Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session Q48: Focus Session: Physics of Proteins: Dynamics and Function III |
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Sponsoring Units: DBIO Chair: Dimitri Antoniou, University of Arizona Room: 217C |
Wednesday, March 4, 2015 2:30PM - 2:42PM |
Q48.00001: Investigation at the atomic level of homologous enzymes reveals distinct reaction paths Ioanna Zoi, Steven D. Schwartz Bacterial enzymes Escherichia coli and Vibrio cholerae 5' -Methylthioadenosine nucleosidases (MTANs) have different binding affinities for the same transition state analogue. This was surprising as these enzymes share 60{\%} sequence identity, have almost identical active sites and act under the same mechanism. We performed Transition Path Sampling simulations of both enzymes to reveal the atomic details of the catalytic chemical step, to explain the inhibitor affinity differences. Unlike EcMTAN, VcMTAN has multiple distinct transition states, which is an indication that multiple sets of coordinated protein motions can reach a transition state. We also identified the important residues that participate in each enzyme's reaction coordinate and explained their contribution. Subtle dynamic differences manifest in difference of reaction coordinate and transition state structure and also suggest that MTANs differ from most ribosyl transferases. As experimental approaches report averages regarding reaction coordinate information, this study offers, previously unavailable, detailed knowledge to the explanation of bacterial MTANs catalytic mechanism, and could have a significant impact on pharmaceutical design. [Preview Abstract] |
Wednesday, March 4, 2015 2:42PM - 2:54PM |
Q48.00002: Mechanistic model of sodium/proton antiport based on X-ray crystal structures and molecular dynamics simulations Oliver Beckstein, David L Dotson, Chiara Lee, Shoko Yashiro, Povilas Uzdavinys, Christoph von Ballmoos, David Drew, Alexander D. Cameron Na$^{+}$/H$^{+}$ antiporters are membrane proteins that are vital for cell homeostasis but the mechanistic details of their transport mechanism remain unclear, in particular, how Na$^{+}$ and protons bind to the transporter. We recently solved X-ray crystal structures for two such antiporters (NhaA and NapA) in two different conformations of the transport cycle. All-atom molecular dynamics (MD) simulations (for a total simulated time $>10\ \mu$s), indicate that sodium binding is dependent on the charge states of two conserved aspartate residues. A conserved lysine forms a previously unidentified salt bridge with one of the asparates. Under simulated physiological pH the presence of a Na$^{+}$ ion disrupts and breaks the salt bridge in NhaA. To quantify proton binding, we then performed heuristic p$K_{\mathrm{a}}$ calculations on our ensemble of simulations. The calculations support our novel hypothesis that the conserved lysine in these antiporter binds protons in a sodium-dependent manner and thus acts as part of the transport machinery. In conjunction with simulations of the conformational transition we propose a new mechanistic model of ion binding for the CPA2 class of antiporters within the larger framework of the alternating access mechanism of transmembrane transport. [Preview Abstract] |
Wednesday, March 4, 2015 2:54PM - 3:06PM |
Q48.00003: Another Look at the Mechanisms of Hydride Transfer Enzymes from Quantum and Classical Transition Path Sampling Michael Dzierlenga, Dimitri Antoniou, Steven Schwartz The mechanisms involved in enzymatic hydride transfer have been studies for years but questions remain, due to the difficulty in determining the participation of protein dynamics and quantum effects, especially hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and lactate dehydrogenase (LDH). Calculation of the work applied to the hydride during the reaction allows for observation of the change in barrier height due to inclusion of quantum effects. Additionally, the same calculations were performed using deuterium as the transferring particle to validate our methods with experimentally measured kinetic isotope effects. The change in barrier height in YADH upon inclusion of quantum effects is indicative of a zero-point energy contribution, and is evidence that the protein mediates a near-barrierless transfer of the rate-limiting hydride. Calculation of kinetic isotope effects using the average difference in barrier between hydride and deuteride agreed well with experimental results. [Preview Abstract] |
Wednesday, March 4, 2015 3:06PM - 3:18PM |
Q48.00004: Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations Xiaoliang Pan, Steven Schwartz It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD$^+$). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH. [Preview Abstract] |
Wednesday, March 4, 2015 3:18PM - 3:30PM |
Q48.00005: Theory of relaxation dynamics within carotenoids via high frequency stretching modes Vytautas Balevicius, Darius Abramavicius Carotenoids are ubiquitous natural pigment molecules acting as light harvesters in the blue-green region of the spectrum, and at the same time ensuring the photoprotection against excessive light by quenching the triplet state of chlorophylls and singlet oxygen. However, their photophysics is still not fully understood, because the absorption takes place not into the optically dark lowest excited state $S_{1}$, but to the short-lived higher-lying state $S_{2}$. This leads to complicated intramolecular energy redistribution schemes within carotenoids. From the transient absorption experiments it is known that the $S_{1}$ state is populated shortly after the excitation of the $S_{2}$ state (on the time-scale of tens of femtoseconds). The corresponding excited state absorption signal is blue-shifting and narrowing at early times, which is attributed to the vibrational cooling of the $S_{1}$ state. We apply the secular density matrix theory to take into account both the internal conversion from the $S_{2}$ into the $S_{1}$ state and the subsequent relaxation within the manifold of high-frequency vibrational states corresponding to the carbon-carbon stretching modes (C-C and C=C). It allows us to obtain relevant pump-probe spectra in the time range from femto- to picoseconds. [Preview Abstract] |
Wednesday, March 4, 2015 3:30PM - 3:42PM |
Q48.00006: Connecting thermal and mechanical protein (un)folding landscapes Li Sun, Jeffrey Noel, Joanna Sulkowska, Herbert Levine, Jos\'e Onuchic Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying force at both termini. The unfolding time-force relation $\tau $(F) indicates that the unfolding behavior can be characterized into three regimes: barrier-limited low- and intermediate-force regimes, and a barrierless high-force regime. Slope changes of $\tau $(F) separate the three regimes. We show that the behavior of $\tau $(F) can be understood from a two-dimensional free energy landscape projected onto the extension X and the fraction of native contacts Q. In the low-force regime, the unfolding rate is roughly force-independent due to the small (even negative) separation in X between the native ensemble and transition state ensemble (TSE). In the intermediate-force regime, force sufficiently separates the TSE from the native ensemble such that $\tau $(F) roughly follows an exponential relation. The TSE becomes increasingly structured with force. The high-force regime is characterized by barrierless unfolding, approaching a time limit of around 10 $\mu $s. [Preview Abstract] |
Wednesday, March 4, 2015 3:42PM - 3:54PM |
Q48.00007: ABSTRACT WITHDRAWN |
Wednesday, March 4, 2015 3:54PM - 4:06PM |
Q48.00008: Rhodopsin Photoactivation Dynamics Revealed by Quasi-Elastic Neutron Scattering Debsindhu Bhowmik, Utsab Shrestha, Suchhithranga M. C. D. Perera, Udeep Chawla, Eugene Mamontov, Michael Brown, Xiang-Qiang Chu Rhodopsin is a G-protein-coupled receptor (GPCR) responsible for vision. During photoactivation, the chromophore retinal dissociates from protein yielding the opsin apoprotein. What are the changes in protein dynamics that occur during the photoactivation process? Here, we studied the microscopic dynamics of dark-state rhodopsin and the ligand-free opsin using quasielastic neutron scattering (QENS). The QENS technique tracks individual hydrogen atom motion because of the much higher neutron scattering cross-section of hydrogen than other atoms. We used protein with CHAPS detergent hydrated with heavy water. The activation of proteins is confirmed at low temperatures up to 300 K by mean-square displacement (MSD) analysis. The QENS experiments at temperatures ranging from 220 K to 300 K clearly indicate an increase in protein dynamic behavior with temperature. The relaxation time for the ligand-bound protein rhodopsin is faster compared to opsin, which can be correlated with the photoactivation. Moreover, the protein dynamics are orders of magnitude slower than the accompanying CHAPS detergent, which unlike protein, manifests localized motions. [Preview Abstract] |
Wednesday, March 4, 2015 4:06PM - 4:18PM |
Q48.00009: Predicting side-chain conformations of methionine using a hard-sphere model with stereochemical constraints A. Virrueta, J. Gaines, C. S. O'Hern, L. Regan Current research in the O'Hern and Regan laboratories focuses on the development of hard-sphere models with stereochemical constraints for protein structure prediction as an alternative to molecular dynamics methods that utilize knowledge-based corrections in their force-fields. Beginning with simple hydrophobic dipeptides like valine, leucine, and isoleucine, we have shown that our model is able to reproduce the side-chain dihedral angle distributions derived from sets of high-resolution protein crystal structures. However, methionine remains an exception - our model yields a chi-3 side-chain dihedral angle distribution that is relatively uniform from 60 to 300 degrees, while the observed distribution displays peaks at 60, 180, and 300 degrees. Our goal is to resolve this discrepancy by considering clashes with neighboring residues, and averaging the reduced distribution of allowable methionine structures taken from a set of crystallized proteins. We will also re-evaluate the electron density maps from which these protein structures are derived to ensure that the methionines and their local environments are correctly modeled. This work will ultimately serve as a tool for computing side-chain entropy and protein stability. [Preview Abstract] |
Wednesday, March 4, 2015 4:18PM - 4:54PM |
Q48.00010: How can we understand an entire (super)family of proteins? Invited Speaker: Wouter Hoff Understanding how the functional properties of a protein are encoded in its amino acid sequence remains a formidable challenge. We use photoactive yellow protein (PYP) to determine how structure-function relationships can be obtained for an entire (super)family of proteins. PYP is a model system to study fundamental processes in proteins and a prototype for the PAS domain superfamily. It consists of a 100-residue PAS domain with an additional 25-residue N-terminal extension. PYP exhibits a photocycle that is initiated by $p$CA photoisomerization, followed by proton transfer from Glu46 to the $p$CA and a subsequent protein quake during formation of the pB intermediate. These structural changes are driven by the electrostatic epicenter formed by the buried ionized Glu46 side chain and involve partial protein unfolding, including the release of the N-terminal region. Deletion of the N-terminal region slows down pB decay 1,000-fold. We report results on family-wide structure function relationships in PYP. (i) Transplanting mutations that alter the properties of a highly studied PYP to a different PYP homolog are only partially successful, implying sequence context dependence of functional properties. (ii) We find a direct correlation between the strength of the hydrogen bonding between the $p$CA and Glu46 and functional properties of PYPs. The role of Glu46 as the epicenter for driving large conformational changes during pB formation is conserved. (iii) Across the PYP family the N-terminal region is negatively charged while the PAS core is positively charged. The resulting charge-charge interactions are critical for the function the N-terminal region. (iv) We find that residues conserved in the PAS domain superfamily exert their effects through conserved patterns of side chain interactions. [Preview Abstract] |
Wednesday, March 4, 2015 4:54PM - 5:06PM |
Q48.00011: A coarse-grained model to study calcium activation of the cardiac thin filament Jing Zhang, Steven Schwartz Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources. [Preview Abstract] |
Wednesday, March 4, 2015 5:06PM - 5:18PM |
Q48.00012: Photoinduced conformational changes to porphyrin-bound albumin reduces albumin binding to Osteonectin Sarah Rozinek, Robert Thomas, Lorenzo Brancaleon Much work has shown light-induced structural changes to proteins are possible. For instance, we have previously shown that, small secondary and tertiary structural changes occur to albumin when it is bound (non-covalently) to meso-tetrakis(4-sulfonatophenyl)porphyrin (TSPP) and irradiated with a low intensity laser. Further study of this light-induced protein modification could advance the understanding of albumin's structure/function relationship. Then, this structural modification technique might be implemented to deactivate unwanted protein functions or even to bestow non-native protein properties. A necessary step toward this goal is to determine if and how protein function is affected once its structure is modified. The current study aims to explore the light-induced conformational change to TSPP-bound albumin by testing its ability to bind the biologically relevant albumin receptor, Osteonectin. In this Affinity-Depletion experiment, Osteonectin has been covalently attached to magnetic beads, forming an affinity column. TSPP-albumin will non-covalently bind the column, and we predict that the light-induced change to albumin will cause a reduction in binding to Osteonectin. This loss of binding ability would mean a deactivation of albumin's natural cellular functions. [Preview Abstract] |
Wednesday, March 4, 2015 5:18PM - 5:30PM |
Q48.00013: Probing second hydration shell of ionic solutions using Gigahertz to Terahertz spectroscopy Deepu George, Chola Regmi, Shengfeng Cheng, Nguyen Vinh Understanding the nature of ionic solvation sheds light into the role of ions in determining the activities of biomolecules in living environment. The dynamics of water around simple structures like ions may be a good starting point in understanding the dynamics of water around much more complex macro molecules. Here we expand on our previous studies on ionic solutions by further extending the radiation frequency region as well as by looking at ions with different sizes. Using two complimentary techniques which cover the frequency range from 6 GHz up to 3 THz, we have measured the femtosecond to picosecond dynamics of weakly bound waters around cations in the first group of the periodic table. By choosing solutions of chloride salts, we have kept the influence of anions the same while varying only the size of cations. Our results confirm our previous studies on pure water dynamics showing the existence of three different relaxation processes. While the relaxation times remain more or less the same, their amplitudes change with a change in salt concentration. Together with molecular dynamics, we give an estimation of the structure of the first as well as the second hydration shells of ions in liquid water. [Preview Abstract] |
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