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To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tibs.2009.09.006 Byline: Mark T. Young Abstract: P2X receptors are non-selective cation channels gated by extracellular ATP. They play key roles in various physiological processes such as nerve transmission, pain sensation and the response to inflammation, making them attractive drug targets for the treatment of inflammatory pain. The recent report of the three-dimensional (3D) crystal structure of zebrafish P2X4.1 represents a step change in our understanding of these membrane ion channels, where previously only low-resolution structural data and inferences from indirect structure-function studies were available. The purpose of this review is to place previous work within the context of the new 3D structure, and to summarize the key questions and challenges which await P2X researchers as we move into the post-structure era. Author Affiliation: School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2009.07.044 Byline: Erik Martinez-Hackert (1), Wayne A. Hendrickson (1)(2) Keywords: PROTEINS; CELLBIO Abstract: Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes. Author Affiliation: (1) Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA (2) Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA Article History: Received 22 December 2008; Revised 28 March 2009; Accepted 31 July 2009 Article Note: (miscellaneous) Published: September 3, 2009

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tins.2009.01.004 Byline: Uri Ashery, Noa Bielopolski, Boaz Barak, Ofer Yizhar Abstract: Priming is the process by which vesicles become available for fusion at nerve terminals and is modulated by numerous proteins and second messengers. One of the prominent members of this diverse family is tomosyn. Tomosyn has been identified as a syntaxin-binding protein; it inhibits vesicle priming, but its mode of action is not fully understood. The inhibitory activity of tomosyn depends on its N-terminal WD40-repeat domain and is regulated by the binding of its SNARE motif to syntaxin. Here, we describe new physiological information on the function of tomosyn and address possible interpretations of these results in the framework of the recently described crystal structure of the yeast tomosyn homolog Sro7. We also present possible molecular scenarios for vesicle priming and the involvement of tomosyn in these processes. Author Affiliation: Department of Neurobiology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.06.024 Byline: Scott M. Stagg (1)(2)(6), Paul LaPointe (2), Abbas Razvi (2), Cemal Gurkan (2)(5), Clinton S. Potter (1)(2), Bridget Carragher (1)(2), William E. Balch (2)(3)(4) Keywords: CELLBIO; PROTEINS Abstract: Using cryo-electron microscopy, we have solved the structure of an icosidodecahedral COPII coat involved in cargo export from the endoplasmic reticulum (ER) coassembled from purified cargo adaptor Sec23-24 and Sec13-31 lattice-forming complexes. The coat structure shows a tetrameric assembly of the Sec23-24 adaptor layer that is well positioned beneath the vertices and edges of the Sec13-31 lattice. Fitting the known crystal structures of the COPII proteins into the density map reveals a flexible hinge region stemming from interactions between WD40 [beta]-propeller domains present in Sec13 and Sec31 at the vertices. The structure shows that the hinge region can direct geometric cage expansion to accommodate a wide range of bulky cargo, including procollagen and chylomicrons, that is sensitive to adaptor function in inherited disease. The COPII coat structure leads us to propose a mechanism by which cargo drives cage assembly and membrane curvature for budding from the ER. Author Affiliation: (1) National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA (2) Departments of Cell Biology and Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA (3) Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA (4) The Institute for Childhood and Neglected Disease, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA (5) Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, International Airport Avenue #6, Ayios Dhometios, Nicosia, Cyprus (6) Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA Article History: Received 20 February 2008; Revised 1 May 2008; Accepted 9 June 2008 Article Note: (miscellaneous) Published: August 7, 2008

Crystal structures of LeuT, a bacterial homologue of mammalian neurotransmitter transporters, show a molecule of bound substrate that is essentially exposed to the extracellular space but occluded from the cytoplasm. Thus, there must exist an alternate conformation for LeuT in which the substrate is accessible to the cytoplasm and a corresponding mechanism that switches accessibility from one side of the membrane to the other. Here, we identify the cytoplasmic accessibility pathway of the alternate conformation in a mammalian serotonin transporter (SERT) (a member of the same transporter family as LeuT). We also propose a model for the cytoplasmic-facing state that exploits the internal pseudosymmetry observed in the crystal structure. LeuT contains two structurally similar repeats (TMs1-5 and TMs 6-10) that are inverted with respect to the plane of the membrane. The conformational differences between them result in the formation of the extracellular pathway. Our model for the cytoplasm-facing state exchanges the conformations of the two repeats and thus exposes the substrate and ion-binding sites to the cytoplasm. The conformational change that connects the two states primarily involves the tilting of a 4-helix bundle composed of transmembrane helices 1, 2, 6, and 7. Switching the tilt angle of this bundle is essentially equivalent to switching the conformation of the two repeats. Extensive mutagenesis of SERT and accessibility measurements, using cysteine reagents, are accommodated by our model. These observations may be of relevance to other transporter families, many of which contain internal inverted repeats. alternating access mechanism | neurotransmitter:sodium symporters | serotonin | structural modeling | structural repeats

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tips.2007.11.009 Byline: Brian Kobilka (1), Gebhard F.X. Schertler (2) Abstract: G-protein-coupled receptors (GPCRs) constitute a large family of structurally similar proteins that respond to a chemically diverse array of physiological and environmental stimulants. Until recently, high-resolution structural information was limited to rhodopsin, a naturally abundant GPCR that is highly specialized for the detection of light. Non-rhodopsin GPCRs for diffusible hormones and neurotransmitters have proven more resistant to crystallography approaches, possibly because of their inherent structural flexibility and the need for recombinant expression. Recently, crystal structures of the human [beta].sub.2 adrenoceptor have been obtained using two different approaches to stabilize receptor protein and increase polar surface area. These structures, together with the existing structures of rhodopsin, represent an important first step in understanding how GPCRs work at a molecular level. Much more high-resolution information is needed for this important family of membrane proteins, however: for example, the structures of GPCRs from different families, structures bound to ligands having different efficacies, and structures of GPCRs in complex with G proteins and other signaling molecules. Methods to characterize the dynamic aspects of the GPCR architecture at high resolution will also be important. Author Affiliation: (1) Departments of Molecular and Cellular Physiology and Medicine, Stanford University School of Medicine, 279 Campus Drive, Stanford, Palo Alto, CA 94305, USA (2) MRC Laboratory of Molecular Biology, Cambridge, CB2 0QT, UK

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tibs.2006.10.002 Byline: Johannes L. Bos Abstract: Epac1 and Epac2 are cAMP-dependent guanine-nucleotide-exchange factors for the small GTPases Rap1 and Rap2, and are known to be important mediators of cAMP signaling. The recent determination of the crystal structure of Epac2 has indicated a mechanism for the activation of the multi-domain Epac proteins. In addition, these proteins have been implicated in various cellular processes such as integrin-mediated cell adhesion and cell-cell junction formation, the control of insulin secretion and neurotransmitter release. In most of these processes, cAMP signaling through protein kinase A (PKA) is also involved, stressing the interconnectivity between Epac- and PKA-mediated signaling. Author Affiliation: Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tips.2006.08.005 Byline: Alastair J. Barr, Stefan Knapp Abstract: Protein tyrosine phosphatases (PTPs) have key roles in a diverse range of cellular processes, and their dysregulation is associated with several human diseases. Many PTPs are recognized as potential drug targets; however, inhibitor development has focused only on a small number of enzymes, most notably PTP1B for type II diabetes and obesity, and MKP1 and CDC25 for cancer. The future challenge of selective-inhibitor development for PTPs will be significantly facilitated by the recent rapid progress in the structural biology of the 'PTPome'. In this article, we focus on the family of mitogen-activated protein kinase (MAPK)-specific tyrosine phosphatases - PTPN5 [also called striatal-enriched phosphatase (STEP)], PTPN7 (also called hematopoietic PTP) and PTPRR (also called PC12 PTP or STEP-like PTP) - and discuss approaches for achieving selectivity for the MAPK-PTPs at the molecular level using recently determined high-resolution X-ray crystal structures. We believe that the development of specific inhibitors would provide a valuable set of experimental pharmacological tools for investigating the physiological role of these phosphatases and exploring their emerging role in human disease. Author Affiliation: Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, OX3 7LD, UK

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.08.029 Byline: Sheng Ye (1), Yang Li (1), Liping Chen (1), Youxing Jiang (1) Abstract: MthK is a prokaryotic Ca.sup.2+-gated K.sup.+ channel that, like other ligand-gated channels, converts the chemical energy of ligand binding to the mechanical force of channel opening. The channel's eight ligand-binding domains, the RCK domains, form an octameric gating ring in which Ca.sup.2+ binding induces conformational changes that open the channel. Here we present the crystal structures of the MthK gating ring in closed and partially open states at 2.8 A, both obtained from the same crystal grown in the absence of Ca.sup.2+. Furthermore, our biochemical and electrophysiological analyses demonstrate that MthK is regulated by both Ca.sup.2+ and pH. Ca.sup.2+ regulates the channel by changing the equilibrium of the gating ring between closed and open states, while pH regulates channel gating by affecting gating-ring stability. Our findings, along with the previously determined open MthK structure, allow us to elucidate the ligand gating mechanism of RCK-regulated K.sup.+ channels. Author Affiliation: (1) Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA Article History: Received 16 February 2006; Revised 8 May 2006; Accepted 11 August 2006 Article Note: (miscellaneous) Published: September 21, 2006

We report data on the composition and crystal structure of the most K-rich (3.61 wt% [K.sub.2]O) natural clinopyroxene yet discovered. The studied crystal was found as a tiny inclusion in garnet from a garnet-clinopyroxene rock of the Kumdy-Kol microdiamond mine, Kokchetav complex, Northern Kazakhstan. Microprobe analysis yields the formula ([Ca.sub.0.61][Fe.sub.0.13] [Mg.sub.0.04][Mn.sub.0.01][K.sub.0.17][Na.sub.0.05]) (Al.sub.0.61][Mg.sub.0.39])([Si.sub.1.61][Al.sub.0.39])[O.sub.6.00]. Lattice parameters are: a = 9.773(1), b = 8.926(1), c = 5.269(1) [Angstrom], [beta] = 105.75(1)[degrees]. The structure was refined up to [R.sub.all] = 2.42% using 982 independent reflections. Substitution of K for Ca causes significant modification of the average structure. No evidence for an additional M2' position was found. Crystal-chemical characteristics are compared with published data on both natural and synthetic K-bearing clinopyroxenes.

Single-crystal X-ray diffraction data, collected from a sartorite crystal from Lengenbach (Binntal, Valais, Switzerland), yielded a ninefold superstructure: space group P[2.sub.1]/c; a = 37.71 (2), b = 7.898(3), c = 20.106(8)[Angstrom] [beta] = 101.993(7)[degrees]; [R.sub.1] = 6.08% for 6293 reflections with I > 2[[sigma].sub.I]. The sample is an [N.sub.1,2] = 3,3 sartorite homologue and the refined formula [Pb.sub.8][Tl.sub.1.5][As.sub.17.5][S.sub.35] compares very well with the empirical formula [Pb.sub.8.2][Tl.sub.1.4][As.sub.17.5][Sb.sub.0.5][S.sub.35] obtained from electron microprobe analyses. It has a high T1 content, up to 6.5 wt%. In a coupled substitution approximately 1.5 [Tl.sup.+]replace about 0.5 [As.sup.3+] and 1 PbS. The refined structure has 35 S atoms pfu instead of the expected 36 S (= 9 x 4 S, from Pb[As.sub.2][S.sub.4]). The incorporation of substantial amounts of [Tl.sup.+] into Pb[As.sub.2][S.sub.4]) is essential for the type and periodicity of superstructures in sartorite. The refined superstructure can be interpreted as a so-called 'lock-in' structure with a composition that yields a commensurate lattice for a mineral that usually has an incommensurate lattice. No commensurate periodicity could be found for a second crystal with about 0.5 Tl apfu.

Research has been conducted on the transhydrogenase domain I of Rhodospirillum rubrum transhydrogenase. The high-resolution structures of this domain have been determined with NADH bound and in the absence of NAD(H) and the single-crystal spectrophotometry has been used to determine NADH presence.

Research has been conducted on the dichloroferrous complexes. The crystal structures of these complexes investigated via the use of (super)1 H NMR and UV-visible spectroscopies and the complexes' conductivity which demonstrates that they remain neutral in solution are discussed.

Research has been conducted on the recombinant human fibrinogen fragment D. The crystal structures of this fibrinogen has been investigated in the presence and absence of peptide ligands and the details are reported.

Research has been conducted on the hypothetical protein YdcE from Escherichia coli. The crystal structure analysis of this protein demonstrate that it is a dimer and that it has structural diversity within the 4-oxalocrotonate tautomerase family.

Research has been conducted on the 1,2-dihydrodiazete ring system. The hypothesis that these compounds might be aromatic has been tested experimentally and computationally and their X-ray crystal structure and alkene-like reactivity are discussed.

Research has been conducted on the diisopropyl azodicarboxylate. The cycloaddition reaction of this compound with the cyclic phosphites carried out in producing pentacoordinate phosphoranes as crystalline solids is described.

Research has been conducted on the square-planar platinum(II) complexes. The results of the X-ray crystallographic analysis indicate that bis{1-(9-anthracene)}phosphiranedithioplatinum(II) complexes have different molecular and crystal structures.

Research has been conducted on dichlorogallane (HGaCl (sub)2) (sub)2. The preparation of this compound from gallium trichloride and triethylsilane and its crystal structure determined via single crystal X-ray diffraction are discussed.

Research has been conducted on the salts. Results indicate that the charge-transfer ethylenedithiotetrathiafulvalenoquinone-1,3-dithiolemethide charge-transfer salts containing FeBr (sub)4 (super)- and GaBr (sub)4 (super)- counteranions have been obtained as needle crystals with almost identical structures.

Research has been conducted on the vanadyl pyrophosphate' large transparent blue crystals. The study of their growth from a phosphorus pentoxide flux and of their single-crystal X-ray structure is presented.

Functional RNAs often form compact structures characterized by closely packed helices. Crystallographic analysis of several large RNAs revealed a prevalent interaction in which unpaired adenosine residues dock into the minor groove of a receptor helix. This A-minor motif, potentially the most important element responsible for global RNA architecture, has also been suggested to contribute to the fidelity of protein synthesis by discriminating against near-cognate tRNAs on the ribosome. The specificity of A-minor interactions is fundamental to RNA tertiary structure formation, as well as to their proposed role in translational accuracy. To investigate A-minor motif specificity, we analyzed mutations in an A-minor interaction within the Tetrahymena group I self-splicing intron. Thermodynamic and x-ray crystallographic results show that the A-minor interaction strongly prefers canonical base pairs over base mismatches in the receptor helix, enabling RNA interhelical packing through specific recognition of Watson-Crick minor groove geometry.

Research has been conducted on the vanadium(IV) silicate. The synthesis of this compound has been carried out via the use of high-pressure, high-temperature hydrothermal method and the results indicate that this compound's structure is different from those of the synthetic silicate and of the natural mineral polymorphs.

Research has been conducted on the ClO (sub)2 Au(ClO (sub)4) (sub)4. The crystal structure of this complex has been determined via the use of the Rietveld analysis of powder X-ray diffraction data and the details are reported.

Research has been conducted on the Me (sub)2 GeCl (sub)2. The molecular structure of this compound and its C-Ge-C angle have been investigated via the use of ab initio quantum calculations in studying the molecule's deviation from geometry in the gas phase and in the crystalline state and the details are reported.

Research has been conducted on the metastable binary compound with the skutterudite crystal structure. The synthesis of this compound from the modulated elemental reactants carried out via amorphous intermediate is described.

Research has been conducted on Bacillus stearothermophilus D-hydantoinase. The apo-crystal structure of this enzyme has been investigated in providing the insight into the stereochemistry of the hydrolysis enantioselectivity and the details are reported.

Research has been conducted on the hydrogen-bonded one-dimensional supramolecular array and a 3D network with a large tunnel. Results indicate the coordination of the crown ether moieties with the metal ions in both complexes.

Research has been conducted on the paramagnetic pyridine derivatives. The structural and magnetic analyses of these compounds have been carried out and the results indicate that the lattice rearrangement temperature dependence can be affected by the evolution of magnetic properties.

Research has been conducted on the fullerene complexes. The preparation of fullerene mixed crystals with Co and Zn tetraarylporphyrins carried out in the presence of ferrocene is described.

The reproducible degradation of thin polymer films in the presence of an analyte or a reaction product of an analyte has potential applications in the development of highly sensitive, disposable biosensors. In this study, a novel combination of quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS) has been developed to monitor the degradation of thin polymer films. Unlike a conventional QCM, the instrument described here allows rapid in situ measurement of quartz crystal impedance spectra. Simultaneously, classical electrochemical impedance spectra are measured in situ, affording the polymer film capacitance and bulk resistance. The combination of QCM impedance and classical EIS provides a wealth of information about the process of degradation of thin polymer films such as mass variation, swelling, delamination, viscoelasticity, and pore formation. Three different systems have been analyzed with this experimental setup; in two of the systems, polymer degradation was promoted by hydrolytic enzymes, and in the third one by a pH change. The results obtained show that the degradation of these three systems follows very different mechanisms. It is also underlined how the complementary information obtained by the two techniques allows a detailed description of the dissolution process.

Research has been conducted on the helical segment 8 of rhodopsin. The structural properties of of this helical segment and their effect on rhodopsin functions have been investigated and are discussed.

Research has been conducted on the hydrogen bonds. The features common to all hydrogen bonds termed hydrogen bridges in this article for their ability to interact without borders are discussed..

Research has been conducted on the blue ultramarine pigments. The results of the quantitative study of these pigments carried out in determining the S (sub)3 (super)- chromophore concentration are discussed.

Research has been conducted on the acetone and ketodiester alpha-cleavage and decarbonylation reactions. The thermochemical analysis of these reactions has been carried out via the use of the density functional method and the radical-stabilizing abilities of the ketone substituents have been investigated.

Research has been conducted on the diol synthesis. Results indicate that their X-ray crystal structures have been determined and the role of the crystal engineering in the hydroxy group hydrogen bonding has been investigated.

Research has been conducted on the mixed alkali oxo sulfato vanadium(V) compound. The X-ray analysis of this compound has been carried our and the results are presented.

Research has been conducted on the N-methyliminobis(methylenephosphonic acid). The reaction of this compound with divalent metal acetates has been carried out under different conditions and the results indicate that it has produced metal diphosphonates with different structures.

Research has been conducted on the divalent metal complexes with the N-(phosphonomethyl)iminodiacetic acid. The synthesis and structural characterization of these complexes have been performed and the details are reported.