Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session S11: Focus Session: Physics of Proteins III |
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Sponsoring Units: DBIO DPOLY Chair: Andrea Markelz, SUNY Buffalo Room: 203 |
Thursday, March 6, 2014 8:00AM - 8:12AM |
S11.00001: What is the Origin of Internal Friction in Unfolded Proteins? Garegin Papoian, Ignacia Echeverria The unfolded state is being increasingly recognized as critical to many biological processes. There are many proteins that are found only transiently in the unfolded state, eventually folding into globular structures. Other proteins, called intrinsically disordered proteins (IDPs), may be unfolded even when carrying out important biological functions. Despite its ubiquitousness, the unfolded ensemble is not fully understood. In this work, we have investigated the origin of friction for the unfolded proteins undergoing conformational diffusion. We used extensive all-atom molecular dynamics simulations to study the dynamics of the unfolded cold-shock protein (CSP) from Thermotoga maritima at different solvent viscosities and at different denaturant concentrations. We systematically analyzed the reconfiguration dynamics of relevant structural features such as dihedral angle rotations, hydrogen bonds and hydrophobic contacts forming and breaking. The results of our calculations are broadly consistent with the corresponding experimental measurements. Our findings have important implications for the folding kinetics of proteins, especially under physiological conditions. [Preview Abstract] |
Thursday, March 6, 2014 8:12AM - 8:24AM |
S11.00002: Photoinduced Localized Unfolding of Tubulin Dimers Bound to a Water Soluble Porphyrin and the Search for Binding Location Using Docking Simulations Guided by a Combination of Resonance Raman Spectroscopy and Density Functional Theory Brady McMicken, Lorenzo Brancaleon, Robert Thomas The ability to modify the conformation of a protein by controlling its partial unfolding may have practical applications such as inhibiting its function. One method of locally unfolding a protein involves the use of a photosensitizer non-covalently bound to a protein which triggers photochemical reactions upon irradiation leading to protein conformational changes. We investigate the photoinduced conformational changes of tubulin mediated by a bound water soluble porphyrin which acts as a photosensitizer. Also of interest is how conformational changes of tubulin affect its function such as forming microtubules and the mechanism responsible for the structural change. To better understand the conformational change we must find the binding location between the porphyrin and protein. Density functional theory calculations will be combined with Resonance Raman spectroscopy to correlate the changes in vibrational modes of the porphyrin with changes in its physical structure upon binding to tubulin. This will allow us to determine the distorted conformation of the porphyrin when bound to tubulin which will subsequently be used in docking simulations to find the most likely binding configuration. [Preview Abstract] |
Thursday, March 6, 2014 8:24AM - 8:36AM |
S11.00003: Structure and DNA-binding of meiosis-specific protein Hop2 Donghua Zhou, Hem Moktan, Roberto Pezza Here we report structure elucidation of the DNA binding domain of homologous pairing protein 2 (Hop2), which is important to gene diversity when sperms and eggs are produced. Together with another protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. However, the structural and biochemical bases for the function of Hop2 and Mnd1 have not been well understood. As a first step toward such understanding, we recently solved the structure for the N-terminus of Hop2 (1-84) using solution NMR. This fragment shows a typical winged-head conformation with recognized DNA binding activity. DNA interacting sites were then investigated by chemical shift perturbations in a titration experiment. Information of these sites was used to guide protein-DNA docking with MD simulation, revealing that helix 3 is stably lodged in the DNA major groove and that wing 1 (connecting strands 2 and 3) transiently comes in contact with the minor groove in nanosecond time scale. Mutagenesis analysis further confirmed the DNA binding sites in this fragment of the protein. [Preview Abstract] |
Thursday, March 6, 2014 8:36AM - 9:12AM |
S11.00004: Metal ion coupled protein folding and allosteric motions Invited Speaker: Wei Wang Many proteins need the help of cofactors for their successful folding and functioning. Metal ions, i.e., Zn$^{2+}$, Ca$^{2+}$, and Mg$^{2+}$ etc., are typical biological cofactors. Binding of metal ions can reshape the energy landscapes of proteins, thereby modifying the folding and allosteric motions. For example, such binding may make the intrinsically disordered proteins have funneled energy landscapes, consequently, ensures their spontaneous folding. In addition, the binding may activate certain biological processes by inducing related conformational changes of regulation proteins. However, how the local interactions involving the metal ion binding can induce the global conformational motions of proteins remains elusive. Investigating such question requires multiple models with different details, including quantum mechanics, atomistic models, and coarse grained models. In our recent work, we have been developing such multiscale methods which can reasonably model the metal ion binding induced charge transfer, protonation/deprotonation, and large conformational motions of proteins. With such multiscale model, we elucidated the zinc-binding induced folding mechanism of classical zinc finger and the calcium-binding induced dynamic symmetry breaking in the allosteric motions of calmodulin [1,2]. In addition, we studied the coupling of folding, calcium binding and allosteric motions of calmodulin domains. In this talk, I will introduce the above progresses on the metal ion coupled protein folding and allosteric motions. \\[4pt] [1] Li WF, Zhang J, Wang J, and Wang W, Metal-Coupled Folding of Cys2His2 Zinc-Finger, J. Am. Chem. Soc. 130 (2008) 892-900;\\[0pt] [2] Tan C, Li WF, Wang W, and Thirumalai D, Dynamic symmetry breaking during allosteric transitions in Calmodulin is driven by quantized dehydration of Ca2$+$ ions, (2013) submitted. [Preview Abstract] |
Thursday, March 6, 2014 9:12AM - 9:24AM |
S11.00005: Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex Yangzhong Qin, Dongping Zhong Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined in nanospace but mostly highly mobile. Here, we report our studies of interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local sidechain fluctuations in the apo, binary and ternary states of Dpo4, we observed that the DNA binding interface and active site is dynamically solvent accessible and the interfacial water dynamics are slightly slow but similar to the surface hydration water fluctuations on picosecond time scales. Our MD simulations also show the binding interface full of water molecules and nonspecific weak interactions with protein and DNA. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation while the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase. [Preview Abstract] |
Thursday, March 6, 2014 9:24AM - 9:36AM |
S11.00006: Accessible surface area of proteins from purely sequence information and the importance of global features Eshel Faraggi, Yaoqi Zhou, Andrzej Kloczkowski We present a new approach for predicting the accessible surface area of proteins. The novelty of this approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Rather, sequential window information and the global monomer and dimer compositions of the chain are used. We find that much of the lost accuracy due to the elimination of evolutionary information is recouped by the use of global features. Furthermore, this new predictor produces similar results for proteins with or without sequence homologs deposited in the Protein Data Bank, and hence shows generalizability. Finally, these predictions are obtained in a small fraction (1/1000) of the time required to run mutation profile based prediction. All these factors indicate the possible usability of this work in de-novo protein structure prediction and in de-novo protein design using iterative searches. [Preview Abstract] |
Thursday, March 6, 2014 9:36AM - 9:48AM |
S11.00007: Excited State Electronic Structure of Fluorescent Proteins Revealed by Two-Dimensional Double Quantum Coherence Spectroscopy Patrick Konold Red fluorescent proteins (RFPs) are nearly ideal probes for monitoring subcellular processes with extremely high spatial and temporal precision. Modern derivatives with increased brightness are sought to further enhance imaging applicability, however, photostability issues represent a universal obstacle towards RFP development. In this work, we employed Two-Dimensional Double Quantum Coherence (2D2Q) spectroscopy to probe the excited state electronic structure of mKate, a widely used RFP. Our results help explain the excited state absorption contributions observed in spectrally resolved transient grating measurements that ultimately relate to excited state photophysics thought to modulate the dark state conversion and irreversible photobleaching processes leading to poor brightness. Moreover, we contrast results across a panel of point mutants of the S158 residue and find a connection between chromophore-sidechain interactions and the position of energy levels in the doubly excited manifold. Such observations highlight the role of the protein environment in tuning excited state photophysics and may provide a clue for engineering more photostable RFPs. [Preview Abstract] |
Thursday, March 6, 2014 9:48AM - 10:00AM |
S11.00008: Spectroscopic Monitoring of Proton Transfer in Green Fluorescent Protein J. Timothy Sage, Mannis O'Brien, Bridget Salna, Benabbas Abdelkrim, Paul M. Champion, Jasper van Thor Vibrational spectroscopy is an ideal probe for proton transfer in biological molecules because of its sensitivity to the motion of protons, which are difficult to track with more direct structural methods such as X-ray crystallography. Previous time-resolved infrared measurements provided direct experimental evidence for Glu 222 as the excited state proton acceptor following excitation of green fluorescent protein (GFP). Here, we use infrared cryospectroscopy to characterize a low quantum yield photochemical channel that leads to decarboxylation of Glu 222 coupled with proton transfer to complete the methyl group on the resulting $\alpha$-aminobutyric acid residue. The \emph{irreversible} nature of this process allows us to obtain infrared data at much higher sensitivity and over an extended frequency range. Difference spectra recorded over the full 1000-4000 cm$^{-1}$ range at 100 K probe perturbations of internal water molecules and nearby amino acids as well as the chromophore. We identify vibrational frequencies that probe hydrogen bonding along the ``proton wire'' that connects the chromophore to Glu 222. [Preview Abstract] |
Thursday, March 6, 2014 10:00AM - 10:12AM |
S11.00009: Correlated Protein Motion Measurements of Dihydrofolate Reductase Crystals Mengyang Xu, Katherine Niessen, James Pace, Vivian Cody, Andrea Markelz We report the first direct measurements of the long range structural vibrational modes in dihydrofolate reductase (DHFR). DHFR is a universal housekeeping enzyme that catalyzes the reduction of 7,8-dihydrofolate to 5,6,7,8-tetra-hydrofolate, with the aid of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH). This crucial enzymatic role as the target for anti-cancer [methotrexate (MTX)], and other clinically useful drugs, has made DHFR a long-standing target of enzymological studies. The terahertz (THz) frequency range (5-100 cm$^{-1}$), corresponds to global correlated protein motions. In our lab we have developed Crystal Anisotropy Terahertz Microscopy (CATM), which directly measures these large scale intra-molecular protein vibrations, by removing the relaxational background of the solvent and residue side chain librational motions. We demonstrate narrowband features in the anisotropic absorbance for mouse DHFR with the ligand binding of NADPH and MTX single crystals as well as Escherichia coli DHFR with the ligand binding of NADPH and MTX single crystals. [Preview Abstract] |
Thursday, March 6, 2014 10:12AM - 10:24AM |
S11.00010: Structure-based simulations of kinesin motor domain for the study and characterization of its different microtubule and ligand-binding states Srirupa Chakraborty, Wenjun Zheng Kinesins are molecular motors acting as enzyme-based nanomachines that transport intracellular cargo along microtubules (MT). To obtain a detailed structural and energetic picture of the various conformations of the kinesin motor domain, we built atomistic models using available crystal structures, homology modeling and flexible fitting into cryo-electron microscopy (EM) maps. These models depict the various biochemical states of the kinesin head, such as - with the neck-linker docked and undocked in the MT-free state, and the different nucleotide (ADP, ATP and APO) bound states in the kinesin-MT complex. Here we perform molecular dynamics simulation techniques and large-scale computational probing of differences in these states, by an exhaustive search of interactions that differ between them, identify key residues in the active site and binding interface, and investigate the binding free-energy between kinesin and MT, and kinesin and ligand to compare with experimentally obtained results. [Preview Abstract] |
Thursday, March 6, 2014 10:24AM - 11:00AM |
S11.00011: Allosteric Ligand Binding and Anisotropic Energy Flow in Albumin Invited Speaker: Brian Dyer Protein allostery usually involves propagation of local structural changes through the protein to a remote site. Coupling of structural changes at remote sites is thought to occur through anisotropic energy transport, but the nature of this process is poorly understood. We have studied the relationship between allosteric interactions of remote ligand binding sites of the protein and energy flow through the structure of bovine serum albumin (BSA). We applied ultrafast infrared spectroscopy to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic flow through the protein structure following input of thermal energy into the flexible ligand binding sites. We also observe anisotropic heat flow through the structure, without local heating of the rigid helix bundles that connect these sites. We will discuss the implications of this efficient energy transport mechanism with regard to the allosteric propagation of binding energy through the connecting helix structures. [Preview Abstract] |
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