Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session J35: Protein Water Interactions |
Hide Abstracts |
Sponsoring Units: DBP DCP DCOMP Chair: Andrea Markelz, University of Buffalo Room: Colorado Convention Center 405 |
Tuesday, March 6, 2007 11:15AM - 11:27AM |
J35.00001: Oscillatory Growth of Ice Crystals Observed in a Solution of Antifreeze Glycoprotein Yoshinori Furukawa, Yoshihiro Nishimura, Salvador Zepeda, Hiroyuki Nakaya, Etsuro Yokoyama One-directional growth experiments of ice crystals in an aqueous solution of antifreeze glycoprotein (AFGP) were carried out using a growth cell made of thin glass capillaries. When the interface tips of ice crystals were constructed by prismatic planes, the interface position changed periodically with time. These phenomena were not observed for the growth of basal planes in the AFGP solution or for the growth of ice crystals in pure water. We first observed the oscillatory growth of ice crystals in the AFGP solution. Fluorescent labeled AFGP molecules were also used to observe the diffusion, incorporation, and segregation of the solute at the interface, in the solid and in solution. The periodic incorporation of AFGP molecules were clearly observed in conjunction with the growth rate changes. [Preview Abstract] |
Tuesday, March 6, 2007 11:27AM - 11:39AM |
J35.00002: A model of self-oscillatory growth of ice crystals in antifreeze glycoprotein solutions Etsuro Yokoyama, Yoshinori Furukawa We discuss that~ an oscillatory crystal growth is observed not only in the growth of an ice crystal from AFGP solution but also in the motion of steps on the surface of ice crystals in the presence of AFGP molecules. Our model of the oscillatory growth of crystals accounts for two elementary processes relevant to the growth: 1) an interface kinetic processes for transformation into a crystalline phase at the interface, and 2) a diffusion process for the transport of latent heat liberated at the growing interface. In this talk, we propose the hypothesis of a hysteresis behavior of growth rate to explain the formation of periodic structures of a growing crystal without a change of external conditions.~ ~The self-oscillatory growth in the presence of AFGP adsorbed molecules can occur because of the coupling of interface kinetics to the transport of latent heat under constant growth conditions. [Preview Abstract] |
Tuesday, March 6, 2007 11:39AM - 11:51AM |
J35.00003: Antifreeze Protein (AFP) and Antifreeze Glycoprotein (AFGP) Kinetics at the Ice/Solution Interface Salvador Zepeda, Hiroyuki Nakaya, Yukihiro Uda, Etsuro Yokoyama, Yoshinori Furukawa AFPs and AFGPs found in some fish, plants and insects are a necessary tool for surviving sub-freezing environments. They occur in a wide range of compositions and structure, but to some extent they all accomplish the same functions: they suppress the freezing temperature, inhibit recrystallization, and modify ice crystal growth. Here, we observe the exact location of AFGPs, Type I and Type III AFPs by 1-directional growth experiments using fluorescence and phase contrast microscopy as well as free growth experiments using 3-d confocal microscopy. In all cases, the proteins clearly adsorb at the interface. By comparing the fluorescent image with the corresponding phase contrast image we find that AFGPs incorporate only into the solid in veins and not into the ice lattice structure. Type I AFPs show similar behavior as AFGPs, but type III AFPs adsorb to specific planes within the ice lattice. We have also calculated the diffusion constants and the surface adsorption concentration from both types of experiments. Our results indicated that the different types of AFPs or AFGPs accomplish essentially the same function in slightly different ways and that it is not necessary for the protein adsorption to the ice interface to be as rigid as once thought. [Preview Abstract] |
Tuesday, March 6, 2007 11:51AM - 12:03PM |
J35.00004: Protein slaving to the solvent and the relation to hydrodynamics P. W. Fenimore, Guo Chen, B. H. McMahon Protein motions can be categorized by the nature of their coupling to solvent dynamics. Some protein motions, including the final ligand binding process in myoglobin (Mb), are largely independent of solvent fluctuations. Others, such as entry and exit of ligands from Mb require Debye-like $\alpha$ fluctuations in the solvent to proceed. A third class of motions, including the r.\ m.\ s.\ displacments of atoms are controlled by solvent $\beta$ fluctuations. We show that a slaving picture of protein dynamics, $k_{\mathrm{protein}} = k_\alpha/n$, where $n$ is a nearly T-independent factor, known to be as large as $10^5$, is consistent with an essentially hydrodynamic picture of $\alpha$-slaved protein motions. Consistency with hydrodynamics (i.\ e.\ the Stokes-Einstein equation) can be demonstrated by considering changes to protein stability caused by ordinary experimental protocols for measuring viscosity- and T-dependent protein dynamics data. The decomposition of protein dynamics into several discrete classes suggests modelling techniques to simplify the simulation of protein dynamics. [Preview Abstract] |
Tuesday, March 6, 2007 12:03PM - 12:15PM |
J35.00005: Dynamics of Lysozyme in a Glycerol-Water system Pavan Ghatty, Gustavo Carri Bio-preservation of proteins is of great commercial and academic interest. A variety of sugars have been found to be effective in preserving the structure of proteins. This has been attributed and in some cases proved to their ability to form strong hydrogen bonds with proteins thus restricting their motion. The work presented here explores the hypothesis that glycerol, a tri-alcohol curbs the motion of protein. \newline \newline We have carried out a 10ns Molecular Dynamics simulation to study the phenomenon. The structure of Lysozyme (PDB code 193L) has been studied in three solutions of 10, 20 and 30 {\%} by weight of glycerol in water. \newline \newline Glycerol molecules in all three solutions have shown a tendency to agglomerate around the protein. Strong hydrogen bonding has also been observed between glycerol molecules and the protein. With increasing time, the g(r) of glycerol molecules around proteins shows two peaks with increasing prominence suggesting the movement of glycerol cluster to positions closer to the protein surface. [Preview Abstract] |
Tuesday, March 6, 2007 12:15PM - 12:27PM |
J35.00006: An extended dynamical solvation shell around proteins. Seung Joong Kim, Simon Ebbinghaus, Matthias Heyden, Xin Yu, Udo Heugen, Martin Gruebele, David Leitner, Martina Havenith Water solvating biomolecules in organisms has different properties from the bulk. Such solvation shells can be characterized by a variety of structural and dynamical measures. The fundamental question of biomolecule hydration is: how far out into the solvent does the influence of the biomolecule reach? We use terahertz absorption spectroscopy of the five helix bundle protein Lambda Repressor 6-85, coupled with molecular dynamics simulations, to show that correlated water motion at a sub-psec time scale persists to distances of at least 20 angstrom. We show this by determining that bulk water, water molecules mainly interacting with a single protein molecule, and water molecules interacting with more than one protein molecule have different absorption signatures in the THz frequency range, leading to an experimentally detectable non-monotonic dependence of the absorption coefficient on protein concentration. This trend is supported in the calculations, which further show that long-distance hydration is a dynamical effect correlating many water molecules, not one that noticeably perturbs the structural distribution of one or a few water molecules from the bulk value. [Preview Abstract] |
Tuesday, March 6, 2007 12:27PM - 12:39PM |
J35.00007: Structural and dynamical properties of water in hydrophobic confinement, as probed by \textit{ab-initio }molecular dynamics. Giancarlo Cicero, Jeffrey C. Grossman, Eric Schwegler, Galli Giulia Unraveling the microscopic properties of water confined in small channels will help understand fluid flow and transport at the nanoscale, and will shed light on the solvation of biomolecules. To date most of the properties of confined water are poorly understood and, in many cases, controversial. We present a first principles computational study of prototype systems ---water confined between graphene sheets and inside carbon nanotubes-- which have received widespread experimental attention and for which, however, such basic questions as diffusion at the nanoscale, and characteristics of the hydrogen bonded network remain unanswered. Our simulations show that the liquid density substantially increases at the water/surface interface, and that water diffusion is faster in highly confined structures, due to a decrease of the dipole moment in interfacial water molecules and correspondingly a decrease in H-bond network strength. We propose that many effects attributed to confinement in the past are actually interfacial effects due to subtle electronic structure rearrangements, and that these are amenable to vibrational and x-ray absorption spectroscopy investigations. [Preview Abstract] |
Tuesday, March 6, 2007 12:39PM - 12:51PM |
J35.00008: Basal Plane Affinity of an Insect Antifreeze Protein N. Pertaya, S.Y. Gauthier, P.L. Davies, I. Braslavsky sbwAFP is a powerful antifreeze protein (AFP) with high thermal hysteresis activity that protects spruce budworm (sbw) from freezing during harsh winters in the spruce and fir forests of USA and Canada. Different types of antifreeze proteins have been found in many other species and have potential applications in cryomedicine and cryopreservation. When an ice crystal is cooled in the presence of AFP below the non-equilibrium freezing point the crystal will suddenly and rapidly grow in specific directions. Hyperactive antifreezes like sbwAFP expand perpendicular to the c-axis (in the plane of the a-axes), whereas moderately active AFPs, like type III from fish, grow in the direction parallel to the c-axis. It has been proposed that the basis for hyperactivity of certain AFPs is that they bind and accumulate on the basal plane to inhibit c-axial growth. By putting fluorescent tags on these two types of AFPs we have been able to directly visualize the binding of different types of AFPs to ice surfaces. We do indeed find that the insect AFP accumulates on the basal plane of an ice crystal while type III AFP does not. Supported by CIHR and BNTI. [Preview Abstract] |
Tuesday, March 6, 2007 12:51PM - 1:03PM |
J35.00009: Study of Hydrogen Bond and Dipolar Interaction in Water-like Fluid with Toy Model Y.S. Jho, C.S. Chang, P.A. Pincus, M.W. Kim Hydrogen bond and dipolar interaction, which originated from the high polarizability of asymmetric water-like molecules, give rise to anomalous properties. Anionic interface of water-like fluid is understandable as a result of hydrogen bond and excluded interactions of OH$^{-}$ and H$_{3}$O$^{+}$. Range of dipolar interaction reaches over several water-like molecule size. And, the interaction between dipole and ion affects on about 20 times longer than the size of water-like molecule. Therefore, the interaction between charged particles within this range shows different behavior compared to interaction in a uniform dielectric medium. Toy model gives physical insights and helps comprehensions to complex phenomena. In this study we give the numerical simulation to investigate these phenomena. [Preview Abstract] |
Tuesday, March 6, 2007 1:03PM - 1:15PM |
J35.00010: Density and Structure of Water under Confinement as Determined using Monte Carlo Simulations Sumit Sharma, Sanat K. Kumar The structure and local density of water is thought to play an important role in phenomena such as protein adsorption. These properties of water under confinement between surfaces can be significantly different from those of bulk water. A change in the water's structure, which is coupled to a change in the local density of the confined water in equilibrium with the bulk water, can create an attractive or repulsive force between the planar surfaces. This force itself can dominate the mechanism of adsorption when adsorbing molecules are within close proximity from adsorbent. In order to probe the effects of confinement further, Grand Canonical ensemble Monte Carlo (GCMC) simulations of Single Point Charge Enhanced (SPC/E) water confined between two planar surfaces of differing hydrophobicity, ranging from hydrophobic to hydrophilic, have been performed. The dependence of the water's structure and local density on the hydrophobicity and distance between the two planar surfaces has been determined. Further, the effect of surface curvature will also be examined. [Preview Abstract] |
Tuesday, March 6, 2007 1:15PM - 1:27PM |
J35.00011: The protein hydration transition Yunfen He, Joseph Knab, Jing-Yin Chen, Andrea Markelz We previously reported the hydration transition in the THz dielectric response for native state hen egg white lysozyme (HEWL). As hydration increases the response slowly increases until at 0.25h (gm water/gm protein) the absorbance and index sharply increase. The hydration level coincides with the filling of the first solvation shell. The THz dielectric response arises from relaxational and resonant vibrational response, where the vibrational response corresponds to delocalized structural motions sensitive to the conformation and the environment. We examine the contribution of low frequency vibrational modes to the hydration transition by calculating the normal mode density as a function of solvent content using CHARMM. We find that the density of low frequency modes increases with the increasing solvent content, but this increase does not show the transition seen experimentally. We discuss that another source for the hydration transition in the THz response may be the hydration dependence of the activation energy for glass-like beta fluctuations that contribute to the relaxational response. [Preview Abstract] |
Tuesday, March 6, 2007 1:27PM - 1:39PM |
J35.00012: Inverted Solubility of the Pro 23 to Val Mutant of Human $\gamma $D Crystallin-- Altered Phase Diagram from a Single Amino Acid Substitution and the Effect of PEG J.J. McManus, A. Lomakin, M. Basan, O. Ogun, A. Pande, J. Pande, G.B. Benedek Many genetic cataracts are the result of single point mutations in the amino acid sequence of lens crystallin proteins. The P23T mutation in human $\gamma $D-crystallin (HGD) is associated with several different cataract phenotypes. The solubility of the protein shows an inverse temperature dependence. This is in contrast with the native protein. The replacement of Thr23 with a Ser or a Val residue shifts the location of the inverted solubility line to higher concentrations [1]. We describe the phase diagram of the P23V mutant of HGD, which exhibits aggregation, crystallization and liquid-liquid phase separation (LLPS). We have used QLS to probe the interactions of the protein in the soluble region of the phase diagram. We have developed a model to describe the observed retrograde solubility of the protein. Using PEG we introduce a so-called ``depletion interaction'' to further investigate the origin of the retrograde solubility. [1] A. Pande, O. Anunziata, N. Asherie, O. Ogun, G.B. Benedek, J. Pande, \textit{Biochemistry} \textbf{44}, 2491-2500 (2005). [Preview Abstract] |
Tuesday, March 6, 2007 1:39PM - 1:51PM |
J35.00013: Free energy study of uranyl complexes across water-oil and water-oil+tri-butyl phosphate (TBP) interfaces Manori Jayasinghe, Thomas L. Beck Free energy profiles of heavy metal ion complexes, UO$_{2}$ (NO$_{3})_{2}$, UO$_{2}$ (NO$_{3})_{2}$TBP$_{2}$, and TBP, across the water-hexane and water hexane+TBP (50{\%}/50{\%}) interfaces, were calculated from molecular dynamics simulations. These complexes and interfaces are relevant to recently developed heavy-ion separation techniques. The solute complex with TBP, UO$_{2}$ (NO$_{3})_{2}$TBP$_{2}$, shows strong interfacial activity in contrast to the free energy barrier for UO$_{2}$ (NO$_{3})_{2}$ at the water-hexane interface. Increased TBP concentration in the oil phase reduces the interfacial activity and better solvates the ion complexes and their ligands. The solute complex with TBP oriented parallel to the water-hexane+TBP interface binds more strongly to the hexane+TBP phase than to the pure hexane phase. The (un-complexed) TBP orientational probability distribution shows the polar head buried in water, while the nonpolar tails are buried in the oil phase, and hence TBP exhibits interfacial activity. The calculated density profiles at the interface show that TBP acts not only as a carrier for uranyl transport across the interface, but also as an ``interface modifier''. Our simulation results are in agreement with the recent study of uranyl transport across chemically modified membranes with TBP based metal ion carriers. [Preview Abstract] |
Tuesday, March 6, 2007 1:51PM - 2:03PM |
J35.00014: Differential Dielectric Spectroscopy of Protein Solutions: Observation of Protein Interactions Brian Mazzeo, Andrew Flewitt Observation of a protein-protein interaction is illustrated by dielectric measurements on rabbit IgG (190 $\mu $g/ml) and Protein A (19 $\mu $g/ml) by a homemade dielectric cell and HP 4194A impedance analyzer. Frequency shifts of ratios 2.0 and 1.6 with respect to the individual relaxation characteristics of IgG and Protein A were obtained by dielectric spectroscopy, which has historically been used to determine the properties of solvated biomolecules to measure the hydrodynamic and electrical properties of individual proteins and of solution. Dielectric relaxation theory predicts changes in the dielectric relaxation characteristics of proteins due to protein interactions resulting in larger hydrodynamic volumes. Experimentally, bovine serum albumin, protein A, and rabbit IgG were added sequentially to phosphate buffer and the incremental dielectric changes were measured. The differential dielectric response, as a biophysical technique, gives insight into the interaction of the added protein with biomolecules in solution and can indicate the presence of protein-protein interactions. [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