Structure (v.17, #9)

In This Issue (ix-x).

The Piston Rises Again by Joseph J. Falke; Annette H. Erbse (1149-1151).
Previous evidence has indicated that the transmembrane signal in bacterial chemoeceptors is carried by the piston displacement of a membrane-spanning signaling helix. Hendrickson and coworkers (Cheung and Hendrickson, 2009; Moore and Hendrickson, 2009) now provide structural evidence that suggests piston transmembrane signaling is widely conserved in bacterial receptors that control ubiquitous two-component signaling pathways.

Polyglutamine Dances the Conformational Cha-Cha-Cha by Jason Miller; Earl Rutenber; Paul J. Muchowski (1151-1153).
While polyglutamine repeats appear in dozens of human proteins, high-resolution structural analysis of these repeats in their native context has eluded researchers. Kim et al. now describe multiple crystal structures and demonstrate that polyglutamine in huntingtin dances through multiple conformations.

Keeping an Eye on Membrane Transport by TR-WAXS by Jeff Abramson; Vincent Chaptal (1153-1155).
In this issue of Structure, Andersson et al. apply time-resolved wide angle X-ray scattering (TR-WAXS) to follow light-induced conformational changes for both bacteriorhodopsin and proteorhodopsin and probe real-time dynamics at atomic resolution.

The Nuclear Pore Complex Has Entered the Atomic Age by Stephen G. Brohawn; James R. Partridge; James R.R. Whittle; Thomas U. Schwartz (1156-1168).
Nuclear pore complexes (NPCs) perforate the nuclear envelope and represent the exclusive passageway into and out of the nucleus of the eukaryotic cell. Apart from their essential transport function, components of the NPC have important, direct roles in nuclear organization and in gene regulation. Because of its central role in cell biology, it is of considerable interest to determine the NPC structure at atomic resolution. The complexity of these large, 40–60 MDa protein assemblies has for decades limited such structural studies. More recently, exploiting the intrinsic modularity of the NPC, structural biologists are making progress toward understanding this nanomachine in molecular detail. Structures of building blocks of the stable, architectural scaffold of the NPC have been solved, and distinct models for their assembly proposed. Here we review the status of the field and lay out the challenges and the next steps toward a full understanding of the NPC at atomic resolution.

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings by Malene Ringkjøbing Jensen; Phineus R.L. Markwick; Sebastian Meier; Christian Griesinger; Markus Zweckstetter; Stephan Grzesiek; Pau Bernadó; Martin Blackledge (1169-1185).
Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.
Keywords: PROTEINS;

The Orientation of a Tandem POTRA Domain Pair, of the Beta-Barrel Assembly Protein BamA, Determined by PELDOR Spectroscopy by R. Ward; M. Zoltner; L. Beer; H. El Mkami; I.R. Henderson; T. Palmer; D.G. Norman (1187-1194).
The outer membrane β-barrel trans-membrane proteins in gram-negative bacteria are folded into the membrane with the aid of polypeptide transport-associated (POTRA) domains. These domains occur, and probably function, as a tandem array situated on the periplasmic side of the outer membrane. Two crystal structures and one NMR study have attempted to define the structure and articulation of the POTRA domains of the Escherichia coli, prototypic Omp85 protein BamA. We have used pulsed electron paramagnetic resonance (EPR) to determine the distance and distance distribution between (1-Oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate spin labels (MTSSL), placed across the domain interface of the first two POTRA domains of BamA. Our results show tightly defined interdomain distance distributions that indicate a well-defined domain orientation. Examination of the known structures revealed that none of them fitted the EPR data. A combination of EPR and NMR data was used to generate converged structures with defined domain-domain orientation.
Keywords: PROTEINS;

Histidine kinase receptors respond to diverse signals and mediate signal transduction across the plasma membrane in all prokaryotes and certain eukaryotes. Each receptor is part of a two-component system that regulates a particular cellular process. Organisms that use trimethylamine-N-oxide (TMAO) as a terminal electron acceptor typically control their anaerobic respiration through the TMAO reductase (Tor) pathway, which the TorS histidine kinase activates when sensing TMAO in the environment. We have determined crystal structures for the periplasmic sensor domains of TorS receptors from Escherichia coli and Vibrio parahaemolyticus. TorS sensor domains have a novel fold consisting of a membrane-proximal right-handed four-helical bundle and a membrane-distal left-handed four-helical bundle, but conformational dispositions differ significantly in the two structures. Isolated TorS sensor domains dimerize in solution; and from comparisons with dimeric NarX and Tar sensors, we postulate that signaling through TorS dimers involves a piston-type displacement between helices.

Secondary Structure of Huntingtin Amino-Terminal Region by Mee Whi Kim; Yogarany Chelliah; Sang Woo Kim; Zbyszek Otwinowski; Ilya Bezprozvanny (1205-1212).
Huntington's disease is a genetic neurodegenerative disorder resulting from polyglutamine (polyQ) expansion (>36Q) within the first exon of Huntingtin (Htt) protein. We applied X-ray crystallography to determine the secondary structure of the first exon (EX1) of Htt17Q. The structure of Htt17Q-EX1 consists of an amino-terminal α helix, poly17Q region, and polyproline helix formed by the proline-rich region. The poly17Q region adopts multiple conformations in the structure, including α helix, random coil, and extended loop. The conformation of the poly17Q region is influenced by the conformation of neighboring protein regions, demonstrating the importance of the native protein context. We propose that the conformational flexibility of the polyQ region observed in our structure is a common characteristic of many amyloidogenic proteins. We further propose that the pathogenic polyQ expansion in the Htt protein increases the length of the random coil, which promotes aggregation and facilitates abnormal interactions with other proteins in cells.

Insights into How Nucleotide-Binding Domains Power ABC Transport by Simon Newstead; Philip W. Fowler; Paul Bilton; Elisabeth P. Carpenter; Peter J. Sadler; Dominic J. Campopiano; Mark S.P. Sansom; So Iwata (1213-1222).
The mechanism by which nucleotide-binding domains (NBDs) of ABC transporters power the transport of substrates across cell membranes is currently unclear. Here we report the crystal structure of an NBD, FbpC, from the Neisseria gonorrhoeae ferric iron uptake transporter with an unusual and substantial domain swap in the C-terminal regulatory domain. This entanglement suggests that FbpC is unable to open to the same extent as the homologous protein MalK. Using molecular dynamics we demonstrate that this is not the case: both NBDs open rapidly once ATP is removed. We conclude from this result that the closed structures of FbpC and MalK have higher free energies than their respective open states. This result has important implications for our understanding of the mechanism of power generation in ABC transporters, because the unwinding of this free energy ensures that the opening of these two NBDs is also powered.

Probing the Accessibility of the Mn4Ca Cluster in Photosystem II: Channels Calculation, Noble Gas Derivatization, and Cocrystallization with DMSO by Azat Gabdulkhakov; Albert Guskov; Matthias Broser; Jan Kern; Frank Müh; Wolfram Saenger; Athina Zouni (1223-1234).
Using the 2.9 Å resolution structure of the membrane-intrinsic protein-cofactor complex photosystem II (PSII) from the cyanobacterium Thermosynechococcus elongatus, we calculated and characterized nine possible substrate/product channels leading to/away from the Mn4Ca cluster, where water is oxidized to dioxygen, protons, and electrons. Five narrow channels could function in proton transport, assuming that no large structural changes are associated with water oxidation. Four wider channels could serve to supply water to or remove oxygen from the Mn4Ca cluster. One of them might be regulated by conformational changes of Lys134 in subunit PsbU. Data analyses of Kr derivatized crystals and complexes with dimethyl sulfoxide (DMSO) confirm the accessibility of the proposed dioxygen channels to other molecules. Results from Xe derivatization suggest that the lipid clusters within PSII could serve as a drain for oxygen because of their predominant hydrophobic character and mediate dioxygen release from the lumen.
Keywords: PROTEINS;

Subunit Architecture of Multiprotein Assemblies Determined Using Restraints from Gas-Phase Measurements by Tara L. Pukala; Brandon T. Ruotolo; Min Zhou; Argyris Politis; Raluca Stefanescu; Julie A. Leary; Carol V. Robinson (1235-1243).
Protein interaction networks are becoming an increasingly important area of research within structural genomics. Here we present an ion mobility-mass spectrometry approach capable of distinguishing the overall subunit architecture of protein complexes. The approach relies on the simultaneous measurement in the gas phase of the mass and size of intact assemblies and subcomplexes. These data are then used as restraints to generate topological models of protein complexes. To test and develop our method, we have chosen two well-characterized homo-dodecameric protein complexes: ornithine carbamoyl transferase and glutamine synthetase. By forming subcomplexes related to the comparative strength of the subunit interfaces, acquiring ion mobility data, and subsequent modeling, we show that these “building blocks” retain their native interactions and do not undergo major rearrangement in either solution or gas phases. We apply this approach to study two subcomplexes of the human eukaryotic initiation factor 3, for which there is no high-resolution structure.
Keywords: PROTEINS;

Probing the “Dark Matter” of Protein Fold Space by William R. Taylor; Vijayalakshmi Chelliah; Siv Midtun Hollup; James T. MacDonald; Inge Jonassen (1244-1252).
We used a protein structure prediction method to generate a variety of folds as α-carbon models with realistic secondary structures and good hydrophobic packing. The prediction method used only idealized constructs that are not based on known protein structures or fragments of them, producing an unbiased distribution. Model and native fold comparison used a topology-based method as superposition can only be relied on in similar structures. When all the models were compared to a nonredundant set of all known structures, only one-in-ten were found to have a match. This large excess of novel folds was associated with each protein probe and if true in general, implies that the space of possible folds is larger than the space of realized folds, in much the same way that sequence-space is larger than fold-space. The large excess of novel folds exhibited no unusual properties and has been likened to cosmological dark matter.
Keywords: PROTEINS;

Structural Polymorphism of the ParM Filament and Dynamic Instability by Vitold E. Galkin; Albina Orlova; Chris Rivera; R. Dyche Mullins; Edward H. Egelman (1253-1264).
Segregation of the R1 plasmid in bacteria relies on ParM, an actin homolog that segregates plasmids by switching between cycles of polymerization and depolymerization. We find similar polymerization kinetics and stability in the presence of either ATP or GTP and a 10-fold affinity preference for ATP over GTP. We used electron cryo-microscopy to evaluate the heterogeneity within ParM filaments. In addition to variable twist, ParM has variable axial rise, and both parameters are coupled. Subunits in the same ParM filaments can exist in two different structural states, with the nucleotide-binding cleft closed or open, and the bound nucleotide biases the distribution of states. The interface between protomers is different between these states, and in neither state is it similar to F-actin. Our results suggest that the closed state of the cleft is required but not sufficient for ParM polymerization, and provide a structural basis for the dynamic instability of ParM filaments.

Structural Dynamics of Light-Driven Proton Pumps by Magnus Andersson; Erik Malmerberg; Sebastian Westenhoff; Gergely Katona; Marco Cammarata; Annemarie B. Wöhri; Linda C. Johansson; Friederike Ewald; Mattias Eklund; Michael Wulff; Jan Davidsson; Richard Neutze (1265-1275).
Bacteriorhodopsin and proteorhodopsin are simple heptahelical proton pumps containing a retinal chromophore covalently bound to helix G via a protonated Schiff base. Following the absorption of a photon, all-trans retinal is isomerized to a 13-cis conformation, initiating a sequence of conformational changes driving vectorial proton transport. In this study we apply time-resolved wide-angle X-ray scattering to visualize in real time the helical motions associated with proton pumping by bacteriorhodopsin and proteorhodopsin. Our results establish that three conformational states are required to describe their photocycles. Significant motions of the cytoplasmic half of helix F and the extracellular half of helix C are observed prior to the primary proton transfer event, which increase in amplitude following proton transfer. These results both simplify the structural description to emerge from intermediate trapping studies of bacteriorhodopsin and reveal shared dynamical principles for proton pumping.