251
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Mochida K, Shinozaki K. Genomics and bioinformatics resources for crop improvement. PLANT & CELL PHYSIOLOGY 2010; 51:497-523. [PMID: 20208064 PMCID: PMC2852516 DOI: 10.1093/pcp/pcq027] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 03/01/2010] [Indexed: 05/19/2023]
Abstract
Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.
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252
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McMahon HA, Alfieri KN, Clark KAA, Londergan CH. Cyanylated Cysteine: A Covalently Attached Vibrational Probe of Protein-Lipid Contacts. J Phys Chem Lett 2010; 1:850-855. [PMID: 20228945 PMCID: PMC2836368 DOI: 10.1021/jz1000177] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 02/05/2010] [Indexed: 05/05/2023]
Abstract
Cyanylated cysteine, or beta-thiocyanatoalanine, is an artificial amino acid that can be introduced into peptides and proteins by post-translational chemical modification of solvent-exposed cysteine side chains, and thus it can be used in any protein with a suitable expression and mutagenesis system. In this study, cyanylated cysteine is introduced at selected sites in two model peptides that have been shown to bind to membrane interfaces: a membrane-binding sequence of the human myelin basic protein and the antimicrobial peptide CM15. Far-UV circular dichroism indicates that the secondary structures of the bound peptides are not influenced by introduction of the artificial side chain. Infrared spectra of both systems in buffer and exposed to dodecylphosphocholine micelles indicate that the CN stretching absorption band of cyanylated cysteine can clearly distinguish between membrane burial and solvent exposure of the artificial side chain. Since infrared spectroscopy can be applied in a wide variety of lipid systems, and since cyanylated cysteine can be introduced into proteins of arbitrary size via mutagenesis and post-translational modification, this new probe could see wide use in characterizing the protein-lipid interactions of membrane proteins.
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Affiliation(s)
- Heather A. McMahon
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041
| | - Katherine N. Alfieri
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041
| | - Katherine A. A. Clark
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041
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253
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Janik R, Ritz E, Gravelle A, Shi L, Peng X, Ladizhansky V. Interresidue carbonyl-carbonyl polarization transfer experiments in uniformly 13C,15N-labeled peptides and proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 203:177-84. [PMID: 20060344 DOI: 10.1016/j.jmr.2009.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 12/16/2009] [Indexed: 05/04/2023]
Abstract
In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly (13)C,(15)N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600MHz. To match HORROR condition over all powder orientations, variable amplitude radio frequency (RF) fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing long-range interresidue connectivities (e.g., (N[i]-CO[i-2])) are demonstrated on the model peptide N-acetyl-valine-leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.
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Affiliation(s)
- Rafal Janik
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ont, Canada
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254
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Schneider R, Etzkorn M, Giller K, Daebel V, Eisfeld J, Zweckstetter M, Griesinger C, Becker S, Lange A. Die native Konformation des N-Terminus des humanen spannungsabhängigen Anionenkanals VDAC1. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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255
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Woys AM, Lin YS, Reddy AS, Xiong W, de Pablo JJ, Skinner JL, Zanni MT. 2D IR Line Shapes Probe Ovispirin Peptide Conformation and Depth in Lipid Bilayers. J Am Chem Soc 2010; 132:2832-8. [DOI: 10.1021/ja9101776] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ann Marie Woys
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Yu-Shan Lin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Allam S. Reddy
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Wei Xiong
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Juan J. de Pablo
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - James L. Skinner
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, and Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
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256
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Shi L, Lake EM, Ahmed MA, Brown LS, Ladizhansky V. Solid-state NMR study of proteorhodopsin in the lipid environment: Secondary structure and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2563-74. [DOI: 10.1016/j.bbamem.2009.09.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/16/2009] [Accepted: 09/21/2009] [Indexed: 11/26/2022]
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257
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Ladizhansky V. Homonuclear dipolar recoupling techniques for structure determination in uniformly 13C-labeled proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2009; 36:119-128. [PMID: 19729285 DOI: 10.1016/j.ssnmr.2009.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 07/21/2009] [Indexed: 05/28/2023]
Abstract
In solid-state NMR magic angle spinning is often used to remove line broadening associated with anisotropic interactions, such as chemical shift anisotropy and dipolar couplings. Dipolar recoupling refers to sequences of pulses designed to reintroduce dipolar interactions that are otherwise averaged by magic angle spinning. One of the key applications of homonuclear (and heteronuclear) dipolar recoupling is for the purpose of protein structure determination. Recoupling experiments, originally designed for applications in spin-pair labeled samples, have been revised in recent years for applications in samples with extensive or uniform incorporation of isotopic labels. In these samples multiple internuclear distances can in principle be probed simultaneously, but the dipolar truncation effects (i.e. attenuation of the effects of weak couplings by strong ones) circumvent such measurements. In this article we review some of the recent developments in homonuclear recoupling methods that allow overcoming this problem.
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Affiliation(s)
- Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada.
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258
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Mainz A, Jehle S, van Rossum BJ, Oschkinat H, Reif B. Large Protein Complexes with Extreme Rotational Correlation Times Investigated in Solution by Magic-Angle-Spinning NMR Spectroscopy. J Am Chem Soc 2009; 131:15968-9. [DOI: 10.1021/ja904733v] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andi Mainz
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Stefan Jehle
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Barth J. van Rossum
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Bernd Reif
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
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259
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Solid-state (2)H and (15)N NMR studies of side-chain and backbone dynamics of phospholamban in lipid bilayers: investigation of the N27A mutation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:210-5. [PMID: 19840770 DOI: 10.1016/j.bbamem.2009.09.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 09/18/2009] [Accepted: 09/30/2009] [Indexed: 11/23/2022]
Abstract
Phospholamban (PLB) is an integral membrane protein regulating Ca(2+) transport through inhibitory interaction with sarco(endo)plasmic reticulum calcium ATPase (SERCA). The Asn27 to Ala (N27A) mutation of PLB has been shown to function as a superinhibitor of the affinity of SERCA for Ca(2+) and of cardiac contractility in vivo. The effects of this N27A mutation on the side-chain and backbone dynamics of PLB were investigated with (2)H and (15)N solid-state NMR spectroscopy in phospholipid multilamellar vesicles (MLVs). (2)H and (15)N NMR spectra indicate that the N27A mutation does not significantly change the side-chain or backbone dynamics of the transmembrane and cytoplasmic domains when compared to wild-type PLB. However, dynamic changes are observed for the hinge region, in which greater mobility is observed for the CD(3)-labeled Ala24 N27A-PLB. The increased dynamics in the hinge region of PLB upon N27A mutation may allow the cytoplasmic helix to more easily interact with the Ca(2+)-ATPase; thus, showing increased inhibition of Ca(2+)-ATPase.
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260
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Expression and purification of a recombinant amyloidogenic peptide from transthyretin for solid-state NMR spectroscopy. Protein Expr Purif 2009; 70:101-8. [PMID: 19796687 DOI: 10.1016/j.pep.2009.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/22/2009] [Accepted: 09/23/2009] [Indexed: 11/17/2022]
Abstract
We describe the expression and purification of a model amyloidogenic peptide comprising residues 105-115 of human transthyretin (TTR105-115). Recombinant TTR105-115, which does not contain any non-native residues, was prepared as part of a fusion protein construct with a highly soluble B1 immunoglobulin binding domain of protein G (GB1), with typical yields of approximately 4 mg/L of uniformly (13)C,(15)N-enriched HPLC-purified peptide per liter of minimal media culture. Amyloid fibrils formed by recombinant TTR105-115 were characterized by transmission electron microscopy and solid-state NMR spectroscopy, and found to be comparable to synthetic TTR105-115 fibrils. These results establish recombinant TTR105-115 as a valuable model system for the development of new solid-state NMR techniques for the atomic-level characterization of amyloid architecture.
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261
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Blois TM, Bowie JU. G-protein-coupled receptor structures were not built in a day. Protein Sci 2009; 18:1335-42. [PMID: 19536805 DOI: 10.1002/pro.165] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Among the most exciting recent developments in structural biology is the structure determination of G-protein-coupled receptors (GPCRs), which comprise the largest class of membrane proteins in mammalian cells and have enormous importance for disease and drug development. The GPCR structures are perhaps the most visible examples of a nascent revolution in membrane protein structure determination. Like other major milestones in science, however, such as the sequencing of the human genome, these achievements were built on a hidden foundation of technological developments. Here, we describe some of the methods that are fueling the membrane protein structure revolution and have enabled the determination of the current GPCR structures, along with new techniques that may lead to future structures.
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Affiliation(s)
- Tracy M Blois
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570, USA
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262
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Cui T, Canlas CG, Xu Y, Tang P. Anesthetic effects on the structure and dynamics of the second transmembrane domains of nAChR alpha4beta2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:161-6. [PMID: 19715664 DOI: 10.1016/j.bbamem.2009.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 07/31/2009] [Accepted: 08/12/2009] [Indexed: 01/03/2023]
Abstract
Channel functions of the neuronal alpha4beta2 nicotinic acetylcholine receptor (nAChR), one of the most widely expressed subtypes in the brain, can be inhibited by volatile anesthetics. Our Na(+) flux experiments confirmed that the second transmembrane domains (TM2) of alpha4 and beta2 in 2:3 stoichiometry, (alpha4)(2)(beta2)(3), could form pentameric channels, whereas the alpha4 TM2 alone could not. The structure, topology, and dynamics of the alpha4 TM2 and (alpha4)(2)(beta2)(3) TM2 in magnetically aligned phospholipid bicelles were investigated using solid-state NMR spectroscopy in the absence and presence of halothane and isoflurane, two clinically used volatile anesthetics. (2)H NMR demonstrated that anesthetics increased lipid conformational heterogeneity. Such anesthetic effects on lipids became more profound in the presence of transmembrane proteins. PISEMA experiments on the selectively (15)N-labeled alpha4 TM2 showed that the TM2 formed transmembrane helices with tilt angles of 12 degrees +/-1 degrees and 16 degrees +/-1 degrees relative to the bicelle normal for the alpha4 and (alpha4)(2)(beta2)(3) samples, respectively. Anesthetics changed the tilt angle of the alpha4 TM2 from 12 degrees +/-1 degrees to 14 degrees +/-1 degrees , but had only a subtle effect on the tilt angle of the (alpha4)(2)(beta2)(3) TM2. A small degree of wobbling motion of the helix axis occurred in the (alpha4)(2)(beta2)(3) TM2. In addition, a subset of the (alpha4)(2)(beta2)(3) TM2 exhibited counterclockwise rotational motion around the helix axis on a time scale slower than 10(-4) s in the presence of anesthetics. Both helical tilting and rotational motions have been identified computationally as critical elements for ion channel functions. This study suggested that anesthetics could alter these motions to modulate channel functions.
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Affiliation(s)
- Tanxing Cui
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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263
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Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008; 451:596-9. [PMID: 18235504 DOI: 10.1038/nature06528] [Citation(s) in RCA: 481] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 12/06/2007] [Indexed: 12/15/2022]
Abstract
The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses. Binding of amantadine physically occludes the pore, and might also perturb the pK(a) of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.
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