Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session Z46: Focus Session: Physics of Proteins IV |
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Sponsoring Units: DBIO Chair: Andrea Markelz, State University of New York at Buffalo Room: Hilton Baltimore Holiday Ballroom 5 |
Friday, March 22, 2013 11:15AM - 11:51AM |
Z46.00001: Is tertiary structure really required for specific function of a protein? Invited Speaker: Mikio Kataoka A protein is folded into the unique tertiary structure spontaneously based on the information encoded in the amino acid sequence. It has been believed that the unique tertiary structure is required for the expression of its specific function. However, the discovery of intrinsically disordered proteins (IDP) raised a question whether the structure is really required to function. Some IDP's are folded by the recognition and binding of their targets called coupled folding and binding. We have created many mutants of staphylococcal nuclease (SNase) which have interesting properties. One category of mutants cannot take native structures but show enzymatic activity. Another type of mutants takes stable native structures without activity, despite that the active site residues are completely conserved. The former can be regarded as a model system of IDP. They show ligand-induced folding which is similar to the coupled folding and binding. The mechanism of induced folding has been studied intensively by stopped-flow CD. The reason why activity is lost in the latter mutants will be discussed based on the crystal structure. Consequently, I would like to discuss about the relationship among structure, function and dynamics. [Preview Abstract] |
Friday, March 22, 2013 11:51AM - 12:03PM |
Z46.00002: Structure--Function Studies on Receptor Activation of Photoactive Yellow Protein Sandip Kaledhonkar, Shuo Dai, Rachana Rathod, Wouter Hoff, Aihua Xie Biological signaling in cells starts with detection of stimuli from ever changing environment, results in relay of signal, and finishes with particular cellular response. Photoactive yellow protein (PYP) from a salt loving \textit{Halorhodospira halophila} bacterium is a blue light photoreceptor protein for negative phototaxis and a structural prototype of PAS domain superfamily of signaling and regulatory proteins. Upon absorption of a blue photon by its negatively charged $p$-coumaric acid ($p$CA) chromophore, the receptor state (off-state) undergoes photocyclic process, leading to large amplitude protein quake that results in PYP receptor activation. To understand the structural basis of receptor activation we employ time-resolved FTIR spectroscopic techniques combined with site-specific mutation to search for a key residue involved in protein quake. We will discuss the strategies and experimental results in light of hydrogen bonding network, active site structure and protein quake in PYP. The signaling mechanism leaned from PYP may have implication to understand signal transduction in other proteins. [Preview Abstract] |
Friday, March 22, 2013 12:03PM - 12:15PM |
Z46.00003: Reconciling the concurrent fast and slow cycling of proteins on gene promoter Wei Wang, Yaolai Wang, Feng Liu Proteins appeared to cycle on and off the gene promoters with both long and short periods. We proposed a model to explore the dynamics of promoter-protein interactions, which enable gene transcription to proceed orderly and cyclically. We analytically proved that the intervals between two successive productive interactions are less than tens of seconds. Fitting of the model to the experimental data suggests that proteins rapidly cycle on and off the promoter, with the binding time less than several minutes. Different proteins kick in at different phases of the transcriptional cycle, and the percentage of promoters bound by specific proteins in a cell population oscillates with a period of 40min. We thus reconcile the fast and slow cycling of proteins and reveal the essential mechanism of transcription dynamics. [Preview Abstract] |
Friday, March 22, 2013 12:15PM - 12:27PM |
Z46.00004: Dynamics and pathway of electron tunneling in repair of damaged DNA by photolyase Zheyun Liu, Xunmin Guo, Chuang Tan, Jiang Li, Ya-Ting Kao, Lijuan Wang, Aziz Sancar, Dongping Zhong Through electron tunneling, photolyase, a photoenzyme, restores damaged DNA into normal bases. Here, we report our systematic characterization and analyses of three electron transfer processes in thymine dimer restoration by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repairing and for the final electron return to restore the active cofactor and complete the repair photocycle. Significantly, we found that the adenine moiety of the unusual bent cofactor is essential to mediating all electron-transfer dynamics through a super-exchange mechanism, leading to a delicate balance of time scales. The active-site structural integrity, unique electron tunneling pathways and the critical role of adenine assure these elementary dynamics in synergy in this complex photorepair machinery to achieve the maximum repair efficiency close to unity. [Preview Abstract] |
Friday, March 22, 2013 12:27PM - 12:39PM |
Z46.00005: Electronic measurements of single-molecule processing by DNA polymerase I Yongki Choi, Tivoli Olsen, Tolga Gul, Brad Corso, Chengjun Dong, William Brown, Gregory Weiss, Philip Collins A single-molecule nanocircuit technique is applied to continuously monitor DNA replication activity by the enzyme DNA polymerase I (Pol I). Using single copies of Pol I bound to a single-walled carbon nanotube device, an electrical signal was generated to reveal enzymatic function and dynamic variability. Continuous, single-molecule-resolution recordings were obtained for Pol I processing homopolymeric DNA templates over 10 minutes and through \textgreater 10,000 DNA replication events. Processivity of up to 40 nucleotide bases was directly observed, and statistical analysis of the recordings determined key kinetic parameters for the enzyme's open and closed conformations. We observe that the closed complex forms a phosphodiester bond in a highly efficient process \textgreater 99.8{\%} of the time, with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for replication occurs during the enzyme's open state, but with a duration that is nearly twice as long for dATP or dTTP incorporation than for dCTP or dGTP. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase. [Preview Abstract] |
Friday, March 22, 2013 12:39PM - 12:51PM |
Z46.00006: Coupling between Switching Regulation and Torque Generation in Bacterial Flagellar Motor Jianhua Xing, Fan Bai, Tohru Minamino, Zhanghan Wu, Keiichi Namba The bacterial flagellar motor plays a crucial role in both bacterial locomotion and chemotaxis. Recent experiments reveal that the switching dynamics of the motor depend on the rotation speed of the motor, and thus the motor torque, nonmonotonically. Here we present a unified mathematical model that treats motor torque generation based on experimental torque-speed curves and the torque-dependent switching based on the Ising type conformational spread model. The model successfully reproduces the observed switching rate as a function of the rotation speed, and provides a generic physical explanation independent of most details. A stator affects the switching dynamics through two mechanisms: accelerating the conformational flipping rate of individual rotor-switching units, which contributes most when the stator works at a high torque and thus a low speed; and influencing a larger number of rotor-switching units within unit time, whose contribution is the greatest when the motor rotates at a high speed. Consequently, the switching rate shows a maximum at intermediate speed, where the above two mechanisms find an optimal output. The load-switching relation may serve as a mechanism for sensing the physical environment, similar to the chemotaxis mechanism for sensing the chemical environment. [Preview Abstract] |
Friday, March 22, 2013 12:51PM - 1:03PM |
Z46.00007: ABSTRACT WITHDRAWN |
Friday, March 22, 2013 1:03PM - 1:15PM |
Z46.00008: Investigating a simple model of protein folding for evidence of self-organized criticality Joelle Murray, Andrew Cleland, Addison Wisthoff Protein folding is a complex, multi-faceted process with many drivers. Systems of this type are ubiquitous in nature and many behave as self-organizing critical (SOC) systems. Does protein folding exhibit self-organizing critical behavior? To answer this question, we developed a simple model of the folding process and searched for evidence of self-organized critical behavior. Furthermore, we investigated whether or not the parameters defining self-organization can shed light on the protein folding process. [Preview Abstract] |
Friday, March 22, 2013 1:15PM - 1:27PM |
Z46.00009: Investigating the nature of folded protein structure with the aid of crystalline and amorphous models Deniz Turgut, Osman Okan, Angel Garcia, Rahmi Ozisik Three-dimensional structure of a protein is closely tied with its function. Understanding the folded shape of a protein provides crucial information both in identifying the function and engineering custom proteins that will perform desired functions. In the current work, based on the symmetries present in the local neighborhood of residues in the folded protein structure, we investigated the possibility of creating protein-like structures from crystalline and amorphous models. Parameters like Radial Distribution Function and Bond Orientational Order Parameter [Steinhardt PJ, Nelson DR, Ronchetti M, Phys Rev B 1983, 28, 784] were used to identify the similarities between the created model structures and over 400 folded protein structures. The results show both similarities and differences between folded protein structures and those obtained from crystalline or amorphous models. [Preview Abstract] |
Friday, March 22, 2013 1:27PM - 1:39PM |
Z46.00010: The Dynamical Transition and DNA hybridization Deepu George, Katherine Niessen, Andrea Markelz Terahertz spectroscopy has contributed to the understanding of the so-called biomolecular dynamical transition [1,2], which has been related to the anharmonic motions necessary to biomolecular function. It has been established that the 220 K transition is associated with solvent dynamics. Recently there has been some evidence that correlated motions of proteins also contribute to the THz response, and possibly a lower temperature dynamical transition arises from internal molecular motions. Here we examine how the temperature dependent THz response changes upon binding of single stranded DNA polynucleotide chains. THz time-domain spectroscopy (THz TDS) transmission measurements are performed on solution phase single stranded DNA (5 bases in length) for a specific sequence GCGCG, its complement CGCGC, and the hybridized pair. Our preliminary results show that while we have consistent decrease in the net dielectric response with binding, the dynamical transition does not change.\\[4pt] [1] Y. He et al ``Protein Dynamical Transition Does Not Require Protein Structure,'' Phys. Rev. Lett., vol. 101, p. 178103, 2008.\\[0pt] [2] F. Lipps et al ``Hydration and temperature interdependence of protein picosecond dynamics,'' Phys. Chem. Chem. Phys. vol. 14, pp. 6375-6381, 2012. [Preview Abstract] |
Friday, March 22, 2013 1:39PM - 1:51PM |
Z46.00011: The power of hard-sphere models for proteins: Understanding side-chain conformations and predicting thermodynamic stability Alice Qinhua Zhou, Corey O'Hern, Lynne Regan We seek to dramatically improve computational protein design using minimal models that include only the dominant physical interactions. By modeling proteins with hard-sphere interactions and stereochemical constraints, we are able to explain the side-chain dihedral angle distributions for Leu, Ile, and other hydrophobic residues that are observed in protein crystal structures. We also consider inter-residue interactions on the distribution of side-chain dihedral angles for residues in the hydrophobic core of T4 lysozyme. We calculate the energetic and entropic contributions to the free energy differences between wildtype T4 lysozyme and several mutants involving Leu to Ala substitutions. We find a strong correlation between the entropy difference and the decrease in the melting temperature of the mutatants. These results emphasize that considering both entropy and enthalpy is crucial for obtaining a quantitative understanding of protein stability. [Preview Abstract] |
Friday, March 22, 2013 1:51PM - 2:03PM |
Z46.00012: Role of the different factors contributing to long lived quantum coherence in the FMO complex Nayeli Zuniga-Hansen, Russell Ceballos, Mark S. Byrd The Fenna-Matthews-Olson (FMO) complex is one of the most widely studied photosynthetic complexes. It occurs as a trimer with three identical subunits that contain eight bacteriochlorphylls embedded in a protein environment. The observation of long lived quantum coherence and the remarkably high efficiency with which energy transfer takes place in the FMO complex has brought much attention to try to understand the mechanism behind it. We study the different factors that contribute to the long lived coherence in this complex by looking at the interplay of different parameters within the intermediate regime, where the strength of the coupling to the environment is comparable to the strength of the coupling between the sites of the system. We attempt to verify if the environmental modes due to the protein backbone have an effect on the energy transfer or if it is inherently robust due to its structure. [Preview Abstract] |
Friday, March 22, 2013 2:03PM - 2:15PM |
Z46.00013: Dielectric response of hydrated proteins Dmitry Matyushov We study dipolar susceptibility of hydrated proteins, representing the average dipole moment induced at the hydrated protein by a uniform external field. This parameter shows remarkable variation among proteins. We find a negative value of the dipolar susceptibility for some proteins, which implies a dia-electric dipolar response and negative dielectrophoresis. Such proteins, even though carrying significant permanent dipole moments, repel from the electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. We therefore suggest that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending approximately 2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is found for the electrostatic potential. The model is applied to the analysis of light absorption by protein solutions in the THz window of radiation. Here we also find significant deviations of the absorption coefficient from the predictions of traditional theories. [Preview Abstract] |
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