Biophest, a joint meeting of Biophysics groups at Arizona State University and the University of Arizona, will take place on March 30, 2019 at the ASU Tempe campus and is hosted by the Center for Biological Physics. This annual event allows scientists from Arizona with an interest in biological physics to meet for a day of short talks, posters and lively discussion. We especially welcome presentations from graduate students and postdocs, and also from researchers from biology and bioengineering whose interests overlap with biological physics.
General Program Schedule Biophest 2019, March 30th
Venue: Arizona State University, Tempe Campus, Physical Sciences F Wing, 1st floor
8:00 AM Breakfast
8:50 AM - 10:30 AM Morning Session 1 Session Chairs :
Zeliha Kilic & Steven Fried
8:50 AM - 9:50 AM
Keynote Speaker : M. Thomas Record, Jr. (University of Wisconsin - Madison)
Keynote Lecture : E. coli as a Chemical and Osmotic System: Large Changes in Cytoplasmic Salt Ion, Solute and Biopolymer Concentrations in Response to Osmotic Stress
Abstract : E. coli is remarkable in that it grows over a very wide range of osmotic conditions, from almost-fresh water to brine. To accomplish this, E. coli varies the cytoplasmic amounts of various small solutes (including trehalose; also proline, trimethyl glycine, or ectoine when available) and ions (K+, Glu-, putrescine) over wide ranges by transport or synthesis. The cytoplasmic membrane is freely permeable to water and turgor pressures across the cell wall/outer membrane are small. Hence amounts and types of small solutes present, and their interactions with cytoplasmic biopolymers and other solutes, determine the amount of water in the cytoplasm, which determines cytoplasmic volume and biopolymer concentration. Intriguingly, the growth rate at different osmotic conditions (varied with NaCl, which is not transported) is found to correlate directly with the amount of cytoplasmic water and inversely with the amount of cytoplasmic K+. I’ll summarize these results and discuss possible explanations for the observed correlations.
9:50 AM - 10:10 AM
Speaker : Kristiane Torgesun Pelletier, Rebecca Page (University of Arizona)
Title : Identifying a Novel Allosteric Site in PTP1B
Abstract : A classical paradigm of proteins is that structure predicts function. However, the sequence also plays a critical role. For example, in highly conserved enzyme active sites, the residues responsible for catalysis are often perfectly conserved throughout evolution. In many enzymes, residues outside the active site are also highly conserved, suggesting they may be important for enzyme activity. Here, we describe the identification of a conserved pocket distal from the active site that contributes to Protein Tyrosine Phosphatase 1B (PTP1B) activity. PTP1B is used as a model protein because it is a drug target for both cancer and diabetes, yet inhibitors that target its active site have limited efficacy due to poor bioavailability. Our combination of bioinformatics, enzymatic assays, x-ray crystallographic and NMR spectroscopy led to the discovery of a novel allosteric site on PTP1B that enhances PTP1B intrinsic activity.
10:10 AM - 10:30 AM
Speaker : Paul Campitelli, Banu Ozkan (Arizona State University)
Title : Dynamic Allosteric Residue Coupling (darc) Spots Shed Light on Functional Changes from Sequence Variation
Abstract : Defining the functional impact of protein sequence variation presents a major challenge in biology and genomics and the importance has grown dramatically as unprecedented advances in sequencing complete exomes have yielded tens of thousands of non-synonymous single nucleotide variants (nSNVs) on the human proteome. Currently there are no consistent methods to capture the mechanisms of functional changes as a result of sequence variations, particularly at non-conserved positions and in the absence of large structural changes. We present the dynamic flexibility index (dfi), a measure of residue-specific flexibility and the dynamic coupling index (dci), a technique determining coupling strength between amino acids. We apply our approach to the lactose repressor protein LacI, where substitutions at non-conserved position V52 produce progressive effects on function. dfi captures changes in flexibility in the DNA binding domain and is correlated with binding affinity. We also use dci to identify important dynamic allosteric residue coupling (darc) spots, distally located to the DNA binding domain. darc spot dfi correlates strongly with changes in repression rate as well as DNA binding affinity and shows conformational dynamics at distal sites plays an important role in LacI function.
10:30 AM - 11:00 AM Coffee Break and Poster Presentation Viewing
11:00 AM - 12:00 PM Morning Session 2 Session Chairs :
Akanksha Singh & Reza Nazari
11:00 AM - 11:20 AM
Speaker : Trivikram Molugu, Michael Brown (University of Arizona)
Title : Collective dynamics in phospholipid membranes under osmotic stress
Abstract : Phospholipid membranes are biological liquid crystals exhibiting long-range molecular order . Intermolecular interactions at mesoscopic length scales are key for explaining lipid-protein interactions and biomembrane functioning. Elastic deformations in such materials are manifested as director fluctuations with timescales spanning picoseconds to seconds . Here we examine effects of osmotic stress on liquid-crystalline properties of lipid membranes using NMR relaxation methods. Membrane osmotic stress was monitored by addition of osmolytes and gravimetric dehydration. Solid-state 2H longitudinal (R1Z) and transverse quadrupolar-echo decay (R2QE ) rates were measured for acyl-chain-perdeuterated lipid multilamellar dispersions. Plots of R1Z rates versus squared segmental order parameters (SCD) follow an empirical linear function (square-law) suggesting the emergence of 3-D director fluctuations . Slopes of these plots are sensitive to osmotic stress and invariant under temperature variation. Linear trends were also observed for rates but limited to segments deeper in the bilayer. Enhanced rates and their temperature dependence indicate additional relaxation contributions from slower dynamics. The dependence of on near the headgroup suggests the onset of 2-D surface undulations. Membrane composition at the transition of 3-D to 2-D collective fluctuations has important implications for biomembrane functioning. The observed slow dynamics are due to mesoscopic phenomena that explain bulk material properties, where the connection between mechanical properties and NMR relaxation involves the fluctuation dissipation theorem. Restricted water accessibility into bilayer may suppress slow dynamic modes at high osmotic stress. Analogous studies with cholesterol in raft-like lipid mixtures  report on membrane compositions relevant for biomembrane function. Osmotic stress-mediated lipid dynamics thus opens a new window to exploring their coupling to biomembrane function.
 T.R. Molugu et al. (2017) Chem. Rev. 117, 12087.
 Leftin, A. et al. (2011) BBA 1808, 818.
 T.R. Molugu et al. (2016) Chem. Phys. Lipids 199, 39.
11:20 AM - 11:40 AM
Speaker : Fiona Naughton, Oliver Beckstein (Arizona State University)
Title : Substrate Binding and Conformational Changes of the Bile Acid Symporter ASBTNM
Abstract : Bile acids are synthesised from cholesterol in the body to aid with digestion, but are largely recycled via reabsorption in the intestine through transporters such as the apical sodium-dependent bile acid transporter (ASBT). These transporters are thus attractive drug targets for the treatment of hypercholesterolaemia and type II diabetes, and are of interest as vehicles for drug delivery to the cell following oral administration. ASBT uses the sodium gradient to drive movement of bile acids across the cell membrane, operating through an alternating access mechanism. Although structures of bacterial homologues of ASBT have been determined in both inward and outward facing conformations, many details remain unclear, including the binding of the bile acid substrate and the nature of the conformational transition. We have used computational and experimental methods to examine details of ASBT function on an atomistic scale. Homology modelling and docking were used to generate apo and substrate-bound structures of the ASBT homologue from Neisseria meningitidis (ASBTNM) in both the inward and outward facing conformations. Molecular dynamics (MD) simulations were performed to investigate substrate binding and compared to structural results from X-ray crystallography. Structural transition pathways were explored with biased MD simulations. Through our work, we characterise substrate binding and potential transition pathways between the inward and outward facing structures of ASBTNM as an initial step towards an understanding of the molecular mechanism of sodium-driven symport in ASBT.
11:40 AM - 12:00 PM
Speaker : Fathima Doole, Abhishek Singharoy, Michael Brown, Minkyu Kim (University of Arizona/Arizona State University)
Title : Designing Biopolymer Tethers for Antimicrobial Peptides to Enhance its Stability and Activity
Abstract : Remedies for health associated infectious diseases entails innovations in cost-effective alternatives, industrial-scale synthesis, non-cytotoxicity, and non-biodegradability. We propose a smart biopolymer composed of an antimicrobial peptide (AMP) and a scaffold made from elastin-like polypeptide chains. Direct immobilization of AMPs onto a biomaterial surface reduces its bioactivity; in contrast, surface attachment of AMPs via tethers increases bioactivity and enhances stability. We hypothesize that unstructured hydrophilic protein linkers will behave similarly to conventional hydrophilic polymer tethers. Unstructured hydrophilic protein tethers have been designed using atomistic MD simulation and will be tested experimentally. To obtain an insight how the designed protein tether impact on AMP activity, its mechanism should be probed. The AMP human cathelicidin LL-37  is known to be in equilibrium between various oligomeric states, ranging from monomers to heptamers. Using the visualization tool VMD, these oligomeric states were modeled starting from the available dimeric LL-37 structure (PDB#:5NNM). The structure prediction server Robetta was employed in conjuction to predict energetically important amino acid residues (hot spots) involved in protein-protein interfaces of the modeled structures. Molecular Dynamic Flexibility Fitting (MDFF) was utilized with the available PDB structure (PDB#:2YMK) of the hexameric AMP channel dermcidin to fit the hexameric LL-37 structure. The CHARMM GUI membrane builder was subsequently utilized to simulate the membrane around the hexameric structure. Deducing the orientation of the oligomeric structure in the membrane and adding the protein tether  allows us to observe its impact on the LL-37-membrane interactions. A complete model of this system will allow the design of unstructured hydrophilic protein tethers and aid in understanding the effects of these tethers on AMP conformation as well as bacterial toxicity.
 K.A. Henzler-Wildman et al. (2004) Biochemistry 43, 8459.
 D.J. Callahan et al. (2012) Nano Lett.12, 2165.
12:00 PM - 2:00 PM Lunch Break and Poster Presentation Viewing
2:00 PM - 3:00 PM Afternoon Session 1 Session Chairs :
Anna Eitel & Viren Pattni
2:00 PM - 2:20 PM
Speaker : Senthil Ganesan, Wolfgang Peti (University of Arizona)
Title : Dynamic Activation and Regulation of the Mitogen-activated protein kinase p38
Abstract : Enzymes, including kinases, require conformational and dynamic changes to perform their biological function. Conformational changes associated with the function are well-documented using X-ray crystallography and NMR spectroscopy. However, dynamic changes associated with allostery and catalysis are only beginning to be established. NMR spectroscopy is the method of choice for these studies as it reports directly on protein dynamics/motions across different time scales (ns to s).
Mitogen-activated protein kinases (MAPKs), including p38, belong to the family of ser/thr protein kinases that are essential for cell differentiation and autophagy. p38, becomes activated by phosphorylation of two residues (TxY) in its activation loop. Substrate binding occurs at a recognition sequence, commonly referred to as the D-motif or the Kinase Interaction Motif (KIM). Despite extensive efforts, the molecular mechanism of activation, including how p38 dynamics are correlated with activity and regulation, remains unclear. Here, we use auto-correlated 15N fast (ns-ps) and intermediate timescale (µs-ms) dynamics measurements to understand the activation and regulation of p38. We present relaxation data on five different p38 states – along the activation trajectory, measured at two different magnetic fields (11.7 and 19.96 T) that provide detailed information how dynamics at defined timescales are modulated and lead to p38 activation.
2:20 PM - 2:40 PM
Speaker : Bethany Kartchner, Jeremy Mills (Arizona State University)
Title : A novel approach to integrate protein dynamics into computational enzyme design methods
Abstract : The ability to rationally design enzymes from scratch remains a major challenge in the field of protein engineering. Namely, despite many years of concerted effort in the field, the activities of designed enzymes are almost universally orders of magnitude less efficient than their naturally occurring counterparts. A likely explanation for this is that the well-established link between protein dynamics and both catalytic ability and substrate specificity is not considered, even in state-of-the-art enzyme design methods. This is a consequence of the fact that the computational expense required to simulate these motions has long precluded their inclusion in the enzyme design process. However, the Ozkan laboratory at ASU recently developed computational methods that enable a protein’s unique dynamic profile to be generated with minimal computational expense. This suggests that, for the first time, protein dynamics can be considered during the enzyme design process, representing a potential solution to the previous challenges. We chose to explore this hypothesis using the model enzyme TEM-1 β-lactamase. We first calculated the dynamics profiles of TEM-1 and many of its ancestral homologues. By clustering these profiles, we identified residues that are directly coupled to the active site through extended dynamic networks despite being far removed from it in 3-dimensional space. To test the importance of these residues on catalysis, the Rosetta computational protein design software was used to re-engineer the environments surrounding these residues and were re-analyzed post design. Many designs exhibited predicted dynamic profiles that resembled those of ancient, less specialized, variants of TEM-1. Five of these designed proteins were experimentally characterized in the laboratory and three were found to exhibit properties similar to the ancestral variant. This suggests that, in addition to providing a better understanding of the relationship between catalysis and dynamics in enzymes, our novel computational methods could be used to design more efficient, novel enzymes with far-reaching applications in numerous fields.
2:40 PM - 3:00 PM
Speaker : Daisuke Inoue, Rizal Hariadi (Arizona State University)
Title : Biomolecular motors induce lattice defects and promote monomer exchange in microtubules
Abstract : Microtubules are dynamic bio-polymers, which grow and shrink by addition and removal of tubulin dimers at their tips. Within the microtubule shaft, dimers adopt a densely packed and highly ordered crystal-like lattice structure, which is generally not considered to be dynamic. Biomolecular motors, kinesin and dynein moves along microtubule and exert force to the shaft. However, it has been unclear how the force exerted by molecular motors impact on the shaft stability and dynamics. Here we report that the mechanical work of molecular motors can remove tubulin dimers from the lattice and rapidly destroy microtubules. This effect was not observed when free tubulin dimers were present in the assay. Using fluorescently labelled tubulin dimers we found that dimer removal by motors was compensated for by the insertion of free tubulin dimers into the microtubule lattice. This self-repair mechanism allows microtubules to survive the damage induced by molecular motors as they move along their tracks. Our study reveals the existence of coupling between the motion of kinesin and dynein motors and the renewal of the microtubule lattice.
3:00 PM - 3:30 PM Coffee Break and Poster Presentation - Contest Voting
3:30 PM - 4:50 PM Afternoon Session 2 Session Chairs :
Christine Lewis & Nikita Kumari
3:30 PM - 3:50 AM
Speaker : Julio Candañedo, John Spence (Arizona State University)
Title : Outrunning Electron Beam Damage in Softmatter
Abstract : The Ultra-fast Electron Diffraction (UED) method offers a compact, inexpensive alternative to the XFEL, using both nuclear and electronic scattering from the target potential unlike weak X-ray scattering from the electron density. Recent MeV diffraction cameras have produced sub-10 fs pulses containing about 105 electrons per pulse. We consider prospects for out- running radiation damage using 3 MeV UED pulses, elastically scattered for solid group 18 crystals. Our aim is to use Adiabatic MD (AMD) simulations of the damage process as it evolves to plot as a function of pulse duration. In this way, we study the experimental conditions (e.g. electron source emittance, fluence, and duration) needed to outrun damage using UED. Group 18 solids are chosen for their simplicity, they only interact dispersively. These simulations serve as a stepping stone for more complicated simulations e.g. proteins. The output of the AMD would be the Mean Square Deviation (MSD) and the Radial Distribution Function (RDF), these are explained in the analysis section.
3:50 PM - 4:10 PM
Speaker : Ian Kenney, Oliver Beckstein (Arizona State University)
Title : Formalism for coupled equilibria: statistical mechanics and applications
Abstract : The thermodynamics of a system of coupled equilibria is determined by the free energy of the system's states. While experimental data and computer simulation can tell us the free energy difference between a system's states, physical constraints, such as energy conservation, may not be accounted for when building a thermodynamic cycle from these data. We develop a method for the aggregation of these data in order to determine a system's state free energies up to an arbitrary constant. Given a thermodynamic cycle defined by experimental or computationally determined equilibrium constants, maximum likelihood estimation yields the free energy difference between the system's states without having to sidestep data points with large variances. The use of this method enforces that any closed path within the cycle sums to zero free energy difference. The method was applied considering the problem of competitive binding of sodium and protons in the binding site of a sodium/proton antiporter membrane protein. The method was also applied to a set of molecules to determine macroscopic pKa values where the deprotonation energies were determined quantum mechanically.
4:10 PM - 4:30 PM
Speaker : Sean Seyler, Steve Presse (Arizona State University)
Title : Transport of sub-micron particles in liquids: hydrodynamic memory effects can boost efficiency
Abstract : Recent experiments have motivated a reexamination of Brownian motion, as it is known that hydrodynamic memory and colored thermal noise emerge when resolving short spatiotemporal scales, leading to a substantially different picture of the dynamics. We investigate the problem of particle transport through a liquid at low Reynolds number, where we account for the Basset-Boussinesq force and added mass effect induced by unsteady particle motion while reincorporating thermal fluctuations so as to satisfy fluctuation-dissipation. The resulting fluctuating Basset-Boussinesq-Oseen equation is solved numerically using an efficient method based on Markovian embedding, which captures both the long-tailed hydrodynamic decay of the memory kernel and the colored noise spectrum to an arbitrary level of precision. Using this numerical model, we apply time- and space-periodic driving forces—to sub-micron particles with neutral buoyancy in liquid water—and directly compute net displacements, velocities, and drag forces under steady state conditions. From these basic quantities, we measure an effective friction and compare the predictions of conventional Stokes/Langevin dynamics with the hydrodynamic effects captured by the fluctuating BBO equation. We find that when the driving force period is on the order of the Stokes/Brownian relaxation time, the effective friction is generally lower when hydrodynamic memory effects are present. Our results suggest that accounting for hydrodynamic memory in modeling the transport of vesicles by molecular motors like kinesin, for instance, will modify estimates of motor transport efficiency.
4:30 PM - 4:50 PM
Speaker : Houpu Li, Quan Qing (Arizona State University)
Title : Precise ERK activation by local AC electric field
Abstract : Amplitude, duration, and frequency of activation of the extracellular-signal-regulated kinase (ERK) pathway code diverse spectrum of information at cell, tissue and organism levels to instruct cells to migrate, proliferate, or differentiate. Synchronized frequency control of ERK activation would provide a powerful approach to regulate cell behaviors. In this study we demonstrated modulation of ERK activities using alternative current (AC) electric fields (EFs) in a new frequency range applied through high-k dielectric passivated microelectrodes with single-cell resolution. Both the amplitude and frequency of ERK activation can be precisely controlled, synchronized and modulated. The ERK activation in our system is independent of Faradaic currents and electroporation, thus excluding previously suggested mechanisms of ERK activation by pH, reactive oxygen species and other electro-chemical reaction. Further experiments pinpointed a mechanism of phosphorylation site of EGF receptor to activate the EGFR-ERK pathway that is independent of epidermal growth factor (EGF). AC EFs provide a new strategy to precisely control the dynamics of ERK activation, which may serve as a powerful platform for control of cell behaviors with implications in wide range of biomedical applications.
4:50 PM - 5:00 PM Presentation of Awards and Closing Remarks
- Nikita Kumari
- Tushar Modi
Sarah Johnson e-mail: email@example.com tel.: 480-965-4108