Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session Q14: Invited Session: Physics of Proteins: New Insights on Hydrogen Bonding and Proton Transfer |
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Sponsoring Units: DBIO DCOMP Chair: Wouter Hoff, Oklahoma State University Room: 301-303 |
Wednesday, March 5, 2014 2:30PM - 3:06PM |
Q14.00001: Functional Dynamics and Proton Transfer in Proteins Invited Speaker: Steven Boxer Internal proton transfer between an enzyme and substrate is a common feature of many enzyme mechanisms. Likewise, internal proton transfer between the chromophore of green fluorescent protein (GFP) and amino acids on the inside of the beta barrel are important both in the ground and excited state. I will discuss an interesting connection between the proton transfer dynamics in GFP and those in an enzyme, ketosteroid isomerase (KSI), bound to substrate analogs. In both cases there is a tug of war between the protein and bound substrate analog or chromophore that depends on their affinities for a proton and which can be tuned either by changing the substrate/chromophore or the protein. This can be observed in the ground state by optical methods (absorption and IR) as well as by nmr, or in the excited state by time-resolved fluorescence or visible pump-IR probe measurements. In both cases the proton dynamics have important functional consequences. [Preview Abstract] |
Wednesday, March 5, 2014 3:06PM - 3:42PM |
Q14.00002: Proton transfer and water exchange in the green fluorescent protein Invited Speaker: Noam Agmon The green fluorescent protein (GFP) is the only naturally occurring protein in which excited-state proton-transfer has been identified. Upon excitation, a proton is ejected from its chromophore, travelling through the ``privileged water molecule'' (PWM) and Ser205 to Glu222, on a 10 ps timescale or faster. However, time-resolved fluorescence from the chromophore exhibits a $t^{-\alpha }$ power-law decay extending into the ns regime. With increasing temperature, $\alpha $ switches from 1/2 (below 230 K) to 3/2 (above it). This has been interpreted as pseudo one-dimensional proton hopping along an internal ``proton wire,'' with an activated process that opens a ``doorway'' for proton escape to solution at the higher temperatures [1]. To identify such putative pathways, we have developed a computer code mapping all ``proton wires'' within a protein structure. Applying it to a X-ray GFP structure of 0.9 Angstrom resolution [2], a proton wire indeed continues from Glu222 along the axis of the GFP ``barrel,'' connecting to a negatively charged surface patch (a ``proton collecting antenna''?). This might explain the t$^{-1/2}$ behavior. However, a direct escape pathway opening from the chromophore to solution is not readily identified in the X-ray structure. Here we report molecular dynamics results showing that the PWM escapes to solution on the 100 ps timescale. This occurs by fluctuations of the beta-sheet, creating an opening through which water molecules can leave and enter the protein. The exact pathway of the PWM on its way in and out has been identified, as well as the water-exchange kinetics that follows a stretched-exponential time behavior.\\[4pt] [1] Agmon, N. \textit{J. Phys. Chem. B} 2007, \textbf{111}, 7870.\\[0pt] [2] Shinobu, A.; Palm, G. J.; Schierbeek, A. J.; Agmon, N. \textit{J. Am. Chem. Soc.} 2010, \textbf{132}, 11093. [Preview Abstract] |
Wednesday, March 5, 2014 3:42PM - 4:18PM |
Q14.00003: Principles and Dynamics of Proton Transfer in Proteins Invited Speaker: Aihua Xie Proton transfer is broadly employed in protein functions, not only in energy transformation but also in biological signaling and enzymatic catalysis. Unlike electron transfer which has been well understood for nearly two decades, some key questions regarding the physical mechanism of proton transfer remains elusive after extensive studies. We will report a proof of concept study on principles and dynamics of proton transfer and its applications in proteins. In addition, we will discuss how to apply time-resolved infrared structural biology to probe and explore proton transfer during protein functions. [Preview Abstract] |
Wednesday, March 5, 2014 4:18PM - 4:54PM |
Q14.00004: Proton transfer pathways in Photosystem II Invited Speaker: Hiroshi Ishikita Using quantum mechanics/molecular mechanics calculations and the 1.9-{\AA} crystal structure of Photosystem II (Umena, Y., Kawakami, K., Shen, J.-R., and Kamiya, N. (2011) Nature 473, 55-60), we investigated the H-bonding environment of the redox active tyrosine, TyrD and obtained insights that help explain its slow redox kinetics and the stability of TyrD radical. The water molecule distal to TyrD, 4 {\AA} away from the phenolic O of TyrD (O$_{\mathrm{TyrD}})$, corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to O$_{\mathrm{TyrD,}}$ corresponds to the presence of the unoxidised tyrosine. The H$^{+}$ released upon oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasi-irreversible, explaining the great stability of the TyrD radical. A symmetry-related proton pathway associated with TyrZ is pointed out and this is associated with one of the Cl$^{-}$ sites. This may represent a proton pathway functional in the water oxidation cycle. [Preview Abstract] |
Wednesday, March 5, 2014 4:54PM - 5:30PM |
Q14.00005: Contribution of Hydrogen Bonds to Protein Stability Invited Speaker: Nick Pace I will discuss the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, $\Delta (\Delta $G), for a series of hydrogen bonding mutants in four proteins: villin head piece subdomain (VHP) containing 36 residues, a surface protein from \textit{Borrelia burgdorferi} (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A (1.1{\AA}), Y51F(1.5{\AA}), and T95A(1.3{\AA}). The structures are very similar to wild type RNase Sa and the hydrogen bonding partners always form intermolecular hydrogen bonds to water in the mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions: 1) Hydrogen bonds contribute favorably to protein stability. 2) The contribution of hydrogen bonds to protein stability is strongly context dependent. 3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. 5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein. [Preview Abstract] |
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