Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session U22: Focus Session: Nonequilibrium Fluctuations in Biomolecules |
Hide Abstracts |
Sponsoring Units: DPOLY Chair: Christy Landes, University of Houston Room: Morial Convention Center 214 |
Thursday, March 13, 2008 8:00AM - 8:36AM |
U22.00001: Driving proteins and DNA with mechanical forces: Pushing, pulling, and squeezing molecules using computer simulations. Invited Speaker: In living organisms, proteins and other biopolymers are often subjected to mechanical forces. Some of those forces are strong enough to cause proteins to unfold. For example, proteins driven across transmembrane pores may only enter the pores after they are mechanically denatured. Mechanically driven protein unfolding is often a non-equilibrium, irreversible process; Nature often takes advantage of the energy dissipation associated with such irreversible phenomena. For example, the ability of certain protein domains to dissipate large amounts of energy in the process of their mechanical unfolding is exploited in natural fibers and adhesives, which, as a result, display a remarkable combination of toughness and strength that is rarely achieved in artificial materials. In this talk, I will report on theoretical studies and computer simulations of several types of mechanical processes involving biopolymers. Examples include mechanical unfolding of proteins pulled at their ends, translocation of polymers across transmembrane pores, and stochastic dynamics of knots in tensioned polymer chains. I will discuss some of the computational challenges associated with the disparity between the time scales of simulation and experiments, comment on the molecular origins of high mechanical resistance displayed by some proteins, and compare our results with single-molecule pulling experiments. [Preview Abstract] |
Thursday, March 13, 2008 8:36AM - 8:48AM |
U22.00002: Fluorescent resonant energy transfer: Correlated fluctuations of donor and acceptor Zhi-Gang Yu Mounting evidence suggests that in single-molecule flurescent resonant energy transfer (FRET) measurements, correlation between fluctuations in donor and acceptor may be important. We present a general theory to describe this correlation and its effect on the FRET rate [1]. The correlation arises from low-energy excitations (e.g. acoustic phonons) of the molecule to which a donor-acceptor pair is attached, and results in an effective interaction between local environments or baths associated with the donor and the acceptor. The correlation is found to reduce the transfer rate, in particular at short donor-acceptor distances. The theory can quantitatively explain recent measurements of polyproline peptides. [1] Z. G. Yu, J. Chem. Phys. {\bf 27}, 20xxxx (Communications) (2007). [Preview Abstract] |
Thursday, March 13, 2008 8:48AM - 9:00AM |
U22.00003: The water effects on long-distance charge transfer in polypeptides Nikolai Sergueev, Alexander Demkov Long-range electron transfer (ET) is one of the most intriguing reactions occurring in biological systems. Recent experiments indicate that water play an important role in the mechanism of charge transfer in proteins. In this talk we present the first-principles study of the effect of intervening water molecules on the electron tunneling processes in simple polypeptide bridges. The ET rate is related to the probability current that is computed using density functional theory and nonequilibrium Green's function formalism which takes into account the inelastic electron-phonon scattering in the bridge. Our results suggest that the effect of water is two fold. First, the insertion of water molecules changes the conformational and dynamic properties of the polypeptide molecule. Second, the presence of water modifies the electrostatics of the bridge. Both effects are found to have a significant effect on the electron transfer rate. [Preview Abstract] |
Thursday, March 13, 2008 9:00AM - 9:12AM |
U22.00004: In$_{2}$O$_{3}$ nanowire based field effect transistor for biological sensors. Zhongming Zeng, Kai wang, Weilie Zhou Semiconductor nanowires (NWs) are attracting considerable attention due to their nanoscale dimensions and enormous surface-to-volume ratios. Many applications have been demonstrated in toxic gas, protein, small molecule and viruses sensing because of their superior sensing performances. Indium oxide (In$_{2}$O$_{3})$ NWs have been successfully applied for toxic gas and small organic molecule sensing. In our experiment, In$_{2}$O$_{3}$ NWs based field effect transistors (FET) are fabricated for virus (Ricin) detections. Single-crystalline In$_{2}$O$_{3}$ NWs with diameters around 100 nm were synthesized by the thermal evaporation. The nanodevice based on In$_{2}$O$_{3}$ NWs bridges the source/drain electrodes with a channel length of $\sim $5 $\mu $m. Basic transport properties of devices were measured before biological detection. The I-V curves with the gate voltage V$_{g}$=0 shows good ohmic contact and the resistance is about 10 M$\Omega $. The back-gate effect on the conductivity showed that In$_{2}$O$_{3}$ NW is working as $n$-type channel with obvious back-gate effect, which is much stronger than the reported results. The nanodevices used as virus detection will be also discussed. [Preview Abstract] |
Thursday, March 13, 2008 9:12AM - 9:24AM |
U22.00005: Messenger RNA sequence and the translation process --a particle transport perspective Jiajia Dong, Beate Schmittmann, Royce K.P. Zia The translation process in bacteria has been under intensive study. A key question concerns the quantitative effect of different elongation rates, associated with different codons, on the overall translation efficiency. Starting with a simple particle transport model, the totally asymmetric simple exclusion process (TASEP), we incorporate the essential components of the translation process: Ribosomes, cognate tRNA concentrations, and messenger RNA (mRNA) templates correspond to particles, hopping rates, and the underlying lattice, respectively. Using simulations and mean-field approximations to obtain the stationary currents (the protein production rates) associated with different mRNA sequences, we are especially interested in the effect of slow codons, i.e., codons which are associated with rare tRNAs and are therefore translated very slowly. As the first step, we look at a ``designed sequence'' with one and two slow codons and quantify the marked impact of their spatial distribution to the currents. Extending the results to several mRNA sequences taken from real genes, we argue that an \textit{effective translation rate} including the information from the vicinity of each codon needs to be taken into consideration when seeking an efficient strategy to optimize the protein production. [Preview Abstract] |
Thursday, March 13, 2008 9:24AM - 9:36AM |
U22.00006: Sticky-sphere model for phase separation of mixtures of the eye lens proteins gamma-B and alpha crystallin: non-monotonic dependence on mutual attraction George Thurston, Maurino Bautista, David Ross, Vern Lindberg, Hossein Shahmohamad We apply a multi-component extension of the Baxter sticky-sphere model to aqueous solutions of the eye lens proteins gamma-B crystallin and alpha crystallin. These mixtures show liquid-liquid phase separation influenced by gamma-B/gamma-B attraction, gamma-B/alpha size disparity and gamma-B/alpha attraction. We examine the dependence of the upper-consolute spinodal temperature surface on gamma-B/alpha attraction, previously found to influence stability. Gamma-B crystallin is modeled with a temperature-dependent stickiness parameter that reproduces both static light scattering and small-angle neutron scattering near its critical point. Alpha crystallin is modeled as a hard sphere. We find that the Barboy-Tenne model shows a non-monotonic dependence of the spinodal temperature surface on gamma-B/alpha attraction that is qualitatively consistent with recent molecular dynamics simulation results. Hard-sphere or very attractive gamma-B/alpha interactions lead to instability, and the spinodal surface shows a minimum in an intermediate range of gamma-B/alpha attraction strength. We examine the nature of the two types of instability. [Preview Abstract] |
Thursday, March 13, 2008 9:36AM - 9:48AM |
U22.00007: Structural Isotopic Effects in the smallest chiral amino acid: Observation of a structural phase transition in fully deuterated alanine. Heloisa Bordallo, Joelma de Souza, Paulo de Tarso, Dimitri Argyriou A first study of possible changes instigated by deuteration in amino acids was carried out using neutron diffraction, inelastic neutron scattering and Raman scattering in L-alanine, C$_{2}$H$_{4}$(NH$_{2})$COOH. Careful analysis of the structural parameters shows that deuteration of L-alanine engenders significant geometric changes as a function of temperature, which can be directly related to the observation of new lattice vibration modes in the Raman spectra. The combination of the experimental data suggests that C$_{2}$D$_{4}$(ND$_{2})$COOD undergoes a structural phase transition (or a structural rearrangement) at about 170 K. Considering that this particular amino acid is a hydrogen-bonded system with short hydrogen bonds (O{\ldots}H $\sim $ 1.8 {\AA}), we evoke the Ubbelohde effect to conclude that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions. The structural differences suggest distinct relative stabilities for the hydrogenous and deuterated L-alanine. De Souza et al. - Journal of Physical Chemistry B (Letters) \textbf{111}, 5034-39 (2007) [Preview Abstract] |
Thursday, March 13, 2008 9:48AM - 10:00AM |
U22.00008: Exploring the Electrical Conductivity of Myoglobin Debin Li, David Lederman, Peter M Gannett The electrical conductance of single myoglobin proteins was measured to study its electron transfer properties. We examined the electronic properties of myoglobin, using apomyoglobin (myoglobin without a heme group) as a reference. The differential conductivity of the proteins deposited on Pt nanometer-scale electrodes was measured using a lock-in technique as a function of bias and gate voltages. Nano- electrodes were fabricated by creating small Pt channels 100 nm - 300 nm wide via e-beam lithography and then creating a break junction by electromigration at low temperatures (4 K - 77 K). The conductance of apomyoglobin was very different from that of myoglobin, with a predominant peak at ~50 meV. On the other hand, myoglobin had a rich structure that we surmise results from the presence of the heme group. [Preview Abstract] |
Thursday, March 13, 2008 10:00AM - 10:12AM |
U22.00009: Selective binding affinity of cationic antimicrobial peptides for lipid membranes: roles of peptide charge and hydrophobicity Sattar Taheri-Araghi, Bae-Yeun Ha Antimicrobial peptides selectively disrupt microbial membranes through hydrophobic insertion into the outer layers, which are known to carry a large fraction of anionic lipids. When the peptides are cationic, as is often the case, the interplay between hydrophobic and electrostatic interactions determines the selective binding affinity (thus antimicrobial activity) of the peptides. Here we present a detailed theoretical picture of how the selective binding is influenced by such factors as the charge and hydrophobicity of the peptides and the elasticity of target membranes. This effort not only accounts for some of the general trends observed in experimental studies, but it also leads to a theoretical model for optimizing the selectivity and antimicrobial activity. [Preview Abstract] |
Thursday, March 13, 2008 10:12AM - 10:24AM |
U22.00010: Excitation dynamics in purple bacteria photosynthetic membranes under different light adaptation conditions Felipe Caycedo, Ferney Rodriguez, Luis Quiroga Photosynthetic membranes in {\it R. Sphaeriodes} purple bacteria adapt to light growth conditions such as the intensity level of radiation, which determine their amount of Reaction Centers (RCs), and also their global architecture. In any case, for both high and low intensity conditions the trend for core (LH1) and antenna (LH2) complexes clustering is mantained. Using a F\"orster hopping model for excitation transfer, we analize different adapted membranes for which we report results for the yield and lifetime of excitations under continuous illumination levels. We show that complexes stoichiometry obey to efficiency optimization under RC biochemical cycle constraints. By constrast to common belief, complexes aggregation does not directly show any strong dependence on excitation efficiency observables. [Preview Abstract] |
Thursday, March 13, 2008 10:24AM - 10:36AM |
U22.00011: Microscopic Electrohydrodynamics of DNA electrophoresis Aleksei Aksimentiev, Binquan Luan Gel electrophoresis is currently the most successful yet costly method to sequence DNA. Electrophoresis of DNA through solid-state nanopores holds promise for reducing the costs and making personal genomics a reality. The underlying physics of DNA electrophoresis, however, remains controversial. Theoretical models of this process often invoke the notion of the effective charge of a DNA molecule $q_{\mathrm{eff}}$ to account for the reduced electric force on DNA in an external field $E$, i.e. $F= q_{\mathrm{eff}}E$. However, experimental estimates of $q_{\mathrm{eff}}$ can differ from each other by as much as ten times. To clarify the physical origin of the reduction of an electric force on DNA in electrophoresis, we investigated this process through extensive all-atom molecular dynamics simulations. Our results demonstrate that the effective screening of the DNA charge arises from the hydrodynamic drag of the electroosmotic flow, not from the counterion condensation. We show that the effective driving force $F$ of an applied electric field $E$ in a nanopore obeys the same law as in a bulk electrolyte: $F=\xi\mu E$. Here, $\xi$ and $\mu$ are, respectively, the friction coefficient and electrophoretic mobility of DNA that depend on the surface properties of a nanopore, such as its roughness. Based on the above law, a method for determining the effective driving force is suggested that does not require a direct force measurement. [Preview Abstract] |
Thursday, March 13, 2008 10:36AM - 10:48AM |
U22.00012: Multivalent counterions inhibit DNA ejection from viral capsid Toan Nguyen Viral DNA packaged inside a bacteriophage is tighly bent. This stored bending energy of DNA is believed to be the main driving force to eject viral DNA into host cell upon capsid binding. One can control the amount of ejected DNA by subjecting the virus to a solution of PEG8000 molecules. The molecules cannot penetrate the viral capsid, therefore, they exert an osmotic pressure on the virus preventing DNA ejection. Experiments showed that for a given osmotic pressure, the degree of ejection also depends on the concentration of small ions in solution. Interestingly, for multivalent ions (such as Mg2+, Spd3+ or HexCo3+), this dependence is non-monotonic. We propose a simple electrostatic theory to explain this non-monotonic behavior. This is based on the fact that DNA molecules can invert its net charge at high enough multivalent counterion concentration. In other words, as multivalent counterion concentration is increased from zero, charge of DNA molecules change from negative to positive. At the concentration where DNA net charge is zero, the DNA molecules experience an attraction between different segments and DNA ejected amount is reduced. At low or high counterion concentration, DNA segments are charged (negatively or positively), repel each other and DNA ejected amount is increased. Fitting the result of the theory to experimental data, we obtain a numerical value for Mg2+ mediated DNA - DNA attraction energy to be -0.008kT per base. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700