alanine in GAG. These findings provide a possible explanation of the failure of MD force fields in simulations of monomeric GAG and suggest that the above ethanol-induced conformational changes emerge from GAG self-assembly induced by ethanol. [Preview Abstract] |
Sunday, December 6, 2020 1:06PM - 1:18PM |
K01.00005: Examining the Self Assembly of the Villin Headpiece Protein: A Combined Experimental and Molecular Dynamics Study Brian Andrews, Kaho Long, Brigita Urbanc The Villin Headpiece subdomain (VHP36) is a protein that is well studied experimentally and computationally such that its monomeric native structure and ability to self-assemble are well characterized. In this study, we present experimental evidence that VHP36 proteins in solution form a limited number of dimers while the large majority remain monomeric independent of concentration. We then use our in-house coarse-grain Discrete Molecular Dynamics (DMD) package DMD4B-HYDRA which combines discrete potential functionals with a four-bead protein model to observe VHP36 assembly in simulation. Dimers produced from the DMD simulations are converted from the four-bead model to an all-atom structure and their stability is analyzed via all-atom MD simulations in two frequently used MD force fields. Additional simulations of two unfolded VHP36 monomers are also simulated in the same MD force fields to observe the dimerization process in more detail. The purpose of this work is to assess and compare the ability of the MD force fields to capture the dimerization process and search for an explanation regarding the absence of larger order oligomers. [Preview Abstract] |
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