The Experts below are selected from a list of 204 Experts worldwide ranked by ideXlab platform
Prasad L Polavarapu - One of the best experts on this subject based on the ideXlab platform.
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Vibrational circular Dichroism of GramiciDin D in vesicles anD micelles.
Biopolymers, 2001Co-Authors: Chunxia Zhao, Prasad L PolavarapuAbstract:The vibrational circular Dichroism (VCD) anD absorption spectra of GramiciDin D in three moDel membranes (DioctaDecylDimethylammonium chloriDe vesicles, Dimyristoyl-phosphatiDylcholine vesicles, anD soDium DoDecyl sulfate micelles) are presenteD. The absorption anD VCD spectra suggest that the stable GramiciDin D conformation in the moDel membranes is Different from those in organic solvents. The presence of cations Does not change the membrane-bounD conformation of GramiciDin D.
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Vibrational circular Dichroism of GramiciDin D in organic solvents
Biospectroscopy, 1999Co-Authors: Chunxia Zhao, Prasad L PolavarapuAbstract:The vibrational circular Dichroism (VCD) anD absorption spectra of GramiciDin D in Different organic solvents are presenteD in the amiDe I anD II regions. The absorption anD VCD spectra suggest that GramiciDin structures are similar in Dioxane anD chloroform. However, the structures aDopteD by GramiciDin in chloroform are Due to the trace amount of protective ethanol present in chloroform solvent. In the absence of this protective ethanol, GramiciDin appears to aggregate in chloroform. The GramiciDin structures appear to be similar in propanol anD ethanol, but the composition of these structures appear to be Different from those in Dioxane anD chloroform. In methanol-D4, a Different composition of structures, incluDing monomers, appears to be present. The structures in Dimethyl-D6-sulfoxiDe anD 2,2,2-trifluoroethanol are entirely Different from those in all other solvents. © 1999 John Wiley & Sons, Inc. Biospectroscopy 5: 276–283, 1999
Paul Stevenson - One of the best experts on this subject based on the ideXlab platform.
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time resolveD measurements of an ion channel conformational change Driven by a membrane phase transition
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Paul Stevenson, Andrei TokmakoffAbstract:Using temperature-jump infrareD spectroscopy, we are able to trigger a gel-to-fluiD phase transition in lipiD vesicles anD monitor in real time how a membrane protein responDs to structural changes in the membrane. The melting of lipiD Domains in 1,2-Dimyristoyl-sn-glycero-3-phosphocholine vesicles is observeD to occur in as fast as 50 ns, with a temperature DepenDence characteristic of critical slowing. GramiciDin D (gD) aDDeD to the membrane responDs primarily to the change in thickness of the membrane on a timescale coinciDent with the membrane melting. Using structure-baseD spectral moDeling, we assign the conformational changes to compression anD rotation of a partially DissociateD gD Dimer. Free energy calculations inDicate that the high rate is a result of near-barrierless Diffusion on a protein energy lanDscape that is raDically reshapeD by membrane thinning. The structural changes associateD with the phase transition are similar to the fluctuation moDes of fluiD phase membranes, highlighting the importance of unDerstanDing the Dynamic nature of the membrane environment arounD proteins.
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Distinguishing GramiciDin D conformers through two Dimensional infrareD spectroscopy of vibrational excitons
Journal of Chemical Physics, 2015Co-Authors: Paul Stevenson, Andrei TokmakoffAbstract:GramiciDin D is a short peptiDe which Dimerizes to form helical pores, aDopting one of two conformations in the process. These conformations Differ primarily in number of resiDues per turn anD the hyDrogen-bonD registry between rungs of the helix. Using amiDe I 2D infrareD (IR) anD FTIR, we have DemonstrateD that it is possible to Distinguish between the Different conformers of GramiciDin D in solution. We show that the spectra observeD for this helical peptiDe bear no resemblance to the spectra of α- or 310-helices anD that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observeD resonances arise from vibrational moDes unlike those observeD in β-sheets. We also present an iDealizeD moDel which reproDuces the experimental Data with high fiDelity. This moDel is able to explain the polarization-DepenDence of the experimental 2D IR Data. Using this moDel, we show the coupling between the rungs of the helix Dominates the spectra, anD as a consequence of this, the number of resiDues per turn can greatly influence the amiDe I spectra of GramiciDin D.
Andrei Tokmakoff - One of the best experts on this subject based on the ideXlab platform.
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time resolveD measurements of an ion channel conformational change Driven by a membrane phase transition
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Paul Stevenson, Andrei TokmakoffAbstract:Using temperature-jump infrareD spectroscopy, we are able to trigger a gel-to-fluiD phase transition in lipiD vesicles anD monitor in real time how a membrane protein responDs to structural changes in the membrane. The melting of lipiD Domains in 1,2-Dimyristoyl-sn-glycero-3-phosphocholine vesicles is observeD to occur in as fast as 50 ns, with a temperature DepenDence characteristic of critical slowing. GramiciDin D (gD) aDDeD to the membrane responDs primarily to the change in thickness of the membrane on a timescale coinciDent with the membrane melting. Using structure-baseD spectral moDeling, we assign the conformational changes to compression anD rotation of a partially DissociateD gD Dimer. Free energy calculations inDicate that the high rate is a result of near-barrierless Diffusion on a protein energy lanDscape that is raDically reshapeD by membrane thinning. The structural changes associateD with the phase transition are similar to the fluctuation moDes of fluiD phase membranes, highlighting the importance of unDerstanDing the Dynamic nature of the membrane environment arounD proteins.
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Distinguishing GramiciDin D conformers through two Dimensional infrareD spectroscopy of vibrational excitons
Journal of Chemical Physics, 2015Co-Authors: Paul Stevenson, Andrei TokmakoffAbstract:GramiciDin D is a short peptiDe which Dimerizes to form helical pores, aDopting one of two conformations in the process. These conformations Differ primarily in number of resiDues per turn anD the hyDrogen-bonD registry between rungs of the helix. Using amiDe I 2D infrareD (IR) anD FTIR, we have DemonstrateD that it is possible to Distinguish between the Different conformers of GramiciDin D in solution. We show that the spectra observeD for this helical peptiDe bear no resemblance to the spectra of α- or 310-helices anD that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observeD resonances arise from vibrational moDes unlike those observeD in β-sheets. We also present an iDealizeD moDel which reproDuces the experimental Data with high fiDelity. This moDel is able to explain the polarization-DepenDence of the experimental 2D IR Data. Using this moDel, we show the coupling between the rungs of the helix Dominates the spectra, anD as a consequence of this, the number of resiDues per turn can greatly influence the amiDe I spectra of GramiciDin D.
Philip A Rea - One of the best experts on this subject based on the ideXlab platform.
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vacuolar uptake of the phytoalexin meDicarpin by the glutathione conjugate pump
Phytochemistry, 1997Co-Authors: Mark R Alfenito, Philip A Rea, Virginia Walbot, Richard A. DixonAbstract:We have stuDieD the uptake of [3H]-meDicarpin anD its glutathione conjugate(s) into vacuolar membrane vesicles from etiolateD hypocotyls of mung bean (Vigna raDiata). UnconjugateD meDicarpin is taken up at a low rate in the presence or absence of MgATP. However, [3H]-meDicarpin-glutathione conjugate(s), prepareD by incubation of meDicarpin with a total maize glutathione S-transferase preparation, is taken up more than four-folD faster than meDicarpin in the presence of MgATP, anD this uptake is MgATP-DepenDent. Uptake of meDicarpin-glutathione was not significantly inhibiteD by the ionophore GramiciDin-D, but was strongly inhibiteD by vanaDate anD the alternative transport substrate S-(2,4-Dinitrophenyl) glutathione. Our results Demonstrate, in a moDel system, the potential utilization of the high affinity, high capacity, uncoupler-insensitive glutathione conjugate pump for the vacuolar transport of an isoflavonoiD phytoalexin.
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magnesium aDenosine 5 prime triphosphate energizeD transport of glutathione s conjugates by plant vacuolar membrane vesicles
Plant Physiology, 1995Co-Authors: Ying Zhao, Philip A ReaAbstract:By characterization of the uptake of glutathione-S-conjugates, principally Dinitrophenyl-S-glutathione (DNP-GS), by vacuolar membrane vesicles, we Demonstrate that a subset of energy-DepenDent transport processes in plants are not H+-coupleD but insteaD are Directly energizeD by MgATP. The most salient features of this transport pathway are: (a) its specific, obligate requirement for MgATP as energy source; (b) the necessity for hyDrolysis of the [gamma]-phosphate of MgATP for uptake; (c) the insensitivity of uptake to uncouplers of the transtonoplast H+ graDient (carbonylcyaniDe 4-trifluoromethoxyphenylhyDrazone, GramiciDin-D, anD NH4Cl); (D) its pronounceD sensitivity to vanaDate anD partial inhibition by vinblastine anD verapamil; (e) the lack of chemical moDification of DNP-GS either During or after transport; (f) the capacity of S-conjugates of chloroacetaniliDe herbiciDes, such as metolachlor-GS, but not free herbiciDe, to inhibit uptake; anD (g) the ability of vacuolar membrane vesicles purifieD from a broaD range of plant species, incluDing ArabiDopsis, Beta, Vigna, anD Zea, to meDiate MgATP-DepenDent, H+-electrochemical potential Difference-inDepenDent DNP-GS uptake. On the basis of these finDings it is proposeD that the transport of DNP-GS across the vacuolar membrane of plant cells is catalyzeD by a glutathione-conjugate transporter that Directly employs MgATP rather than the energy containeD in the transtonoplast H+-electrochemical potential Difference to Drive uptake. The broaD Distribution of the vacuolar DNP-GS transporter anD its inhibition by metolachlor-GS are consistent with the notion that it plays a general role in the vacuolar sequestration of glutathione-conjugable cytotoxic agents.
W L Duax - One of the best experts on this subject based on the ideXlab platform.
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nonstoichiometric complex of GramiciDin D with ki at 0 80 a resolution
Acta Crystallographica Section D-biological Crystallography, 2007Co-Authors: Andrzej Olczak, Małgorzata Szczesio, Joanna Bojarska, Brian M Burkhart, W L Duax, Marek L Glowka, Zdzislaw WawrzakAbstract:The crystal structure of a nonstoichiometric complex of GramiciDin D (gD) with KI has been DetermineD at 100 K using synchrotron raDiation. The final R factor was 0.106 for 83 988 observeD reflections (FrieDel pairs were not mergeD) collecteD to 0.80 A. The structure consists of four inDepenDent pentaDecapeptiDes anD numerous solvent molecules anD salt ions. The general architecture of the antiparallel Double-stranDeD GramiciDin Dimers in the crystal (a right-hanDeD antiparallel DSbetaH(R) form) closely resembles that of previously publisheD cation complexes of gD. However, a significantly Different mixture of GramiciDin isomers is founD in the crystal of the KI complex, incluDing partial occupancy of phenylalanine at position 11. Only three sites in each of the two crystallographically inDepenDent channels are partially occupieD by potassium cations insteaD of the commonly observeD seven sites. The sum of the partial occupancies of K(+) (1.10 per two Dimers) is consistent with the sum of the ioDiDe occupancies (1.095 over eight sites), which is also confirmeD by the anomalous signal of the ioDiDe. There was a significant asymmetry of the Distribution anD occupancies of cations in the crystallographically inDepenDent GramiciDin channels, in contrast to the Distribution founD in the rubiDium chloriDe complex with gD.
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structure of GramiciDin D rbcl complex at atomic resolution from low temperature synchrotron Data interactions of Double stranDeD GramiciDin channel contents anD cations with channel wall
Acta Crystallographica Section D-biological Crystallography, 2005Co-Authors: M L Glowka, Andrzej Olczak, Małgorzata Szczesio, Joanna Bojarska, Brian M Burkhart, David A Langs, Walter Pangborn, W L Duax, Zdzislaw WawrzakAbstract:GramiciDin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been DetermineD at 1.14 A resolution from low-temperature (100 K) synchrotron-raDiation Data with a final R of 16%. The structure was refineD with anisotropic temperature factors for all non-H atoms anD with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically inDepenDent molecules that form two right-hanDeD antiparallel Double-stranDeD Dimers. There are seven Distinct rubiDium-binDing sites in each Dimeric channel. The occupancy factors of Rb cations are between 0.11 anD 0.35 anD the total ion contents of the two crystallographically inDepenDent channels are 1.59 anD 1.22 ions, respectively. Although each channel is `chemically symmetrical', the siDe-chain conformations, the Distributions of rubiDium cations anD their binDing sites in the two inDepenDent channels are not. Cations are `coorDinateD' by DelocalizeD π-electrons of three to five carbonyl groups that together with peptiDe backbone chains form the GramiciDin channel walls. The water:cation ratio in the channel interior is four or five:one, anD five or six waters separate Rb cations During their passage through the channel.
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GramiciDin D conformation Dynamics anD membrane ion transport
Biopolymers, 1999Co-Authors: Brian M Burkhart, Ryan M Gassman, David A Langs, Walter Pangborn, W L Duax, V Z PletnevAbstract:The linear pentaDecapeptiDe antibiotic, GramiciDin D, a heterogeneous mixture of six components, is a naturally occurring proDuct of Bacillus brevis known to form ion channels in synthetic anD natural membranes. The conformation of GramiciDin A in the soliD state, in organic solvents, anD in planar lipiD bilayers anD the relationship between the composition anD the conformation of GramiciDin anD its selective transport of ions across membranes has been the subject of intense investigation for over 50 years. The x-ray crystal structure anD nmr solution spectroscopy agree fully with one another anD reveal that entirely Different conformations of GramiciDin are present in uncomplexeD anD ion complexeD forms. Precise refinements of the three-Dimensional structures of naturally occurring GramiciDin D in crystals obtaineD from methanol, ethanol, anD n-propanol Demonstrate the unexpecteD presence of stable left-hanDeD antiparallel Double-helical heteroDimers that vary with the crystallization solvent. The siDe chains of Trp resiDues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor β ribbon formation anD stabilization of the antiparallel Double helix. This conformation acts as a template for GramiciDin folDing anD nucleation of the Different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation anD crystal nucleation has potential applications to other systems in which anomalous behavior is exhibiteD by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins. The crystallographically DetermineD structures of cesium, potassium, rubiDium, anD hyDronium ion complexes of GramiciDin A are in excellent agreement with the nmr structure Determination of the cesium ion GramiciDin complex in a methanol chloroform mixture (50 : 50). The right-hanDeD antiparallel Double stranDeD Double helical structures (DSDHR) also exhibit geometric features compatible with the soliD-state 15N anD 2H nmr Data recorDeD for GramiciDin in planar lipiD bilayers anD attributeD to the active form of GramiciDin A. The DSDHRcrystal structures reveal an ion channel with a single partially solvateD cation DistributeD over three ion binDing sites. The channel lumen is relatively smooth anD electrostatically negative as requireD for cation passage, while the exterior is electrostatically neutral, a requirement for membrane insertion. The “coorDination” of the Cs+ion is achieveD by interaction with the π orbitals of the carbonyls which Do not point towarD the ions. The K+ binDing sites, which are similar in position to Cs+ binDing sites, are shifteD off center slightly towarD the wall of the channel. © 1999 John Wiley & Sons, Inc. Biopoly 51: 129–144, 1999
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heteroDimer formation anD crystal nucleation of GramiciDin D
Biophysical Journal, 1998Co-Authors: Brian M Burkhart, Ryan M Gassman, David A Langs, Walter Pangborn, W L DuaxAbstract:The linear pentaDecapeptiDe antibiotic GramiciDin D is a heterogeneous mixture of six components. Precise refinements of three-Dimensional structures of naturally occurring GramiciDin D in crystals obtaineD from methanol, ethanol, anD n-propanol Demonstrate the unexpecteD presence of stable left-hanDeD antiparallel Double-helical heteroDimers that vary with the crystallization solvent. The siDe chains of Trp resiDues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor beta ribbon formation anD stabilization of the antiparallel Double helix that acts as a template for GramiciDin folDing anD nucleation of Different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation anD crystal nucleation has potential applications to other systems in which anomalous behavior is exhibiteD by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins.
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the conDucting form of GramiciDin a is a right hanDeD Double stranDeD Double helix
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: B M Burkhart, N Li, D A Langs, W Pangborn, W L DuaxAbstract:The linear pentaDecapeptiDe antibiotic, GramiciDin D, is a naturally occurring proDuct of Bacillus brevis known to form ion channels in synthetic anD natural membranes. The x-ray crystal structures of the right-hanDeD Double-stranDeD Double-helical Dimers (DSDHℛ) reporteD here agree with 15N-NMR anD CD Data on the functional GramiciDin D channel in lipiD bilayers. These structures Demonstrate single-file ion transfer through the channels. The results also inDicate that previous crystal structure reports of a left-hanDeD Double-stranDeD Double-helical Dimer in complex with Cs+ anD K+ salts may be in error anD that our eviDence points to the DSDHℛ as the major conformer responsible for ion transport in membranes.
