Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session B40: Proteins: Structure and Function II |
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Sponsoring Units: DBP Chair: Paul Janmey, University of Pennsylvania Room: 412 |
Monday, March 16, 2009 11:15AM - 11:27AM |
B40.00001: Amino Acid Free Energy Decomposition Hui Wang, Michael Fairchild, Dennis Livesay, Donald Jacobs The Distance Constraint Model (DCM) describes protein thermodynamics at a coarse-grained level based on a Free Energy Decomposition (FED) that assigns energy and entropy contributions to specific molecular interactions. Application of constraint theory accounts for non-additivity in conformational entropy so that the total free energy of a system can be reconstituted from all its molecular parts. In prior work, a minimal DCM utilized a simple FED involving temperature-independent parameters indiscriminately applied to all residues. Here, we describe a residue-specific FED that depends on local conformational states. The FED of an amino acid is constructed by weighting the energy spectrums associated with local energy minimums in configuration space by absolute entropies estimated using a quasi-harmonic approximation. Interesting temperature-dependent behavior is found. Support is from NIH R01 GM073082 and a CRI postdoctoral Duke research fellowship for H. Wang. [Preview Abstract] |
Monday, March 16, 2009 11:27AM - 11:39AM |
B40.00002: Surface Induced Self-Assembly of Fibrinogen Fibers in the Absence of Thrombin Jaseung Koo, Miriam Rafailovich, Dennis Galanakis Wound healing is a complex process imitated by the formation of fibrin fibers that are involved in clot formation and fibroblast migration. Normally this process is triggered by thrombin cleavage of the E domain on the fibrinogen molecules, which allows them to spontaneously self-assemble into the fibers. Here we demonstrate that this process can also be initiated in the absence of thrombin. We show that by simply placing the proteins in contact with hydrocarbon functionalized clay surfaces, molecular reorientation occurs which allows fibers to form from the intact fibrinogen protein. Furthermore, using monoclonal antibodies, we determined which regions on the $\alpha $C domains are involved in the formation of the new fibrinogen fibers. This allowed us to extend these findings to general hydrophobic surfaces, such as those presented by most hydrocarbon polymers. On the other hand, the carboxyl terminal part of the A$\alpha $ chain, can interact with amine containing polymers, and suppress formation of the fibers. [Preview Abstract] |
Monday, March 16, 2009 11:39AM - 11:51AM |
B40.00003: On the Rate and Mechanism of Proton Transfer Reactions in Proteins Aihua Xie, Yunxing Li, Edward Manda, Beining Nie, Wouter Hoff, Richard Martin One of the fundamental processes in molecular biology is proton transfer reactions in proteins. Proton transfer is essential for the biological functions of proteins responsible in bioenergetics, biological signaling, and enzymatic catalysis. The mechanism of proton transfer is of great interests in order to understand the structural basis of biological functions. Despite of extensive experimental and computational efforts, it remains elusive what causes a proton to move from the proton donor to the proton acceptor. We will report a proof of concept study regarding a general mechanism of internal proton transfer reactions in proteins. Density functional theory, B3LYP/6-311+G(2d,p), is employed in this study. The results of our study provide deep insights into the structural basis to the rate and mechanism of proton transfer reactions in proteins, such as bacteriorhodopsin and green fluorescence protein. [Preview Abstract] |
Monday, March 16, 2009 11:51AM - 12:03PM |
B40.00004: Probing the reversibility of the Dscam Dimer with Light Scattering and Colloids Jesse Collins, Dietmar Schmucker, Vinothan Manoharan Dscam (Down-syndrome cell adhesion molecule) is a fascinating example of the highly specific interactions unique to biomolecules. The extracellular domain is spliced into over 18,000 isoforms. With few exceptions, each isoform, despite conservation of over 95\% of amino acid residues between isoforms, binds to itself and to no other in the set. We investigate the effect of salt and pH on the reversibility of this interaction. [Preview Abstract] |
Monday, March 16, 2009 12:03PM - 12:15PM |
B40.00005: Using Fluorescence Spectroscopy to Evaluate Hill Parameters and Heterogeneity of Ligand Binding to Cytochromes P450 Glenn A. Marsch, Benjamin Carlson, Jennifer Hansen, Elaine Mihelc, Martha V. Martin, F. Peter Guengerich The cytochromes P450 (CYPs) are hemoproteins that oxidize many drugs and carcinogens. Binding interactions of two CYPs with Nile Red, pyrene, and alpha-naphthoflavone were studied using fluorescence quenching. Upon interaction with CYPs, fluorescence from pyrene excited-state dimers was quenched more efficiently than fluorescence from pyrene monomers. Quenching data was fit to the Hill equation to determine binding affinities and the Hill parameter $n$ for the interaction of substrates with CYPs. All ligands showed strong binding to the CYPs, especially alpha-naphthoflavone, but exhibited little or no cooperativity in the interaction. Modified Stern-Volmer plots were used to confirm binding affinities, and suggested heterogeneous populations of amino acid fluorophores. Fluorescence anisotropy experiments suggest that CYP molecules tumble more rapidly when alpha-naphthoflavone is added. [Preview Abstract] |
Monday, March 16, 2009 12:15PM - 12:27PM |
B40.00006: UV Resonance Raman Excitation Profiles and Depolarization Ratios of Peptide Conformations Bhavya Sharma, Sanford Asher UV resonance Raman spectroscopy is a well established technique for probing peptide and protein secondary structure. Excitation between 180 to 215 nm, within the $\pi $ to $\pi $* electronic transitions of the peptide backbone, results in the enhancement of amide vibrations. We use UVRR excitation profiles and depolarization ratios to examine the underlying peptide bond electronic transitions. The present consensus is that three electronic transitions (n to $\pi $* and two $\pi $ to $\pi $*) occur in simple amides between 230 and 130 nm. In $\alpha $-helices a weak n to $\pi $* electronic transition occurs at 220 nm, while a higher frequency $\pi $ to $\pi $* transition occurs at 190 nm. This $\pi $ to $\pi $* transition undergoes exciton splitting, giving rise to two dipole-allowed transitions: one perpendicular to the helical axis (190 nm) and the second parallel to the axis (205 nm). The melted state of alpha-helices resembles left-handed poly-proline II (PPII) helices. The PPII helix electronic transitions have been defined as an n to $\pi $* transition at $\sim $ 220 nm and a $\pi $ to $\pi $* transition at $\sim $ 200 nm. For beta-sheets, the $\pi $ to $\pi $* transition occurs at $\sim $ 194 nm for parallel and $\sim $196 nm for anti-parallel sheets. n to pi* transition occurs at $\sim $217 nm for both. [Preview Abstract] |
Monday, March 16, 2009 12:27PM - 12:39PM |
B40.00007: UV Resonance Raman Spectral Hydrogen Exchange Studies of Poly-L-Lysine's Conformation Lu Ma, Sanford Asher The rate of exchange of peptide backbone NH group with the hydrogen of aqueous solvents is sensitive to the peptide secondary structure. In this work, we use a continuous flow rapid mixing technique and study H/D exchange rates of the model peptide poly-l-lysine (PLL) using UV resonance Raman spectroscopy. Different conformational equilibria of PLL between the helical ($\alpha $, 3$_{10}$, and $\pi $-helix) and extended conformations (PPII and 2.5$_{1}$-helix) are obtained by controlling solvent pH and salt concentration. The AmII' band of the peptide backbone is used as the deuteration marker. The H/D change rate of PLL provides direct information of the stability of different conformations. Additionally, these results provide insight into backbone conformation fluctuations and how various factors affect the conformation. [Preview Abstract] |
Monday, March 16, 2009 12:39PM - 12:51PM |
B40.00008: Polyglycine in Solution, Random or Ordered? Sergei Bykov, Sanford Asher According to the existing theories during folding, the protein backbone undergoes a transition from unordered (random coil) to ordered (native) conformations. Understanding the nature of the unordered state is one of the key problems in protein folding. Some recent investigations indicate that unfolded peptides and proteins in solution form structures close to PPII helices. Glycine based peptides possess greater conformational freedom due to the lack of the side chains. This high flexibility makes polyglycine an important model system for investigating of the conformational preferences of the polypeptides backbone in solution in general and for understanding the nature of the unfolded states in particular. We utilized UV Resonance and Visible Raman spectroscopy to investigate conformational preferences of glycine based peptides of different lengths in water solution at different conditions. We will discuss conformational preferences of the glycine based peptides in solution, and define the major factors which govern these conformational preferences. [Preview Abstract] |
Monday, March 16, 2009 12:51PM - 1:03PM |
B40.00009: Increase in Mechanical Resistance to Force in a Shear-Activated Protein Eric Botello, Nolan Harris, Huiwan Choi, Zhou Zhou, Angela Bergeron, Jing-fei Dong, Ching-Hwa Kiang von Willebrand factor (VWF) is the largest multimeric adhesion ligand found in human blood. Plasma VWF (pVWF) must be exposed to shear stress, like at sites of vascular injury, to be activated to bind platelets to induce blood clotting. In addition, adhesion activity of VWF is related to its polymer size, with the ultra-large form of VWF (ULVWF) being hyper-active, and forming fibers even without exposure to shear stress. We used the AFM to stretch pVWF, sheared VWF (sVWF) and ULVWF, and monitor the forces as a function of molecular extension. We showed a similar increase in force resistance to unfolding for sVWF and ULVWF when compared to pVWF. The increase in force is reduced when other molecules that are known to disrupt their fibril formation are present. Our results provide evidence that the common higher order structure of sVWF and ULVWF may affect the domain structure that causes difference in their adhesion activity compared to pVWF. [Preview Abstract] |
Monday, March 16, 2009 1:03PM - 1:15PM |
B40.00010: Hydrodynamic and Conformational Properties of Unfolded Proteins Guy Berry Published data on the characterization of unfolded proteins in dilute solutions in aqueous guanidine hydrochloride are analyzed to show that the data are not fit by either the random-flight or wormlike chain models for linear chains. The analysis includes data on the intrinsic viscosity, root-mean-square radius of gyration, from small-angle x-ray scattering, and hydrodynamic radius, from the translational diffusion coefficient. It is concluded that residual structure consistent with that deduced from nuclear magnetic resonance on these solutions can explain the dilute solution results in a consistent manner through the presence of ring-structures, which otherwise have an essentially flexible coil conformation. The ring-structures could be in a state of continual flux and rearrangement. Calculation of the radius of gyration for the random-flight model gives a similar reduction of this measure for chains joined at their endpoints, or those containing loop with two dangling ends, each one-fourth the total length of the chain. This relative insensitivity to the details of the ring-structure is taken to support the behavior observed across a range of proteins. [Preview Abstract] |
Monday, March 16, 2009 1:15PM - 1:27PM |
B40.00011: Stability versus flexibility in the dimerization kinetics and thermodynamics of the GCN4 Leucine zipper Dipak Rimal, Yanxin Liu, Prem Chapagain, Bernard Gerstman We present results of computer simulations that show that too much stability of the native state can have the unwanted side-effect of slower and less reliable folding. The time spent in non-native configurations depends on both the depth of the valleys in the energy landscape and the probability for visiting various regions of the landscape. We present computational results for dimerization of the GCN4 Leucine zipper in which both the helical propensities and the ionic interactions are varied in strength. The results show that when interactions are too strong, they not only beneficially stabilize the native state, but also stabilize non-native configurations that act as kinetic traps. In some cases, intermediate structures become so rigid that the peptide does not have the flexibility necessary to fold to the native state. In other situations, such as high temperature, the chain has superfluous flexibility and can form non-native bonds. If these non-native bonds are too strong, the peptide spends significant time in contorted non-native configurations and folding is slowed and less efficient. Therefore, efficient folding must be a compromise between stability and flexibility. [Preview Abstract] |
Monday, March 16, 2009 1:27PM - 1:39PM |
B40.00012: Intermediate states of globular proteins during temperature-induced folding and unfolding studied using small angle x-ray scattering Jose Banuelos, Jacob Urquidi The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as concentration, degree of crowding from other entities, and solvent medium affect how a protein folds. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for a series of globular proteins. The temporal stability of these ensembles is also under investigation. Trends in the scattering profiles, along with correlations with protein thermodynamics, may help elucidate shared characteristics between all proteins in their folding behavior. [Preview Abstract] |
Monday, March 16, 2009 1:39PM - 1:51PM |
B40.00013: Forced unfolding of proteins within cells -- a proteomic method Brian Chase, Dennis Discher Many cellular activities are mediated by conformational changes in proteins or else involve rearrangement of protein assemblies. These motions are now commonly investigated in vitro as well as at the single-molecule level. But we sought to develop an in-cell method to study these motions and to do so on a proteomic scale. We have been especially interested in studying molecular responses in cells under stress, and we initially developed a labeling technique in the simplest human cell, the red blood cell. The premise is to label cysteines with cell-viable, thiol-reactive fluorophores in both stressed and unstressed cells. Then, differential labeling of proteins would indicate that under stress, previously buried cysteine residues become exposed and thus accessible to the fluorescent probe. Fluorescence imaging and saparations provide initial clues to structures and proteins, but Mass Spectrometry precisely maps the sites that are exposed. Subsequent work on recombinants and in modeling is then used to explain the cell-derived findings, and the method has now been applied to several nucleated cell types. [Preview Abstract] |
Monday, March 16, 2009 1:51PM - 2:03PM |
B40.00014: Energy parameterization of protein coarse-grained models Marcos Betancourt Protein coarse-grained models are simplified representation of proteins that in principle can be used to perform long time scale simulations of protein folding dynamics, thermodynamics, and native structures. The main challenge in realizing these models is to find a physically accurate energy parameterization. Here two approaches are considered for this purpose. The first is the popular knowledge based potential approach, where the energies are extracted from the sequence and structure of known proteins. The advantages and limitations of this approach are examined from the perspective of minimal lattice models. It is concluded that this approach is less accurate in the determination of non-bonded interactions. The other approach involves the straightforward coarse-graining of individual residue pairs by performing molecular dynamics simulations. This approach does not suffer from the approximations involved in knowledge-based potentials and have the advantage that their quality can be controlled. The final energy model is built from a balanced combination of knowledge based potentials and coarse-grained interactions from molecular dynamics. Applications of this model to protein structure prediction are described. [Preview Abstract] |
Monday, March 16, 2009 2:03PM - 2:15PM |
B40.00015: Generalized distance and its application in protein folding Ali Mohazab The concept of Euclidean distance between two points can be generalized to extended objects. The generalized distance $\cal D$ can be used as a reaction coordinate in protein folding process. Here $\cal D$ is compared and contrasted with some well-known reaction coordinates, Q and RMSD and is applied to protein fragments such as alpha helix and beta hairpin. The non-crossing constraint in utilizing $\cal D$ is also discussed. [Preview Abstract] |
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