DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally employed long (400–800 bp) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intra-species genetic variation. We report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterise four million SNPs and four hundred thousand structural variants, many of which are previously unknown. Our approach is effective for accurate, rapid and economical whole genome re-sequencing and many other biomedical applications.

High density lipoprotein (HDL), the carrier of so-called "good" cholesterol, serves as the major athero-protective lipoprotein and has emerged as a key therapeutic target for cardiovascular disease. We applied small angle neutron scattering (SANS) with contrast variation and selective isotopic deuteration to the study of nascent HDL to obtain the low resolution structure in solution of the overall time-averaged conformation of apolipoprotein AI (apoA-I) versus the lipid (acyl chain) core of the particle. Remarkably, apoA-I is observed to possess an open helical shape that wraps around a central ellipsoidal lipid phase. Using the low resolution SANS shapes of the protein and lipid core as scaffolding, an all-atom computational model for the protein and lipid components of nascent HDL was developed by integrating complementary structural data from hydrogen/deuterium exchange mass spectrometry and previously published constraints from multiple biophysical techniques. Both SANS data and the new computational model, the double superhelix model, suggest an unexpected structural arrangement of protein and lipids of nascent HDL, an anti-parallel double superhelix wrapped around an ellipsoidal lipid phase. The protein and lipid organization in nascent HDL envisages a potential generalized mechanism for lipoprotein biogenesis and remodeling, biological processes critical to sterol and lipid transport, organismal energy metabolism, and innate immunity. High density lipoprotein (HDL)2 functions in removal of cholesterol from peripheral tissues, such as within the artery wall, for delivery to the liver and ultimate excretion as biliary cholesterol within the intestinal lumen, a process called reverse cholesterol transport (1, 2). Plasma levels of HDL cholesterol and apolipoprotein AI (apoA-I), the major protein component of HDL, are inversely related to the risk of developing coronary artery disease (3-5). Moreover, genetic alterations that induce changes in apoA-I levels in both animals and humans alter susceptibility for development of atherosclerotic heart disease (3-6). Thus, numerous interventions aimed at enhancing reverse cholesterol transport are being examined as potential novel therapeutic interventions for the prevention and treatment of cardiovascular disease (7,8). Examples include methods for generating new HDL particles through enhanced production or delivery of either intact apoA-I (9, 10) or peptide mimetics of apoA-I (11), as well as modulating interactions between nascent HDL and proteins involved in HDL particle maturation and remodeling for potential therapeutic benefit (12-14). Structural elucidation often serves as the "Rosetta Stone" for enhanced understanding of function. It is thus remarkable that despite its importance to numerous biological and biomedical functions and its current prominent role as a target for therapeutic interventions, to date, the structures of neither the protein nor lipid components of nascent HDL have been directly visualized, and the high resolution structure of the particl...

The antiviral activity of the interferon-induced, double-stranded RNA (dsRNA)-activated protein kinase (PKR) is mediated through dsRNA binding leading to PKR autophosphorylation and subsequent inhibition of protein synthesis. Previous biochemical studies have suggested that autophosphorylation of PKR occurs via a protein-protein interaction and that PKR can form dimers in vitro. Using four independent biophysical and biochemical methods, we have characterized the solution complex formed between PKR and trans-activating region (TAR) RNA, a 57-nucleotide RNA species with double-stranded secondary structure derived from the human immunodeficiency virus type I genome. Chemical cross-linking and gel filtration analyses of PKR⅐TAR RNA complexes reveals that TAR RNA addition increases PKR dimerization and results in the formation of a solution complex with a molecular weight of approximately 150,000. Addition of TAR RNA to PKR results in a quenching of tryptophan fluorescence, indicative of a conformational shift. Through small angle neutron scattering analysis, we show that PKR exists in solution predominantly as a dimer, and has an elongated solution structure. Addition of TAR RNA to PKR causes a significant conformational shift in the protein at a 2:1 stoichiometric ratio of protein to RNA. Taken together, these data indicate that the PKR activation complex consists of a protein dimer bound cooperatively to one dsRNA molecule.

The lysosomal cysteine proteinase cathepsin B (EC 3.4.22.1) plays an important role in protein catabolism and has also been implicated in various disease states. The crystal structures of two forms of native recombinant rat cathepsin B have been determined. The overall folding of rat cathepsin B was shown to be very similar to that of the human liver enzyme. The structure of the native enzyme containing an underivatized active site cysteine (Cys29) showed the active enzyme conformation to be similar to that determined previously for the oxidized form. In a second structure Cys29 was derivatized with the reversible blocking reagent pyridyl disulfide. In this structure large side chain conformational changes were observed for the two key catalytic residues Cys29 and His199, demonstrating the potential flexibility of these side chains. In addition the structure of the complex between rat cathepsin B and the inhibitor benzyloxycarbonyl-Arg-Ser(O-Bzl) chloromethylketone was determined. The complex structure showed that very little conformational change occurs in the enzyme upon inhibitor binding. It also allowed visualization of the interaction between the enzyme and inhibitor. In particular the interaction between Glu245 and the P2 Arg residue was clearly demonstrated, and it was found that the benzyl group of the P1 substrate residue occupies a large hydrophobic pocket thought to represent the S'1 subsite. This may have important implications for structure-based design of cathepsin B inhibitors.

Spherical high density lipoprotein (sHDL), a key player in reverse cholesterol transport and the most abundant form of HDL, is associated with cardiovascular diseases. Small angle neutron scattering with contrast variation was used to determine the solution structure of protein and lipid components of reconstituted sHDL. Apolipoprotein A1, the major protein of sHDL, forms a hollow structure that cradles a central compact lipid core. Three apoA1 chains are arranged within the low resolution structure of the protein component as one of three possible global architectures: (i) a helical dimer with a hairpin (HdHp), (ii) three hairpins (3Hp), or (iii) an integrated trimer (iT) in which the three apoA1 monomers mutually associate over a portion of the sHDL surface. Cross-linking and mass spectrometry analyses help to discriminate among the three molecular models and are most consistent with the HdHp overall architecture of apoA1 within sHDL.Epidemiological studies firmly establish that circulating levels of high density lipoprotein (HDL) cholesterol and apolipoprotein A1 (apoA1), 2 the major protein constituent of HDL particles, are inversely associated with atherosclerotic heart disease risk (1-3). Moreover, genetic studies further confirm a strong mechanistic link between HDL and apoA1 and cardiovascular disease (4 -8). Defined by its buoyant density characteristics, HDL represent a heterogeneous group of particles with varied lipid composition and protein content that participate in diverse biological functions ranging from lipid transport to innate immune functions. For example, HDL serves as an acceptor of cholesterol from peripheral tissue macrophages and promotes lipid transport through delivery of cholesterol to the liver and steroidogenic tissues (9 -11). HDL also mediates systemic anti-inflammatory and anti-oxidant functions (12-14), and HDL-associated proteins can play critical host defense functions (15). ApoA1 represents nearly three-quarters of the protein content of HDL by mass, and it plays a central functional role in facilitating the numerous biological activities of HDL. Typically present at 2-4 molecules/particle depending upon the degree of HDL maturation, apoA1 serves as the fundamental structural element of the particle (16, 17) and is critical for specific interactions with proteins involved in HDL biogenesis (18, 19), maturation and remodeling (20,21), and recognition by target organ receptors (22,23).Because HDL can be generated in a relatively homogenous form, most structural studies of HDL have focused on reconstituted nascent HDL, a particle composed of two molecules of apoA1 associated with phospholipid and free cholesterol (16,17). Early small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) studies of nascent HDL particles were reported nearly 3 decades ago and are consistent with an outer protein layer relative to a central lipid core (24,25). Current structural models of nascent HDL have an anti-parallel apoA1 chain orientation and posit that the protein exists...

The predicted structure and molecular trajectories from over 80 ns molecular dynamics simulation of the solvated double super helix (DSH) model of nascent-high density lipoprotein (HDL) was determined and compared with experimental data on reconstituted nascent HDL obtained from multiple biophysical platforms including small angle neutron scattering (SANS) with contrast variation, hydrogen-deuterium exchange tandem mass spectrometry (H/D-MS/MS), nuclear magnetic resonance spectroscopy (NMR), cross-linking tandem mass spectrometry (MS/MS), fluorescent resonance energy transfer (FRET), electron spin resonance spectroscopy (ESR), and electron microscopy. In general, biophysical constraints experimentally derived from the multiple platforms agree with the same quantities evaluated using the simulation trajectory. Notably, key structural features postulated for the recent DSH model of nascent HDL are retained during the simulation including: 1) the super helical conformation of the anti-parallel apolipoprotein A1 (apoA1) chains; 2) the lipid micellar-pseudolamellar organization; and 3) the solvent exposed Solar Flare loops, proposed sites of interaction with LCAT (lecithin cholesteryl acyltransferase). Analysis of salt bridge persistence during simulation provides insights into structural features of apoA1 that form the backbone of the lipoprotein. The combination of molecular dynamics simulation and experimental data from a broad range of biophysical platforms serves as a powerful approach to study large macromolecular assemblies such as lipoproteins. The present application to nascent HDL validates the DSH model proposed earlier, and suggests new structural details of nascent HDL. 4 To whom correspondence should be addressed: Cleveland State University, 2121 Euclid Avenue, SI 422, Cleveland, OH 44115, or Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, v.gogonea@csuohio.edu or hazens@ccf.org,. SUPPORTING INFORMATION AVAILABLE. The supporting information contains Suplemmental Figures 1 and 2 that depict small angle neutron scattering intensities (I(q)) versus the scattering vector (q), and distance distribution functions (p(r)) versus the distance between scattering centers (r), and low-resolution structures of nascent rHDL in 12% and 42% D 2 O. The Supplemental Table 1 lists experimental and calculated per residue deuterium incorporation factors, H/D exchange rate constants, and residue unfolding constants. This material is available free of charge via the Internet at http://pubs.acs.org. Additionally, the following information is available for download from http://www.lerner.ccf.org/cellbio/hazen/data/ -neutron scattering intensities for HDL samples analyzed in 12% and 42% D 2 O (text files), low resolution structures of nascent HDL (pdb files), and calculated H/D exchange deuterium incorporation factors for all residues in apoA1 dimer (Excel file). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2011 August 31. NIH-PA Author ManuscriptNIH-PA Author Manuscri...

Cholesterol from peripheral tissues, such as within the artery wall, is transported to the liver by high density lipoprotein (HDL) particles, which are continuously remodeled in a process called reverse cholesterol transport ( 1, 2 ). HDL particles are highly heterogeneous, varying in protein and lipid content ( 3 ). Apolipoprotein A1 (apoA1) is Abstract Small-angle neutron scattering (SANS) with contrast variation was used to obtain the low-resolution structure of nascent HDL (nHDL) reconstituted with dimyristoyl phosphatidylcholine (DMPC) in the absence and presence of cholesterol, [apoA1:DMPC (1:80, mol:mol) and apoA1:DMPC:cholesterol (1:86:9, mol:mol:mol)]. The overall shape of both particles is discoidal with the low-resolution structure of apoA1 visualized as an open, contorted, and out of plane conformation with three arms in nascent HDL/dimyristoyl phosphatidylcholine without cholesterol (nHDL DMPC ) and two arms in nascent HDL/dimyristoyl phosphatidylcholine with cholesterol (nHDL DMPC+Chol ). The low-resolution shape of the lipid phase in both nHDL DMPC and nHDL DMPC+Chol were oblate ellipsoids, and fi t well within their respective protein shapes. Modeling studies indicate that apoA1 is folded onto itself in nHDL DMPC , making a large hairpin, which was also confi rmed independently by both cross-linking mass spectrometry and hydrogen-deuterium exchange (HDX) mass spectrometry analyses. In nHDL DMPC+Chol , the lipid was expanded and no hairpin was visible. Importantly, despite the overall discoidal shape of the whole particle in both nHDL DMPC Press, January 23, 2013 DOI 10.1194 The low-resolution structure of nHDL reconstituted with DMPC with and without cholesterol reveals a mechanism for particle expansion Abbreviations: DMPC, dimyristoyl phosphatidylcholine; DSH, double super helix; ESR, electron spin resonance; FRET, fl uorescence resonance energy transfer; HDX, hydrogen-deuterium exchange; LUV, large unilamellar vesicle; nHDL, nascent HDL; nHDL DMPC , nascent HDL/dimyristoyl phosphatidylcholine without cholesterol; nHDL DMPC+Chol , nascent HDL/dimyristoyl phosphatidylcholine with cholesterol; nHDL POPC , nascent HDL/POPC and cholesterol; PC, phosphatidyl choline ; POPC, 1-palmitoyl-2-oleoyl-sn -glycero-3-phosphocholine; q , range of momentum transfer; SANS, small-angle neutron scattering; SCX, strong-cation exchange. Published, JLR Papers in

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