Bulletin of the American Physical Society
APS March Meeting 2010
Volume 55, Number 2
Monday–Friday, March 15–19, 2010; Portland, Oregon
Session W11: Proteins: Structure, Function, and Folding |
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Sponsoring Units: DBP Chair: Margaret Cheung, University of Houston Room: A107-A109 |
Thursday, March 18, 2010 11:15AM - 11:27AM |
W11.00001: Anisotropic mechanical response of the enzyme Guanylate Kinase perturbed by the DNA molecular spring. Chiao-Yu Tseng, Andrew Wang, Giovanni Zocchi Protein molecules are semi-rigid objects with organized but fluctuating conformation. For Guanylate Kinase, which catalyzes phosphoryl transfer between ATP and GMP, a large conformational change upon substrate binding occurs which is essential for enzymatic activity. With a DNA molecular spring stretching the molecule in distinct ways, we demonstrate that the enzymatic functions of substrate binding and phosphoryl transfer can be separately controlled mechanically. Three different attachment points of the DNA spring on the surface of the protein were tested, corresponding to stretching the protein along three different directions. Using activity measurements with titration over substrate concentration, the kinetic parameters (i.e., binding affinity of substrates and catalytic rate constant) based on Michaelis-Menten kinetics were obtained in the presence and absence of the three different mechanical perturbations. [Preview Abstract] |
Thursday, March 18, 2010 11:27AM - 11:39AM |
W11.00002: Protein structure, stability and folding in the cell -- \textit{in silico} biophysical approaches Margaret Cheung How the crowded environment inside a cell affects the structural conformation of a protein with aspherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo. Here we address this question by combining computational and experimental studies of a spherical protein (i.e. apoflavodoxin), a football-shaped protein (i.e., Borrelia burgdorferi VlsE) and a dumbbell-shaped protein (i.e. calmodulin) under crowded, cell-like conditions. The results show that macromolecular crowding affects protein folding dynamics as well as an overall protein shape associated with changes in secondary structures. Our work demonstrates the malleability of ``native'' proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo. [Preview Abstract] |
Thursday, March 18, 2010 11:39AM - 11:51AM |
W11.00003: Membrane-associated folding and unfolding Yana Reshetnyak, Alexander Karabadzhak, Dhammika Weerakkody, Mak Thakur, Gregory Andreev, Donald Engelman, Oleg Andreev We are studying the molecular events that occur when a peptide inserts across a membrane or exits from it. Using pH jumps to trigger insertion/exit of the pHLIP (pH Low Insertion Peptide) to enable kinetic analysis, we show that insertion occurs in several steps, with rapid (0.1 sec) interfacial helix formation followed by a much slower (100 sec) insertion pathway to form a transmembrane helix. The reverse process of unfolding and peptide exit from the bilayer core, which can be induced by a rapid pH jump from acidic to basic, proceeds much faster than folding/insertion and through different intermediate states. In the exit pathway, the helix-coil transition is initiated while the polypeptide is still inside the membrane. We also designed two pHLIP-variants where Asp and Glu residues were removed from the C-terminus, which inserts across the membrane. The variants preserve the same pH-dependent properties of pHLIP peptide interaction with the membrane, but insertion occurs 10-30 times faster than in the case of the parent pHLIP peptide. A kinetic model of peptide-membrane insertion/folding and exit/unfolding will be discussed. The work was supported by grant from the NIH RO1133890 to OAA, DME, YRK. [Preview Abstract] |
Thursday, March 18, 2010 11:51AM - 12:03PM |
W11.00004: First Principles Electronic Structure Investigation of Singlet and Triplet States of Oxyhemoglobin by Hartree-Fock Procedure Combined with Many-Body Perturbation Theory S.R. Badu, Archana Dubey, R.H. Scheicher, N. Sahoo, R.H. Pink, A. Schulte, H.P. Saha, Lee Chow, K. Nagamine, T.P. Das Interest in the possibility of magnetic character of oxyhemoglobin has been recently stimulated by spin-lattice relaxation effects studied [1] by the muon-spin rotation technique. In view of this, we have carried out first-principles electronic structure investigations involving Hartree-Fock theory combined with many body perturbation effects on the singlet and triplet states of oxyhemoglobin. Our results indicates using two recent x-ray structural data [2,3] for oxyhemoglobin that, using only Hartree-Fock theory without correlation effects included, the singlet state lies above the triplet state by about 0.08a.u.[2] and 0.13a.u.[3]. Incorporation of many body effects by perturbation methods reverses the order with the triplet state located 0.18a.u.[2] and 0.14a.u.[3] respectively above the singlet state. Physical reasons for these relative orderings of the singlet and triplet states will be discussed.\\[4pt] [1] K. Nagamine etal. Proc. Acad.Ser.B 83,120(2007).\\[0pt] [2] Massimo Paoli etal. J.Mol. Biol. 256,775(1996).\\[0pt] [3] Sam-Yong Park etal. J.Mol. Biol. 360,690(2006) [Preview Abstract] |
Thursday, March 18, 2010 12:03PM - 12:15PM |
W11.00005: Two-State Model of Allostery With Force Yuriy Pereverzev, Oleg Prezhdo, Evgeni Sokurenko We propose an allosteric model that describes force-induced changes in lifetimes of biological receptor-ligand bonds. Transitions between the two conformations of the allosteric site with applied force lead to changes in the receptor conformation. The ligand bound to the receptor fluctuates between two different potentials formed by the two conformations. The effect of the force on the receptor-ligand interaction potential is described by the Bell mechanism. The probability of detecting the ligand in the bound state is found to depend on two relaxation times of the ligand and allosteric sites. An analytic expression for the bond lifetime is derived as a function force. The model is used to explain the anomalous force and time dependences of integrin-fibronectin bond lifetimes measured by atomic force microscopy (Kong, F. et al J. Cell Biol., 2009, 185, 1275-1284). The analytic expression and model parameters describe very well all anomalous dependences identified in the experiments. [Preview Abstract] |
Thursday, March 18, 2010 12:15PM - 12:27PM |
W11.00006: Cu(II) coordination structure determinants of the fibrillization switch in Abeta peptides Jessica Hernandez-Guzman, Li Sun, Anil Mehta, David Lynn, Kurt Warncke Alzheimer's Disease (AD) is associated with the aggregation and fibrillization of the beta-amyloid protein (Abeta). The coordination of Cu(II) by peptide histidine imidazole sidechains is proposed to play an important role in determining the fibrillization ``switch'' [$1$]. We have developed techniques of powder X-band electron spin echo envelope modulation (ESEEM) spectroscopy to determine the 3D molecular structure of the Cu(II)-histidine imidazole coordination in cryotrapped soluble and fibrillar forms of Abeta peptides, in order to gain insight into the factors that govern fibrillization. We use hybrid optimization-based OPTESIM [$2$] simulation of the double quantum harmonic feature to determine the mutual orientation of the imidazole rings in Cu(II)--bis-imidazole complexes and in Abeta(13-21) peptides. The Cu(II) coordination mode and assembly constraints in fibrils are revealed. [1] Dong , J., et al., \textit{Proc. Natl. Acad. Sci.,} 2007, $104$, 13313. [2] Sun, L., et al., \textit{J. Magn. Reson.} 2009, \underline {\textit{200}}, 21. [Preview Abstract] |
Thursday, March 18, 2010 12:27PM - 12:39PM |
W11.00007: Impact of Salts on Structural Dynamics of Photoactive Yellow Protein Sandip Kaledhonkar, Lorand Kelemen, Aihua Xie Water is essential for protein functions. Solutions with high salt concentration change the stability and solubility of proteins. Despite extensive studies, it remains unclear how salts alter the properties of proteins. We report the effects of different salts on the structural dynamics of photoactive yellow protein (PYP) which is an excellent model system. Time-resolved infrared difference spectroscopic technique is employed to capture the dynamic structural development of this protein upon light stimulation. Our data show that high salt concentration alters the proton transfer pathway and suppress protein conformational changes. We test different models to elucidate how high concentration salts change the structural response of PYP during its light sensing photocycle. The knowledge gained may be applicable to understand the other effects of salts on proteins, which is known as Hofmeister series. [Preview Abstract] |
Thursday, March 18, 2010 12:39PM - 12:51PM |
W11.00008: Position dependence of the trigger sequence in the folding and dimerization of a lattice model coiled-coil peptide Yuba Bhandari, Prem Chapagain, Bernard Gerstman Coiled-coil protein dimerization has been shown to be greatly facilitated by the presence of a trigger segment of amino acids that has a high propensity for forming alpha-helix structure. A three-dimensional lattice model incorporating a Monte Carlo Metropolis Algorithm is used to investigate how the effectiveness of the trigger segment depends on its location in the protein. Heat capacity and free energy were calculated to study the thermodynamics of the folding and~dimerization for different positions of the trigger segment. The simulation results~show that the dimerization is improved when the trigger segment is located near the middle of the chain as compared to near the ends. [Preview Abstract] |
Thursday, March 18, 2010 12:51PM - 1:03PM |
W11.00009: Probing the vibrational dynamics of proteins in liquid water by terahertz absorption spectroscopy Nguyen Quang Vinh, Kevin W. Plaxco, S. JAMES Allen Biomolecules solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz range that contain information on their global and subglobal collective vibrational modes and global dynamical correlations among solvent water molecules and the protein. Measurements in this region, however, are challenging due to due to the strong absorption of water and often sever interference artifacts. In response, we have developed, with Virginia Diode Inc., a highly sensitive Vector Network Analyzer system for probing collective dynamics in aqueous solution. Using this we explore the complex dielectric response from 0.07 to 0.70 THz that directly probes such questions as the hydration level around proteins and the large scale vibrational modes of biological polymers. We make a direct comparison to the existing molecular dynamic simulations and normal mode calculations and investigate the dependence of the low frequency dynamics on protein concentration and solvent pH. Our measurements shed light on the macromolecular motions in a biologically relevant water environment. [Preview Abstract] |
Thursday, March 18, 2010 1:03PM - 1:15PM |
W11.00010: Entropic and Dynamical Origins of Catalysis in a B12 Enzyme Kurt Warncke, Miao Wang The kinetics of the diffusive radical pair separation process in the adenosylcobalamin (coenzyme B12) -dependent ethanolamine ammonia-lyase from \textit{Salmonella typhimurium} at 234-248 K in a dimethylsulfoxide/water cryosolvent system [1] were determined by using time-resolved, full-spectrum electron paramagnetic resonance spectroscopy. Substrate hydrogen isotope effects show that the cofactor cobalt-carbon bond cleavage event rate is rate determining, and that catalysis (relative to solution) is almost entirely entropic. The results challenge the proposed, traditional enthalpy-based mechanisms, and show that delocalized, dynamical sources are central in bond cleavage catalysis. Changes in configurational freedom of surface residues and hydration waters are proposed as the microscopic origin. [1] M. Wang and K. Warncke, \textit{J. Am. Chem. Soc.} 2008, $130$, 4846. [Preview Abstract] |
Thursday, March 18, 2010 1:15PM - 1:27PM |
W11.00011: Copper attachment to a non-octarepeat site in prion protein Miroslav Hodak, Jerry Bernholc Prion protein, PrP, plays a causative role in several neurodegenerative diseases, including mad cow disease in cattle and Creutzfeldt-Jakob disease in humans. The PrP is known to efficiently bind copper ions and this ability has been linked to its function. PrP contains up to six binding sites, four of which are located in the so-called octarepeat region and are now well known. The binding sites outside this region are still largely undetermined, despite evidence of their relevance to prion diseases. Using a hybrid DFT/DFT, which combines Kohn-Sham DFT with orbital-free DFT to achieve accurate and efficient description of solvent effects in ab initio calculations, we have investigated copper attachment to the sequence GGGTH, which represents the copper binding site located at His96. We have considered both NNNN and NNNO types of copper coordination, as suggested by experiments. Our calculations have determined the geometry of copper attachment site and its energetics. Comparison to the already known binding sites provides insight into the process of copper uptake in PrP. [Preview Abstract] |
Thursday, March 18, 2010 1:27PM - 1:39PM |
W11.00012: Determining the Structure of a Cytoplasmic Polyadenylation Element Binding Protein via AMBER9 Alison Saunders The neurons of \textit{Aplysia californica }contain cytoplasmic polyadenylation element binding protein (CPEB). CPEB shows prion-like properties when expressed in yeast cells. Because prions have misfolded and normally folded forms, prions can code in neurons like binary codes in computers, with ``present'' and ``not present'' signals available. CPEB thus provides a candidate protein for the molecular basis of memory. I attempt to determine CPEB's structure, by first threading the known protein sequence around a $\beta $-helical structure. Threading is preformed by hand, and by a program written to minimize the energy cost of building the structure. I then analyze the stability of the thread using the molecular dynamics program AMBER9. I also analyze a protein of only glutamine (PolyQ) in a $\beta $-helical structure to substantiate my use of a $\beta $-helix with the glutamine-rich CPEB. I found PolyQ to be stable in a left-handed $\beta $-helical structure with eighteen residues per turn. A candidate structure for CPEB was located with the same $\beta $-helical structure. [Preview Abstract] |
Thursday, March 18, 2010 1:39PM - 1:51PM |
W11.00013: Determining the structure of Ac-Ala$_n$LysH$^+$ \textit{in vacuo}: computational spectroscopy using DFT Mariana Rossi, Volker Blum, Peter Kupser, Gert von Helden, Frauke Bierau, Gerard Meijer, Matthias Scheffler Well defined secondary structure motifs (e.g., helices) in polypeptides can be systematically studied \textit{in vacuo}, offering a unique ``clean room" condition to quantify the stabilizing intramolecular interactions. Here we address theoretically the structure of alanine polypeptides Ac-Ala$_n$-LysH$^+$ ($n$=5,10,15), for which gas-phase helical structure was indicated in experiment [1]. Using van der Waals (vdW) corrected [2] Density Functional Theory (DFT), we present vibrational spectra and compare to room temperature multiple photon IR spectroscopy data obtained at the FELIX free electron laser. For the longer molecules (n=10,15) $\alpha$-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For Ac-Ala$_5$LysH$^+$, the predicted lowest energy conformer (``g-1'') in vdW corrected DFT (PBE, B3LYP, revPBE) is not a simple helix. However, the harmonic free energy suggests that g-1 and the lowest-energy $\alpha$-helical conformers are energetically close at 300 K, and thus might all coexist in experiment. Consistently, their calculated vibrational spectra agree with experiment, but only if anharmonic effects are included by explicit molecular dynamics simulations. [1] R. Hudgins \emph{et al.}, JACS \textbf{120}, 12974 (1998) [2] A. Tkatchenko, M. Scheffler, PRL \textbf{102}, 073005 (2009) [Preview Abstract] |
Thursday, March 18, 2010 1:51PM - 2:03PM |
W11.00014: (Un)folding of a high-temperature stable polyalanine helix from first principles Volker Blum, Mariana Rossi, Alex Tkatchenko, Matthias Scheffler Peptides \emph{in vacuo} offer a unique, well-defined testbed to match experiments directly against first-principles approaches that predict the intramolecular interactions that govern peptide and protein folding. In this respect, the polyalanine-based peptide Ac-Ala$_{15}$-LysH$^+$ is particularly interesting, as it is experimentally known to form helices \emph{in vacuo}, with stable secondary structure up to $\approx$ 750~K [1]. Room-temperature folding and unfolding timescales are usually not accessible by direct first-principles simulations, but this high $T$ scale allows a rare direct first-principles view. We here use van der Waals corrected [2] density functional theory in the PBE generalized gradient approximation as implemented in the all-electron code FHI-aims [3] to show by Born-Oppenheimer \emph{ab initio} molecular dynamics that Ac-Ala$_{15}$-LysH$^+$ indeed unfolds rapidly (within a few ps) at $T$=800~K and 1000~K, but not at 500~K. We show that the structural stability of the $\alpha$ helix at 500~K is critically linked to a correct van der Waals treatment, and that the designed LysH$^+$ ionic termination is essential for the observed helical secondary structure. [1] M. Kohtani \emph{et al.}, JACS \textbf{126}, 7420 (2004). [2] A. Tkatchenko, M. Scheffler, PRL \textbf{102}, 073005 (2009). [3] V. Blum \emph{et al}, Comp. Phys. Comm. \textbf{180}, 2175 (2009). [Preview Abstract] |
Thursday, March 18, 2010 2:03PM - 2:15PM |
W11.00015: Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles Edward O'Brien, Michele Vendruscolo, Christopher Dobson \textit{In vitro} experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of R$_{g}$ and shape parameters (R$_{g}$ tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform \textit{in silico }temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths. [Preview Abstract] |
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