Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session S4: Photoreceptor and Signal TransductionFocus
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Sponsoring Units: DBIO DPOLY Chair: Wouter Hoff, Oklahoma State University Room: 263 |
Thursday, March 16, 2017 11:15AM - 11:27AM |
S4.00001: Tryptophan-to-Tryptophan Energy Transfer in UV-B photoreceptor UVR8 Xiankun Li, Dongping Zhong UVR8 (UV RESISTANCE LOCUS 8) protein is a UV-B photoreceptor in high plants. UVR8 is a homodimer that dissociates into monomers upon UV-B irradiation (280 nm to 315 nm), which triggers various protective mechanisms against UV damages. Uniquely, UVR8 does not contain any external chromophores and utilizes the UV-absorbing natural amino acid tryptophan (Trp) to perceive UV-B. Each UVR8 monomer has 14 tryptophan residues. However, only 2 epicenter Trp (W285 W233) are critical to the light induced dimer-to-monomer transformation. Here, we revealed, using site-directed mutagenesis and spectroscopy, a striking energy flow network, in which other tryptophan chromophores serve as antenna to transfer excitation energy to epicenter Trp, greatly enhancing UVR8 light-harvesting efficiency. Furthermore, Trp-to-Trp energy transfer rates were measured and agree well with theoretical values. [Preview Abstract] |
Thursday, March 16, 2017 11:27AM - 11:39AM |
S4.00002: Global Picosecond Structural Dynamics of Orange Carotenoid Protein in Photo/Chemical Activated Signaling States Yanting Deng, Mengyang Xu, Hanjun Liu, Robert Blankenship, Andrea Markelz Light availability to photosynthetic organisms changes throughout the day. High light can over-saturate photosynthetic capacity and produce reactive oxygen which damages the photosynthetic apparatus and leads to cell death. Photosynthetic organisms have evolved multiple photo-protective strategies to prevent oxidative damage from light stress. For cyanobacteria, a blue-light photo-sensor orange carotenoid protein (OCP) responds to exposure to intense light. Upon high light stress, OCP converts from the orange inactive form (OCP$^{\mathrm{O}})$ to the red active form (OCP$^{\mathrm{R}})$, with a large conformational change. And OCP$^{\mathrm{R}}$ interacts with the light harvesting antenna phycobilisome (PB), and mediates the energy quenching of PB. We argue that both the susceptibility of OCP to large conformational change and its interaction with PB are associated with changes in the long range picosecond structural flexibility. To investigate the protein flexibility with signaling state dependence, temperature dependent terahertz time domain spectroscopy is performed in the range of 80 -- 290 K on OCP solutions, as a function of illumination and chaotrope (NaSCN) concentration, which produces a long lived red state in the absence of photoexcitation. We characterize the global flexibility by both the net THz absorbance and the dynamical transition temperature, which scales with structural stability, and observed the dynamical transition occurred in the 180-220 K range. [Preview Abstract] |
Thursday, March 16, 2017 11:39AM - 11:51AM |
S4.00003: Temperature dependence of phonons in photosynthesis proteins Mengyang Xu, Dean Myles, Robert Blankenship, Andrea Markelz Protein long range vibrations are essential to biological function. For many proteins, these vibrations steer functional conformational changes. For photoharvesting proteins, the structural vibrations play an additional critical role in energy transfer to the reaction center by both phonon assisted energy transfer and energy dissipation. The characterization of these vibrations to understand how they are optimized to balance photoharvesting and photoprotection is challenging. To date this characterization has mainly relied on fluorescence line narrowing measurements at cryogenic temperatures. However, protein dynamics has a strong temperature dependence, with an apparent turn on in anharmonicity between 180-220 K. If this transition affects intramolecular vibrations, the low temperature measurements will not represent the phonon spectrum at biological temperatures. Here we use the new technique of anisotropic terahertz microscopy (ATM) to measure the intramolecular vibrations of FMO complex. ATM is uniquely capable of isolating protein vibrations from isotropic background. We find resonances both red and blue shift with temperature above the dynamical transition. The results indicate that the characterization of vibrations must be performed at biologically relevant temperatures to properly understand the energy overlap with the excitation energy transfer. [Preview Abstract] |
Thursday, March 16, 2017 11:51AM - 12:27PM |
S4.00004: Direct observation of light-induced structural changes in photoreceptors by dynamic crystallography Invited Speaker: Xiaojing Yang Photoreceptors are signaling proteins that convert a light signal into a biological signal. Photoreceptors use chemically distinct chromophores to capture photons from different wavelengths. When primary photo-events originating in the chromophore propagate, they drive further conformational changes, which alter protein-protein interactions and/or enzymatic activities. Establishing such a sequence of structural events at atomic resolution holds the key to full understanding of the light perception and signaling mechanisms in photoreceptors. Dynamic crystallography is a powerful tool that enables direct observations of protein structural dynamics at atomic resolution. In a dynamic crystallography experiment, a biochemical reaction or a signaling process is initiated in the crystalline state. X-ray diffraction datasets collected before and after the reaction initiation are compared via the difference Fourier method for examination of conformational changes along the reaction coordinates. However, how to acquire useful dynamic information by crystallography remains a major challenge for many biological systems. In my talk, I will present how we apply dynamic crystallography to directly observe light-induced structural changes in different photoreceptor systems. I will discuss how to design and perform dynamic crystallography experiments, how to process and analyze a collection of difference maps in order to extract structural changes and to determine light-induced structural intermediates. This method and its applications to light-sensitive systems would broadly interest the structural biology community who wish to study protein structural dynamics at high resolution [Preview Abstract] |
Thursday, March 16, 2017 12:27PM - 12:39PM |
S4.00005: High-field CW electron paramagnetic resonance spectroscopy with Gd(III) tags for structure-dynamics studies of proteorhodopsin Jessica A. Clayton, Chung-ta Han, C. Blake Wilson, Mian Qi, Adelheid Godt, Daniella Goldfarb, Mark S. Sherwin, Songi Han Proteorhodopsin (PR) is a seven-helical transmembrane protein that functions as a light-activated proton pump. Much of the structure of PR has been mapped by solution-state NMR and X-ray crystallography, however it remains difficult to study protein associations and conformational changes. Here we report development of 240 GHz CW electron paramagnetic resonance (EPR) as a tool to determine inter- and intra-protein distances in the range of 1 – 4 nm under biologically relevant conditions, using S = 7/2 Gd(III)-based complexes as an EPR-active paramagnetic tag. The dipolar coupling between Gd(III) pairs is determined via the width of the central transition in the CW EPR spectrum, allowing for the inference of an interspin distance. Proof-of-principle experiments are demonstrated on “Gd-ruler” molecules, from cryogenic temperatures up to room temperature. First results applying this method to inter-protein measurement of Gd(III) tagged PR oligomers reveals distances consistent with the penta- or hexameric organization determined by crystal structure. Finally, we present progress towards development of measurement methods that will enable observation of light-induced conformational changes in the EF-loop region of PR at temperatures above the protein dynamical transition. [Preview Abstract] |
Thursday, March 16, 2017 12:39PM - 12:51PM |
S4.00006: DFT study of tetracationic 5,10,15,20-tetrakis(1-methyl4-pyridyl)-21H,23H porphyrin Helena Petrilli, Eduardo Suárez, Danilo Pereira, Filipe Lima, Arles Rebaza, Vera Constantino Porphyrins are heterocyclic macrocycle organic compounds with many applications such as photosensitizers for light harvesting and chemical reactions, molecular electronics and enzymatic catalysis. They can be found in biological systems like photosynthesis of light, enzymes, and transport proteins. The porphyrins optical spectra can be characterized by the presence of a dominant so called Soret band plus a Q-band structure, whose positions and shapes offer a method to characterize porphyrins in various environments. Here the electronic and spectroscopic properties of tetracationic 5,10,15,20-tetrakis(1-methyl4-pyridyl)-21H,23H-porphyrin (TMPyP) is investigated in the framework of the DFT. The IR and UV-vis spectra are compared with experimental results. The influence of the environment and functional on the UV-vis spectra is investigated. These results are further discussed to tentative address the TMPyP/Clay interaction. [Preview Abstract] |
Thursday, March 16, 2017 12:51PM - 1:27PM |
S4.00007: Understanding blue-light photoreceptors Invited Speaker: Brian Crane Blue-light sensing proteins coordinate many biological processes that include phototropism, photomorphism, stress responses, virulence and the entrainment of circadian clocks. Three major types of blue-light sensors all bind flavin nucleotides as chromophores, but the photochemistry employed and conformational responses invoked differ considerably among the classes. Nevertheless, photoinduced electron transfer reactions play a key role in many mechanisms. How such reactivity leads to conformational signaling will be discussed for both cryptochromes (CRYs) and light- oxygen- voltage (LOV) domains. In CRYs, blue-light mediated flavin reduction promotes proton transfer within the active center that then leads to displacement of a key signaling element. For LOV proteins, blue light causes formation of a covalent cysteinyl-flavin adduct, which rearranges hydrogen bonding and restructures the N-terminal region of the protein. Interestingly, a new class of LOV-like sensor does not undergo adduct formation and instead can operate by flavin photoreduction, like CRY. Conserved aspects of reactivity in these proteins provide lessons for the design of new photosensors, which may find use as tools in optogenetics [Preview Abstract] |
Thursday, March 16, 2017 1:27PM - 1:39PM |
S4.00008: Putting a photon to biological work: lessons from novel photoactive yellow protein homologs. Wouter Hoff, Miwa Hara, Jie Ren, Masato Kumauchi, Aihua Xie, Delmar Larsen, Tyler Mix, Shojiro Haraguchi, Takahito Shingae, Masashi Unno The photoactive yellow protein (PYP) is a photosensory protein from the bacterium \textit{Halorhodospira halophila} that has been used extensively as a model system for functional protein dynamics and biological signaling. We have been studying PYP homologs from a diverse set of bacteria. The PYP from \textit{Salinibacter ruber} (Srub PYP) revealed a novel ``spectral isotope effect'' when the protein is dissolved in D$_{\mathrm{2}}$O. We were able to assign this effect to H/D exchange of an active side COOH group that forms an ionic hydrogen bond to the deprotonated (negatively charged) light-absorbing chromophore in PYP. Srub PYP also allowed us to measure Raman Optical Activity (ROA) spectra under resonance and pre-resonance conditions. This work revealed that pre-resonance (ROA) spectra are informative for analyzing active site distortions in PYP. Finally, ultrafast pump-probe experiments on three different PYPs revealed that the primary I$_{\mathrm{0}}$ photoproduct observed in Hhal PYP is not populated in some other PYP homologs. This observation has implications for the mechanism of chromophore photoisomerization at the start of the functional photocycle of PYP. These results illustrate how studies of different members of a protein family can lead to novel insights into basic mechanisms underlying protein function [Preview Abstract] |
Thursday, March 16, 2017 1:39PM - 1:51PM |
S4.00009: Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering Utsab R. Shrestha, Debsindhu Bhowmik, Eugene Mamontov, Xiang-Qiang Chu Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein. [Preview Abstract] |
Thursday, March 16, 2017 1:51PM - 2:03PM |
S4.00010: Ballistic Motion of Enzymes that Catalyze Highly Exothermic Reactions Konstantinos Tsekouras, Steve Pressé Recently we proposed that the experimentally observed enhanced diffusion of enzymes catalyzing highly exothermic reactions is a consequence of their mechanism for dissipating reaction energy. More specifically, we proposed that reaction energy spreads out from the reaction site in the form of an acoustic wave which causes the enzyme to asymmetrically deform into the solvent. The solvent reaction propels the enzyme. However, it has been noted that in water, high viscosity should reduce enzyme momentum to zero within a few \textit{ps}, so any diffusion increase should not be observable. Here we provide a model explaining how small volumetric expansions of biomolecules inside water may cause fluid compression that in turn creates regions of low fluid density around the biomolecule. We then investigate the dynamics of the biomolecule in the presence of these perturbations. [Preview Abstract] |
Thursday, March 16, 2017 2:03PM - 2:15PM |
S4.00011: Multistate coarse-grained molecular dynamics for modelling the catalytic cycle of allosteric enzyme. Wenfei Li, Wei Wang, Shoji Takada Biological functions of proteins are often related to their conformational dynamics, therefore, the intrinsic energy landscape. Adenylate kinase (AK), which catalyzes the reversible conversion from ATP and AMP to ADP, has widely been used as a model system of allosteric enzyme to study the role of conformational dynamics in protein functions. However, the underlying mechanism on the interplay between enzymatic turnover and conformational dynamics is not fully understood. In this work we constructed a multistate coarse-grained molecular dynamics model within the framework of the energy landscape theory, with which we have been able to simulate the full catalytic cycle of the AK. Our results demonstrated the tight coupling between the substrate exchange and lid open/closing motions, and their contributions to the final turnover rate. Particularly, we revealed how typical physiochemical factors, such as substrate concentrations, temperatures, and mechanical force, modulate the multistate allosteric motions of the protein and the pathways of the catalytic cycle. [Preview Abstract] |
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