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Vārānasi, India

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Using structures determined for bacterial complex I (refs 7, 8, 9) as a starting point, structures of the 14 highly conserved core subunits and their nine cofactors (a flavin mononucleotide (FMN) and eight iron–sulfur (FeS) clusters) have been determined to medium resolution in complex I from both mammals (for Bos taurus)10 and yeast (Yarrowia lipolytica)11. The arrangement and structures of the 31 supernumerary subunits (constituting half the mammalian complex) are, however, far less well defined. The 5-Å resolution electron cryomicroscopy (cryoEM) structure of B. taurus complex I revealed the supernumerary ensemble wrapped around the core, with 14 supernumerary subunits assigned10. Subsequently, eight further assignments were proposed using the crystallographic structure of subcomplex Iβ (part of the membrane domain)12. Therefore, nine subunits remain unlocated and models for the supernumerary subunits are fragmentary. The complete structure of mammalian complex I is crucial for elucidating the roles of the supernumerary subunits in complex I function and dysfunction. Here, we describe a cryoEM map for B. taurus complex I with an overall resolution of 4.16 Å (Fig. 1a and Extended Data Fig. 1), which enabled modelling of all its 45 subunits and 93% of its 8,515 residues (Extended Data Tables 1, 2). Computational sorting of the particles revealed three major classes, with overall resolutions 4.27 Å (class 1), 4.35 Å (class 2) and 5.60 Å (class 3) (Extended Data Fig. 2), for which the quality of the map in several regions was improved substantially. The different classes represent different states of the complex and analysis of each provides new insights into the mechanism of complex I catalysis. Extended Data Figures 3 and 4 present example densities and we use the class 2 map and model to describe the structure, unless indicated otherwise. Figure 1 presents the structures and locations of all 31 supernumerary subunits in mammalian complex I (see Extended Data Table 3 for subunit–subunit interactions and additional details). The supernumerary subunits are central to the structure, stability and assembly of the complex, and some also have regulatory or independent metabolic roles. The 18 supernumerary transmembrane helices (TMHs) (Fig. 1b) establish a cage around the core membrane domain. Three TMH-containing subunits, B9 (NDUFA3 in the nomenclature for human complex I), B16.6 (NDUFA13) and MWFE (NDUFA1), interact extensively with PGIV (NDUFA8) on the intermembrane-space (IMS) face, enclosing core subunit ND1. Subunit B14.5b (NDUFC2), bound to ND2, contains two different-length TMHs and attaches KFYI (NDUFC1) to the complex. Three TMHs that interact with ND4 are assigned to MNLL (NDUFB1), ESSS (NDUFB11) and SGDH (NDUFB8). Four TMHs, assigned to B17 (NDUFB6), AGGG (NDUFB2), B12 (NDUFB3) and ASHI (NDUFB8), are bound to ND5. The TMHs of ASHI and B15 (NDUFB4, on the side of ND4) cross the ND5 transverse helix, and the four TMHs of B14.7 (NDUFA11) appear to support ND5-TMH16 in anchoring it against ND2. Four subunits confined to the IMS (PGIV, the 15 kDa subunit (NDUFS5), PDSW (NDUFB10) and B18 (NDUFB7)) form a helix latticework (together with SGDH and B16.6) on the IMS face (Fig. 2a). PGIV, the 15 kDa subunit and B18 contain CHCH domains (pairs of helices linked by two disulfide bonds)13 and are canonical substrates for the Mia40 oxidative-folding pathway14; PDSW probably contains two further disulfide bonds. These disulfide bonds form during complex I biogenesis and are probably important for enzyme stability. Thus, the supernumerary cage has evolved to become integral to the structure and stability of the membrane domain. Subunits B14 (NDUFA6) and SDAP-α (NDUFAB1), and B22 (NDUFB9) and SDAP-β (NDUFAB1), constitute matching subdomains on the hydrophilic domain and matrix face of the membrane domain, respectively10, 12, 15 (Fig. 1). SDAP-α and SDAP-β are identical to the mitochondrial acyl-carrier protein (ACP) and exhibit densities consistent with the pantetheine-4’-phosphate group that covalently attaches an acyl chain to Ser44 (refs 16, 17) (Extended Data Fig. 4e). Their ACP recognition helices interact with arginine- and lysine-rich helices in the LYR proteins B14 and B22 (Fig. 2b and Extended Data Fig. 4e) as canonical ACPs interact with the enzymes of fatty-acid biosynthesis18. The 42 kDa subunit (NDUFA10, Fig. 2c) contains a central α/β nucleoside kinase fold with a parallel five-strand β-sheet, plus three extensions that dock it to the matrix face of ND2. Although the active site is accessible and the key nucleoside kinase residues are present19, no activity has been reported. The 39 kDa subunit (NDUFA9, Fig. 2d) is attached to core subunits PSST (NDUFS7) and the 30 kDa subunit (NDUFS3) in the hydrophilic arm. The N-terminal domain of the 39 kDa subunit comprises an α/β short-chain dehydrogenase/reductase fold20 containing an NAD(P)-binding Rossmann fold with a parallel seven-strand β-sheet and density for a bound nucleotide, modelled as NADPH21 (Extended Data Fig. 4). The separate C-terminal domain interacts with the long matrix loop between TMHs 1 and 2 of ND3. The final seven supernumerary subunits adorn the hydrophilic domain (Fig. 1c). Thioredoxin-like B8 (NDUFA2) is attached to the 75 kDa subunit (NDUFS1), and the three-helix bundle of B13 (NDUFA5) to the 30 kDa subunit. The remaining five subunits are located at interfaces. The zinc-binding domain of the 13 kDa subunit (NDUFS6)22 and the four-strand β-sheet and helix of the 18 kDa subunit (NDUFS4) are located where the NADH dehydrogenase domain meets the rest of the complex. All five subunits (the other three are B14.5a (NDUFA7), B17.2 (NDUFA12) and the 10 kDa subunit (NDUFV3)) contain long loops running over the domain surface. A notable example is the extensive loop in B14.5a, which arches up along the TYKY–49 kDa subunit (NDUFS8–NDUFS2) interface, across the 49 kDa subunit, along its interface with the 75 kDa subunit and onto the 30 kDa subunit. The role of the supernumerary subunits in stabilizing interfaces in the hydrophilic domain contrasts sharply with their arrangement into a rigid cage to stabilize the membrane domain. The structures of the mammalian core subunits (Fig. 3a) closely match those of the bacterial subunits7, 8, 9, and contain corresponding mechanistically relevant features. NADH is oxidized by a flavin mononucleotide in the 51 kDa subunit (NDUFV1) (Extended Data Fig. 3c). Electrons then transfer along a chain of FeS clusters to the terminal cluster (N2) and to ubiquinone-10. In mammalian complex I, an unusual dimethylated arginine (Arg85 of the 49 kDa subunit)23 close to N2 probably contributes to its relatively high reduction potential24. In the hydrophilic domain, the large domain of the mammalian 75 kDa subunit differs from that of Thermus thermophilus7 as its fourth sub-domain contains just two short helices separated by a loop of around 30 residues. The core subunit N- and C-terminal extensions also vary between species; in B. taurus the C terminus of the 30 kDa subunit (which loops into a cleft between PSST, the 39 kDa subunit and B14) and the N terminus of TYKY (which wraps around the hydrophilic/hydrophobic domain interface) recapitulate the stabilizing role of the supernumerary subunits. Notably, our cryoEM maps reveal that the 49 kDa subunit N terminus forms a long loop on the surface of the membrane domain (Fig. 3a). This extended conformation explains its susceptibility to proteases25, but it is unlikely to be central to the mechanism because it is not conserved in T. thermophilus, and in Escherichia coli is fused to the C terminus of the 30 kDa subunit. The long matrix loop in ND3, which lies across the front of the hydrophilic domain and is central to the transition between active and de-active states in mammalian complex I (ref. 3), is also resolved (Fig. 3a). Four proton-transfer routes (in ND2, ND4, ND5 (ref. 8), and ND1 + ND4L + ND6 (ref. 9)) have been proposed for the four protons that complex I is generally considered to translocate for each NADH molecule oxidized. ND2, ND4 and ND5 each contain two TMHs interrupted by loops in the central membrane plane (TMH4 and TMH9 in ND2; TMH7 and TMH12 in ND4 and ND5, Fig. 3a and Extended Data Fig. 3). The chain of conserved aspartate, glutamate, lysine and histidine residues that runs along the middle of the membrane domain is now well defined in the mammalian enzyme (Glu143 of ND1, Asp66 and Glu68 of ND3; Glu34 and Glu70 of ND4L; Glu34, Lys105, Lys135 and Lys263 of ND2; Glu123, Lys206, Lys237 and Glu378 of ND4; Glu145, Lys223, His248 and Lys392 of ND5, Fig. 3a). Distortions of the helical structure are observed in TMH3 of ND6, TMH5 of ND2, TMH8 of ND4 and TMH8 of ND5 (Extended Data Fig. 3). These distortions resemble the π–bulge in bacteriorhodopsin but do not satisfy its technical definition26, perhaps owing to the intermediate resolution of the maps. The distortions are centred on glycine pairs in ND6 (62–3) and ND4 (239–40), on a serine pair in ND5 (249–50), and on Trp167 (flanked by two glycine pairs) in ND2. Notably, TMH3 of ND6 is more distorted in the mammalian structure than in T. thermophilus (which contains only one glycine residue)9, such that Phe67 of ND6 is displaced around the helical axis. Ubiquinone-10 binds with its redox-active headgroup close to cluster N2, at the top of a cleft between the 49 kDa subunit and PSST7, 27 (Fig. 3b), while T. thermophilus complex I co-crystallized with decylubiquinone showed it forms hydrogen bonds with His59 and Tyr108 of the 49 kDa subunit9. Here, the side chains of Tyr108 and His59 are poorly resolved, and the conformation of the β1–β2 His59-containing loop is different to that in T. thermophilus (Fig. 3d). It therefore appears that the structural elements that form the binding site are flexible, allowing it to organize around substrates and inhibitors (neither of which are present here). The putative ubiquinone-access channel, identified first in T. thermophilus9, connects the cleft to an entrance in ND1 (between TMH1, an amphipathic helix, and TMH6) and can also be detected here (minimum diameter, 2.9 Å). Alternative entrances, between TMH1 and TMH7, and TMH5 and TMH6 of ND1, are also evident but narrower (minimum diameters, 1.9−2.2 Å). However, the planar ubiquinone ring is approximately 6 Å across, so all the channels in the static structure would have to open to allow it to enter. A structure containing ubiquinone-10 (or a long-chain analogue) is therefore required to confirm its access pathway. In the mammalian complex, further consideration of the most plausible channel (that is, the widest) for ubiquinone reveals a ‘bottleneck’ at the base of the cleft (Fig. 3c). Ubiquinone-10 is highly hydrophobic so most of the channel-lining residues are uncharged and hydrophobic. In contrast, the bottleneck is formed by charged and polar residues including Glu24 and Arg25 (TMH1 of ND1), Arg274 (TMH7 of ND1), and Arg71 and hydroxy-Arg77 (ref. 23) (α2–β2 loop of PSST). Nearby, the TMH5–6 loop of ND1, with many acidic residues, contributes more notably to channel formation in T. thermophilus and Y. lipolytica9, 11. This cluster of charged residues suggests the presence of water molecules and appears to be incompatible with a ubiquinone-10 binding channel. However, the PSST loop was modelled incompletely in T. thermophilus and Y. lipolytica, and the ND1 loop is poorly resolved here, indicating their flexibility. It is possible that conformational changes at the bottleneck, linked to ubiquinone binding and dissociation, contribute to coupling of the redox reaction to proton translocation. When the particles comprising the whole data set were subjected to 3D classification, three major, slightly different classes emerged. Class 3, the smallest, lowest resolution class, is closer to class 1 than class 2 in structure and is characterized by movement of the ND4–ND5 subdomain (relative to class 1, Extended Data Fig. 5 and Extended Data Table 4) and disorder in the ND5 transverse helix and its anchor (TMH16 of ND5). Similar disorder was observed in subcomplex Iβ (ref. 12), which comprises the ND4–ND5 subdomain. We therefore suggest that class 3 is a state in which molecules are in the first stages of dissociation and do not discuss it further. Classes 1 and 2 are related (Fig. 4a) by opposing rotations of the hydrophilic domain and a large section of the membrane domain, relative to the ND1 subdomain (Extended Data Table 4). In class 1, the 42 kDa subunit has moved towards B14 and SDAPα (Fig. 4b), and the 39 kDa subunit has moved relative to ND1. Notably, the long TMH1–2 loop of ND3 is partially disordered (Fig. 4d). This loop is symptomatic of decreased order in class 1 at the hydrophilic-membrane domain junction; the TMH5–6 loop of ND1, the β1–β2 loop of the 49 kDa subunit containing His59, and parts of the C-terminal domain of the 39 kDa subunit are also disordered (Fig. 4c). In addition, the distortion in TMH3 of ND6 is less pronounced in class 1 than class 2. Mammalian complex I exists in different states according to its catalytic status. In the absence of substrates to sustain turnover (such as during hypoxia) it converts spontaneously to its ‘de-active’ state4, a profound resting state that requires slow, reactivating turnovers to regain ‘active’ status. The de-active state is characterized by the ability of cysteine-modifying reagents (such as N-ethylmaleimide) to derivatize Cys39 in the ND3 TMH1–2 loop3. Approximately half the preparation discussed here is susceptible to modification by N-ethylmaleimide. In class 2, the side chain of Cys39 of ND3 is inaccessible to modifying reagents, suggesting class 2 represents an active state of the complex. By contrast, the disordered loop in class 1 (Fig. 4d) is probably mobile and accessible, suggesting class 1 represents a de-active state. Increased disorder in the C-terminal domain of the 39 kDa subunit, and its altered position relative to ND1, support this assignment because both subunits are more exposed to lysine-modifying reagents in the de-active state28. However, the structures of biochemically defined samples are required to confirm these assignments. Different conformations of the ND1 TMH5–6 loop and the β1–β2 loop of the 49 kDa subunit in Y. lipolytica (relative to that in T. thermophilus) were proposed previously as characteristic of the de-active state11, but they vary between our class 2 conformation and that of T. thermophilus (Fig. 3d), and are disordered in class 1. Notably, Y. lipolytica complex I was co-crystallized with a quinazoline inhibitor (Fig. 3d), and cross-linking studies have shown quinazolines interact with sections of the 49 kDa subunit and ND1 that contain the β1–β2 and TMH5–6 loops25. We propose quinazoline binding orders these loops, and the quinazoline-binding site overlaps with (but does not superimpose on) the ubiquinone-binding site. Our interpretation supports biochemical proposals for non-identical but overlapping sites for the myriad inhibitors of ubiquinone reduction29, but does not support an alternative, occluded ubiquinone-binding site in the de-active complex11. The two states of mammalian complex I described support the idea that dynamic, flexible regions at the hydrophilic–membrane domain interface are important for coupling ubiquinone reduction to proton translocation. The class-1-disordered loops in ND1, ND3 and the 49 kDa subunit all contribute to the ubiquinone-binding site (Fig. 4c). Therefore, we attribute lack of catalytic activity in the de-active state to reversible disruption of this site, which can be recovered when the ubiquinone-binding site in the NADH-reduced enzyme reforms around its substrate. During catalysis, the ND3 loop, which originates in the membrane and interacts extensively with the hydrophilic domain, may restrict conformational changes at the domain interface. Changes in the conformation of the loop of the 49 kDa subunit may trigger proton translocation: molecular simulations were used to outline a mechanism in which the ubiquinol dianion deprotonates Tyr108 and His59, breaking a His59–Asp160 hydrogen bond and displacing Asp160 towards the membrane30. In ND1, TMH2–6 replicate the antiporter-like half-channel motif of ND2, ND4 and ND5 (ref. 9). TMH5 resembles a discontinuous TMH, but with its half helix on the matrix side unstructured and continuous with the TMH5–6 loop at the base of the ubiquinone-binding cleft (Fig. 3d). Like α2–β2 in PSST (Fig. 3c), this loop may change conformation upon ubiquinone binding. Furthermore, the loop carries many conserved acidic residues that may collect protons for Glu143 of ND1 (ref. 9). In turn, Glu143 is connected to the chain of charged residues along the membrane domain by Asp66 of ND3 and the dynamic distortion in TMH3 of ND6 (Fig. 3a). Thus, a cascade of events originating from the ubiquinone-binding cleft may couple ubiquinone reduction and protonation to proton translocation. Although all such mechanisms for complex I are currently hypothetical, cryoEM now provides a powerful tool to study individual trapped conformations or separate mixed states computationally in order to determine how conformational changes are initiated, coordinated and propagated.

News Article | August 31, 2016
Site: http://www.rdmag.com/rss-feeds/all/rss.xml/all

U.S. regulators on Tuesday approved the first lower-cost version of Enbrel, a blockbuster anti-inflammatory drug from Amgen that is among the top-selling drugs in the world. The Food and Drug Administration cleared the near-copy of the drug, dubbed Erelzi, developed by Swiss drug giant Novartis, which would not disclose the planned list price for the drug. A month's supply of Enbrel costs roughly $4,000 or more in the U.S., according to figures from GoodRx, a drug pricing website. Enbrel was the fourth best-selling prescription drug in the world for 2015, according to health data firm IMS Health. The FDA approved Novartis' drug for the same diseases listed on Enbrel's label, including rheumatoid arthritis, psoriasis and other immune system disorders. The announcement marks the third FDA approval of a so-called biosimilar drug, the industry term for generic biotech medicines, used to indicate they are not exact copies of the original products. Already available in Europe, the drugs have the potential to generate billions in savings for insurers, doctors and patients. But savings from Enbrel could be delayed for years due to an ongoing legal dispute over the drug, according to analyst reports. Under a court order dated Aug. 11, Amgen Inc. and Sandoz, a unit of Novartis, agreed to a preliminary injunction blocking the launch of Erelzi. Both companies refused to discuss how long that injunction will last. Morgan Stanley analyst Matthew Harrison said the agreement indicates that a trial would not begin until April 2018. Under that timeline, a near-term launch of lower-cost Enbrel "is off the table," he states in a recent note to investors. Erelzi is Novartis' second competitor to an Amgen drug. Last March Novartis won approval for a biosimilar version of Amgen's drug Neupogen — the first biosimilar approved in the U.S. Pfizer won approval to market a second biosimilar in April, a version of Johnson & Johnson's Remicade. Enbrel was Amgen's top-selling drug last year with $5.1 billion in U.S. sales and $5.4 billion worldwide. The injectable medicine was first approved in 1998, part of a class of multi-billion dollar drugs that reduce inflammation and help control the immune system. The class also includes Remicade and AbbVie's Humira, which is also facing potential competition from biologic versions in development. Biotech drugs are powerful, injected medicines produced in living cells that are typically much more expensive than traditional, chemical-based drugs. In 2015, six of the 10 top-selling medicines globally were biotech drugs, with more than $56 billion in combined sales. Content Item Type: NewsSummary:  U.S. regulators approved the first lower-cost version of a blockbuster anti-inflammatory drug from Amgen that is among the top-selling drugs in the world. Featured Image: Contributed Author: By Linda A. Johnson & Matthew Perrone, AP Health Writers, Associated PressTopics: Drug DevelopmentMeta Keywords: Enbrel, drug giant Novartis, lower-cost Enbrel, blockbuster anti-inflammatory drug, best-selling prescription drug, drug pricing website, so-called biosimilar drug, generic biotech medicines, multi-billion dollar drugs, planned list price, top-selling drugs, Amgen drug, biotech drugs, data firm IMS, Amgen Inc., Morgan Stanley analyst, ongoing legal dispute, top-selling drug, top-selling medicines, lower-cost version, Drug Administration, chemical-based drugs, drug Neupogen, FDA approval, U.S. regulators, preliminary injunction, injected medicines, immune system disorders, rheumatoid arthritis, near-term launch, analyst reports, industry term, original products, U.S. Pfizer, exact copies, court order, biosimilar version, injectable medicine, biologic versions, U.S. sales, recent note, Matthew Harrison, potential competition, Erelzi, Remicade, world, savings, health, Johnson, classExclusive: 

Aras R.,IMS | Dutech A.,French Institute for Research in Computer Science and Automation
Journal of Artificial Intelligence Research | Year: 2010

Decentralized planning in uncertain environments is a complex task generally dealt with by using a decision-theoretic approach, mainly through the framework of Decentralized Partially Observable Markov Decision Processes (DEC-POMDPs). Although DEC-POMDPS are a general and powerful modeling tool, solving them is a task with an overwhelming complexity that can be doubly exponential. In this paper, we study an alternate formulation of DEC-POMDPs relying on a sequence-form representation of policies. From this formulation, we show how to derive Mixed Integer Linear Programming (MILP) problems that, once solved, give exact optimal solutions to the DEC-POMDPs. We show that these MILPs can be derived either by using some combinatorial characteristics of the optimal solutions of the DEC-POMDPs or by using concepts borrowed from game theory. Through an experimental validation on classical test problems from the DEC-POMDP literature, we compare our approach to existing algorithms. Results show that mathematical programming outperforms dynamic programming but is less efficient than forward search, except for some particular problems. The main contributions of this work are the use of mathematical programming for DECPOMDPs and a better understanding of DEC-POMDPs and of their solutions. Besides, we argue that our alternate representation of DEC-POMDPs could be helpful for designing novel algorithms looking for approximate solutions to DEC-POMDPs. © 2010 AI Access Foundation. All rights reserved. Source

Agarwal A.,IMS
Indian Journal of Anaesthesia | Year: 2012

There was an era when bark of mandrake plant, boiled in wine was used to administer anesthesia. Ether, after reigning the kingdom of anaesthesiology for more than a century, came to be superseded by newer and newer agents. Anaesthesiology has witnessed tremendous developments since infancy. The introduction of advanced airway adjuncts, labour analgesia, patient controlled analgesia, fbreoptics, Bispectral Index monitors, workstations, simulators and robotic surgeries are only to name a further few. Anaesthesia for robotic surgery received much impetus and is still a dream to come true in many countries. But then, the rapid spin in technology and fast sophistication of medical feld has even surpassed this. The next event to venture is entry of robots into human body made possible by a culmination of intricate medicine and fne technology that is Nanotechnology. This article briefy introduces the feld of nanotechnology in relation to its potential benefts to the feld of anaesthesiology. As with any new tecnique or application, nanotechnology as applied to anaesthesiology has tremendous potential for research and exploration. This article therefore orients the reader's mind towards the immense potential and benefts that can be tapped by carrying out further studies and experimentations.The literature was searched using databases, peer reviewed journals and books for over a period of one year (till December 2011). The search was carried out using keywords as nanotechnology, robotics, anesthesiology etc. Initially a master database was formed including human as well as animal studies. Later on the broad topic area was narrowed down to developments in nanotechnology as applied to anesthesiology. Further filtering of search results were done based on selection of researches and developments relating to local, regional and general anesthesia as well as critical care and pain and palliative care. Source

Gorsky E.,State University of New York at Stony Brook | Mazin M.,IMS
Journal of Combinatorial Theory. Series A | Year: 2013

J. Piontkowski described the homology of the Jacobi factor of a plane curve singularity with one Puiseux pair. We discuss the combinatorial structure of his answer, in particular, relate it to the bigraded deformation of Catalan numbers introduced by A. Garsia and M. Haiman. © 2012 Elsevier Inc. Source

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