Bulletin of the American Physical Society
APS March Meeting 2010
Volume 55, Number 2
Monday–Friday, March 15–19, 2010; Portland, Oregon
Session L27: Focus Session: Confined and Biological Water IV |
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Sponsoring Units: DCP Chair: Shekhar Garde, Rensselaer Polytechnic Institute Room: D137 |
Tuesday, March 16, 2010 2:30PM - 3:06PM |
L27.00001: Dynamics of ubiquitin in the confining environment of a reverse micelle Invited Speaker: We study the hydration and dynamics of a protein (ubiquitin) in the interior of a reverse micelle (RM) that mimics a confining environment. The protein/RM system self assembles starting from a homogeneous system containing water, isooctane a surfactant (AOT) and ions. We find that the hydration of the protein surface and interior are changed, when compared to the protein in water, but the dynamics is only slightly changed. The protein prefers to be located away from the center of the RM and near the AOT charged headgroups. This preference appears to be entropically driven and occurs even when the AOT headgroups are uncharged. Similar behavior was found in alpha helical peptides. [Preview Abstract] |
Tuesday, March 16, 2010 3:06PM - 3:18PM |
L27.00002: Water-mediated energy transport and structure across a protein-protein interface David Leitner Water molecules embedded within proteins or at the interface between globules play a central role in folding and function. We discuss the influence of interfacial water molecules on energy transport and structure, specifically the role of water at the interface between the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis, which binds oxygen cooperatively. We have studied the water-mediated energy transport in this protein with communication maps and nonequilibrium molecular simulations of energy flow, which reveal the disproportionate amount of energy carried by the water molecules, particularly across the interface, i.e., a larger thermal conductivity of the interfacial waters compared with other parts of the protein, promoting hydrogen bond rearrangements at the interface. [Preview Abstract] |
Tuesday, March 16, 2010 3:18PM - 3:30PM |
L27.00003: Size dependence of water-polypeptide interactions: the peptide dynamical transition Andrea Markelz, Rohit Singh, Deepu George Previously we demonstrated that the so-called protein dynamical transition has a size dependence using terahertz time domain spectroscopy [1]. In those results the 200 K onset of low frequency absorbance continued down to penta-alanine, but ceased below this size. However those measurements only covered the 80-290 K range.~ In this work we continue measurements down to 5 K to address the question of the temperature dependence arising for the time scale of motions scaling with the solute size.\\[4pt] [1]Yunfen He, Pei I. Ku, J. R. Knab, J.Y. Chen, and A. G. Markelz, Phys. Rev. Lett. 101, 178103 (2008). [Preview Abstract] |
Tuesday, March 16, 2010 3:30PM - 3:42PM |
L27.00004: Probing the dynamics of amyloidogenic peptides by dielectric relaxation spectroscopy Donald Barry, Fioleda Prifti, Izabela Stroe Fibrillar amyloidogenic structures have been considered for a long time indicators of neurodegenerative diseases. However, it has been proposed recently that amyloid oligomers are in fact the cytotoxic form and more importantly, they exhibit dynamics which differ from the fibrillar form due to the structure of water around these molecular structures. Here, we report dielectric relaxation measurements of non-amyloidogenic and amyloidogenic peptides in deionized water as a function of time and concentration. Our preliminary data show that the dielectric relaxation time of mixtures of deionized water and amyloidogenic peptides is a sensitive indicator of a transition state dominated by soluble oligomers to one characterized by the formation of large fibrils. Over time, this transition shifts the dielectric signal towards large relaxation time values, similar to those in bulk-like water as more molecules are liberated when small oligomers form fibrils. This is in agreement with recent theoretical models.\footnote{F. Despa et al., J. Biol. Phys. (2008) 34, 577 and references herein.} [Preview Abstract] |
Tuesday, March 16, 2010 3:42PM - 4:18PM |
L27.00005: Water in the Protein Interior Invited Speaker: Water expulsion from protein cores is a key step in protein folding, but there is experimental evidence for water in specific protein cavities. Calculations of the thermodynamics of transfer of bulk water into cavities, using MD simulations, have shown that filling of non-polar cavities with water is favored by dispersion forces at the walls of cavities large enough to contain a hydrogen-bonded cluster of at least three water molecules. The free energy of transfer is driven by the energy and not by the entropy. I will discuss the thermodynamics of water transfer into three different protein cavities: (a)a 4-water molecule cluster formed at high pressures in the large cavity of an L99A mutant of T4lysozyme studied previously by Collins et al (PNAS 102,16668-71 (2005)) (b) a 9-water molecule cluster formed at 92C in the largest cavity of the thermostable bacterial protein tetrabrachion predicted to dry at 110C and (c) water in the nonpolar cavity of interleukin 1-$\beta$. The presence of water in the first two proteins was determined in X-Ray crystallographic studies and is supported by negative free energies of transfer. X-Ray and NMR evidence for water in interleukin 1-$\beta$ is less conclusive. Attempts to resolve this problem by calculating the transfer free energy of water from the bulk phase into the cavity will be described. [Preview Abstract] |
Tuesday, March 16, 2010 4:18PM - 4:30PM |
L27.00006: Charge-transfer water potential for solvated protein dynamics Vijay Janardhanam, Godwin Amo-Kwao, Susan R. Atlas Water plays a critical role in simulations of complex structure-function relationships such as the mechanochemistry of molecular motor proteins, wherein solvating water molecules interact with divalent cations such as Mg$^{+2}$, salt bridges, and polar or charged amino acids. Existing fixed-charge and fluctuating charge water models are inadequate in these environments, since they do not support reactive charge transfer with proper long-range dissociation behavior. The charge-transfer embedded atom method (CT-EAM) potential of Valone and Atlas was developed to address these challenges. It includes charge-polarized and ionic embedding terms that describe many-body atomistic interactions as a statistical ensemble of integer-charge excitations; background embedding densities are functions of local pseudoatom electron density distributions that integrate to non-integer charges and evolve dynamically under chemical potential equalization. Here we report first results from simulations of water using the CT-EAM potential of [1] and compare with characteristic properties of the liquid as determined via conventional force fields. [1] K. Muralidharan, S. M. Valone, and S.R. Atlas. arXiv:cond-mat/0705.0857v1, submitted. [Preview Abstract] |
Tuesday, March 16, 2010 4:30PM - 4:42PM |
L27.00007: An Improved Lattice Gas Model of the Hydrophobic Effect Patrick Varilly, Amish Patel, David Chandler Biological systems are characterized by length scales where the hydrophobic effect crosses over from being dominated by volume exclusion to being dominated by interface formation. This crossover behavior, successfully described by Lum-Chandler-Weeks theory, precludes modeling the hydrophobic contribution to solvation free energies of solutes by an effective surface area term, as is done in GBSA-style implicit solvent models in common use in the biological community. Instead, what is needed is a dynamical model of the hydrophobic effect that explicitly captures this crossover behavior, yet is simple enough for use in a biological context. In this work, we extend the simple lattice gas model of ten Wolde and Chandler by correcting its salient deficiencies at small and large length scales. We demonstrate good agreement between our model and explicit-water simulations, particularly at the crossover length scale, and then proceed to apply the theory to model several instances of hydrophobic assembly in biologically-motivated systems. [Preview Abstract] |
Tuesday, March 16, 2010 4:42PM - 5:18PM |
L27.00008: High Pressure Cryocooling of Protein Crystals: The Enigma of Water Invited Speaker: A novel high-pressure cryocooling technique for preparation biological samples for x-ray analysis is described. The method, high-pressure cryocooling, involves cooling samples to cryogenic temperatures (e.g., 100 K) in high-pressure Helium gas (up to 200 MPa). It bears both similarities and differences to high-pressure cooling methods that have been used to prepare samples for electron microscopy, and has been especially useful for cryocooling of macromolecular crystals for x-ray diffraction. Examples will be given where the method has been effective in providing high quality crystallographic data for difficult samples, such as cases where ligands needed to be stabilized in binding sites to be visualized, or where very high resolution data were required. The talk concludes with a discussion of data obtained by high-pressure cryocooling that pertains to two of the most important problems in modern science: the enigma of water and how water affects the activity of proteins. [Preview Abstract] |
Tuesday, March 16, 2010 5:18PM - 5:30PM |
L27.00009: Negative thermal expansion in the Prussian Blue analog, Fe$_{3}$[Co(CN)$_{6}$]$_{2}$.xH$_{2}$O Sourav Adak, Luke Daemen, Heinz Nakotte, Darrick Williams The thermal expansion of the cubic Prussian Blue analog Fe$_{3}$[Co(CN)$_{6}$]$_{2}$.xH$_{2}$O has been studied below room temperature using x-ray and neutron powder diffraction. The water of hydration was found to have a large effect on the thermal expansion behavior of the material, which switches between positive and negative expansion with varying water content while the average cubic structure remains unchanged. Possible connections between local disorder and thermal expansion behavior are discussed. [Preview Abstract] |
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