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1. Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP.

Author

Shivani Ahuja, James Cahill, Kimberly Hartfield, and Matthew R Whorton

Subjects
Medicine, Science
Abstract

Nucleotide-sugar transporters (NSTs) transport nucleotide-sugar conjugates into the Golgi lumen where they are then used in the synthesis of glycans. We previously reported crystal structures of a mammalian NST, the CMP-sialic acid transporter (CST) (Ahuja and Whorton 2019). These structures elucidated many aspects of substrate recognition, selectivity, and transport; however, one fundamental unaddressed question is how the transport activity of NSTs might be physiologically regulated as a means to produce the vast diversity of observed glycan structures. Here, we describe the discovery that an endogenous methylated form of cytidine monophosphate (m5CMP) binds and inhibits CST. The presence of m5CMP in cells results from the degradation of RNA that has had its cytosine bases post-transcriptionally methylated through epigenetic processes. Therefore, this work not only demonstrates that m5CMP represents a novel physiological regulator of CST, but it also establishes a link between epigenetic control of gene expression and regulation of glycosylation.

Published
2021
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2. In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes

Author

James Cahill, Shivani Ahuja, and Matthew Whorton

Subjects
Biology (General), QH301-705.5
Abstract

Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide monophosphate byproducts to the cytoplasm. Mutations in this family of proteins can cause a number of significant cellular pathologies, and wild type members can act as virulence factors for many parasites and fungi. Here, we describe an in vitro assay to measure the transport activity of the CMP-sialic acid transporter (CST), one of seven NSTs found in mammals. While in vitro transport assays have been previously described for CST, these studies failed to account for the fact that 1) commercially available stocks of CMP-sialic acid (CMP-Sia) are composed of ~10% of the higher-affinity CMP and 2) CMP-Sia is hydrolyzed into CMP and sialic acid in aqueous solutions. Herein we describe a method for treating CMP-Sia with a nonselective phosphatase, Antarctic phosphatase, to convert all free CMP to cytidine. This allows us to accurately measure substrate affinities and transport kinetics for purified CST reconstituted into proteoliposomes.

Published
2020
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3. Structural basis for mammalian nucleotide sugar transport

Author

Shivani Ahuja and Matthew R Whorton

Subjects
transporter, glycobiology, Golgi, sialic acid, nucleotide sugar, Medicine, Science, Biology (General), QH301-705.5
Abstract

Nucleotide-sugar transporters (NSTs) are critical components of the cellular glycosylation machinery. They transport nucleotide-sugar conjugates into the Golgi lumen, where they are used for the glycosylation of proteins and lipids, and they then subsequently transport the nucleotide monophosphate byproduct back to the cytoplasm. Dysregulation of human NSTs causes several debilitating diseases, and NSTs are virulence factors for many pathogens. Here we present the first crystal structures of a mammalian NST, the mouse CMP-sialic acid transporter (mCST), in complex with its physiological substrates CMP and CMP-sialic acid. Detailed visualization of extensive protein-substrate interactions explains the mechanisms governing substrate selectivity. Further structural analysis of mCST’s unique lumen-facing partially-occluded conformation, coupled with the characterization of substrate-induced quenching of mCST’s intrinsic tryptophan fluorescence, reveals the concerted conformational transitions that occur during substrate transport. These results provide a framework for understanding the effects of disease-causing mutations and the mechanisms of this diverse family of transporters.

Published
2019
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4. A pilot study to determine out‐of‐pocket expenditures by families of children being treated for cancer at public hospitals in New Delhi, India

Author

Shivani Ahuja, Ramandeep Singh Arora, Alexandra Martiniuk, Sandhya Srinivas, Poonam Bagai, Argerie Tsimicalis, and Sara Lederman

Subjects
Psychiatry and Mental health, medicine.medical_specialty, Oncology, business.industry, Family medicine, medicine, Cost of illness, Cancer, Experimental and Cognitive Psychology, New delhi, medicine.disease, business
Published
2019

5. Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP

Author

Matthew R. Whorton, James Cahill, Kimberly A Hartfield, and Shivani Ahuja

Subjects
0301 basic medicine, Glycosylation, Protein Extraction, Glycobiology, 01 natural sciences, Biochemistry, Epigenesis, Genetic, chemistry.chemical_compound, Gene expression, Sf9 Cells, RNA Processing, Post-Transcriptional, Post-Translational Modification, Liquid Chromatography, Extraction Techniques, Multidisciplinary, Crystallography, DNA methylation, biology, Nucleotides, Organic Compounds, Physics, Chromatographic Techniques, Condensed Matter Physics, Chromatin, Nucleic acids, Chemistry, Bioassays and Physiological Analysis, Cytidine Monophosphate N-Acetylneuraminic Acid, Nucleotide Transport Proteins, Physical Sciences, Crystal Structure, Medicine, Epigenetics, DNA modification, Cytosine, Chromatin modification, Research Article, Chromosome biology, Cytidine monophosphate, Glycan, Cell biology, Science, Spodoptera, Research and Analysis Methods, Methylation, Cell Line, 03 medical and health sciences, Cytidine Monophosphate, Genetics, Animals, Solid State Physics, 010405 organic chemistry, Organic Chemistry, Chemical Compounds, RNA, Biology and Life Sciences, Proteins, Transporter, Biological Transport, DNA, High Performance Liquid Chromatography, 0104 chemical sciences, carbohydrates (lipids), 030104 developmental biology, Pyrimidines, chemistry, Gene Expression Regulation, Transport Inhibition Assay, biology.protein, human activities
Abstract

Nucleotide-sugar transporters (NSTs) transport nucleotide-sugar conjugates into the Golgi lumen where they are then used in the synthesis of glycans. We previously reported crystal structures of a mammalian NST, the CMP-sialic acid transporter (CST) (Ahuja and Whorton 2019). These structures elucidated many aspects of substrate recognition, selectivity, and transport; however, one fundamental unaddressed question is how the transport activity of NSTs might be physiologically regulated as a means to produce the vast diversity of observed glycan structures. Here, we describe the discovery that an endogenous methylated form of cytidine monophosphate (m5CMP) binds and inhibits CST. The presence of m5CMP in cells results from the degradation of RNA that has had its cytosine bases post-transcriptionally methylated through epigenetic processes. Therefore, this work not only demonstrates that m5CMP represents a novel physiological regulator of CST, but it also establishes a link between epigenetic control of gene expression and regulation of glycosylation.

Published
2020

7. Structural Analysis of Bacterial ABC Transporter Inhibition by an Antibody Fragment

Author

Christopher M. Koth, Melissa A. Starovasnik, Mary Kate Alexander, Stephen J. Russell, Danielle L. Swem, Ping Wu, Christine Tam, Shivani Ahuja, Jawahar Sudhamsu, Mireille Nishiyama, and Lionel Rouge

Subjects
chemistry.chemical_classification, Staphylococcus aureus, Reactive oxygen species, Binding Sites, biology, Molecular Sequence Data, Transporter, DNA-binding protein, Cofactor, Enzyme, Bacterial Proteins, chemistry, Biochemistry, Structural Biology, biology.protein, Antibody inhibitor, ATP-Binding Cassette Transporters, Amino Acid Sequence, ABC Transporter Inhibition, Immunoglobulin Fragments, Molecular Biology, Function (biology), Protein Binding
Abstract

SummaryBacterial ATP-binding cassette (ABC) importers play critical roles in nutrient acquisition and are potential antibacterial targets. However, structural bases for their inhibition are poorly defined. These pathways typically rely on substrate binding proteins (SBPs), which are essential for substrate recognition, delivery, and transporter function. We report the crystal structure of a Staphylococcus aureus SBP for Mn(II), termed MntC, in complex with FabC1, a potent antibody inhibitor of the MntABC pathway. This pathway is essential and highly expressed during S. aureus infection and facilitates the import of Mn(II), a critical cofactor for enzymes that detoxify reactive oxygen species (ROS). Structure-based functional studies indicate that FabC1 sterically blocks a structurally conserved surface of MntC, preventing its interaction with the MntB membrane importer and increasing wild-type S. aureus sensitivity to oxidative stress by more than 10-fold. The results define an SBP blocking mechanism as the basis for ABC importer inhibition by an engineered antibody fragment.

Published
2015

8. Cytochrome-P450–Cytochrome-b5 Interaction in a Membrane Environment Changes 15N Chemical Shift Anisotropy Tensors

Author

Shivani Ahuja, Ayyalusamy Ramamoorthy, Manoj Kumar Pandey, Rui Huang, Sang Choul Im, Lucy Waskell, and Subramanian Vivekanandan

Subjects
Nitrogen Isotopes, biology, Chemistry, Cytochrome P450, Nuclear magnetic resonance spectroscopy, Amides, Article, Protein Structure, Tertiary, Surfaces, Coatings and Films, Crystallography, Cytochromes b5, Membrane, Cytochrome P-450 Enzyme System, Cytochrome b5, Materials Chemistry, biology.protein, Animals, Protein Interaction Domains and Motifs, Rabbits, Physical and Theoretical Chemistry, Anisotropy, Nuclear Magnetic Resonance, Biomolecular, Peptide sequence, Protein secondary structure, Magnetic dipole–dipole interaction
Abstract

It has been well realized that the dependence of chemical shift anisotropy (CSA) tensors on the amino acid sequence, secondary structure, dynamics, and electrostatic interactions can be utilized in the structural and dynamic studies of proteins by NMR spectroscopy. In addition, CSA tensors could also be utilized to measure the structural interactions between proteins in a protein-protein complex. To this end, we report the experimentally measured backbone amide-(15)N CSA tensors for a membrane-bound 16.7 kDa full-length rabbit cytochrome-b5 (cytb5), in complexation with a 55.8 kDa microsomal rabbit cytochrome P450 2B4 (cytP4502B4). The (15)N-CSAs, determined using the (15)N CSA/(15)N-(1)H dipolar coupling transverse cross-correlated rates, for free cytb5 are compared with those for the cytb5 bound to cytP4502B4. An overall increase in backbone amide-(15)N transverse cross-correlated rates for the cytb5 residues in the cytb5-cytP450 complex is observed as compared to the free cytb5 residues. Due to fast spin-spin relaxation (T2) and subsequent broadening of the signals in the complex, we could measure amide-(15)N CSAs only for 48 residues of cytb5 as compared to 84 residues of free cytb5. We observed a change in (15)N CSA for most residues of cytb5 in the complex, as compared to free cytb5, suggesting a dynamic interaction between the oppositely charged surfaces of anionic cytb5 and cationic cytP450. The mean values of (15)N CSA determined for residues in helical, sheet, and turn regions of cytb5 in the complex are -184.5, -146.8, and -146.2 ppm, respectively, with an overall average value of -165.5 ppm (excluding the values from residues in more flexible termini). The measured CSA value for residues in helical conformation is slightly larger as compared to previously reported values. This may be attributed to the paramagnetic effect from Fe(III) of the heme in cytb5, which is similar to our previously reported values for the free cytb5.

Published
2013

9. 1H, 13C and 15N resonance assignments for the full-length mammalian cytochrome b5 in a membrane environment

Author

Subramanian Vivekanandan, Shivani Ahuja, Sang Choul Im, Lucy Waskell, and Ayyalusamy Ramamoorthy

Subjects
Phosphorylcholine, Chemistry, Cholesterol, medicine.medical_treatment, Biochemistry, Micelle, Steroid, Cell membrane, chemistry.chemical_compound, Membrane, medicine.anatomical_structure, Membrane protein, Structural Biology, Cytochrome b5, medicine
Abstract

Microsomal cytochrome b5 plays a key role in the oxidation of a variety of exogenous and endogenous compounds, including drugs, fatty acids, cholesterol and steroid hormones. To better understand its functional properties in a membrane mimic environment, we carried out high-resolution solution NMR studies. Here we report resonance assignments for full-length rabbit cytochrome b5 embedded in dodecylphosphocholine micelles.

Published
2013

10. A Model of the Membrane-bound Cytochrome b5-Cytochrome P450 Complex from NMR and Mutagenesis Data

Author

Nataliya Popovych, Nicole Jahr, Stéphanie V. Le Clair, Subramanian Vivekanandan, Angela Bridges, Kazutoshi Yamamoto, Ravi Prakash Reddy Nanga, Sang Choul Im, Ronald Soong, Shivani Ahuja, Lucy Waskell, Jiadi Xu, Rui Huang, and Ayyalusamy Ramamoorthy

Subjects
Models, Molecular, Magnetic Resonance Spectroscopy, Cytochrome, Stereochemistry, Molecular Sequence Data, Heme, Arginine, Biochemistry, Protein Structure, Secondary, Substrate Specificity, Electron Transport, Electron transfer, chemistry.chemical_compound, Cytochrome P-450 Enzyme System, Cytochrome b5, Animals, Amino Acid Sequence, Molecular Biology, Binding Sites, Sequence Homology, Amino Acid, biology, Chemistry, Cell Biology, Nuclear magnetic resonance spectroscopy, Electron transport chain, Protein Structure, Tertiary, Kinetics, Cytochromes b5, Structural biology, Docking (molecular), Multiprotein Complexes, Mutation, Protein Structure and Folding, Biocatalysis, Mutagenesis, Site-Directed, biology.protein, Rabbits, Oxidation-Reduction, Protein Binding
Abstract

Microsomal cytochrome b5 (cytb5) is a membrane-bound protein that modulates the catalytic activity of its redox partner, cytochrome P4502B4 (cytP450). Here, we report the first structure of full-length rabbit ferric microsomal cytb5 (16 kDa), incorporated in two different membrane mimetics (detergent micelles and lipid bicelles). Differential line broadening of the cytb5 NMR resonances and site-directed mutagenesis data were used to characterize the cytb5 interaction epitope recognized by ferric microsomal cytP450 (56 kDa). Subsequently, a data-driven docking algorithm, HADDOCK (high ambiguity driven biomolecular docking), was used to generate the structure of the complex between cytP4502B4 and cytb5 using experimentally derived restraints from NMR, mutagenesis, and the double mutant cycle data obtained on the full-length proteins. Our docking and experimental results point to the formation of a dynamic electron transfer complex between the acidic convex surface of cytb5 and the concave basic proximal surface of cytP4502B4. The majority of the binding energy for the complex is provided by interactions between residues on the C-helix and β-bulge of cytP450 and residues at the end of helix α4 of cytb5. The structure of the complex allows us to propose an interprotein electron transfer pathway involving the highly conserved Arg-125 on cytP450 serving as a salt bridge between the heme propionates of cytP450 and cytb5. We have also shown that the addition of a substrate to cytP450 likely strengthens the cytb5-cytP450 interaction. This study paves the way to obtaining valuable structural, functional, and dynamic information on membrane-bound complexes.

Published
2013

11. Determination of 15N Chemical Shift Anisotropy from a Membrane-Bound Protein by NMR Spectroscopy

Author

Manoj Kumar Pandey, Kumar Pichumani, Shivani Ahuja, Sang Choul Im, Lucy Waskell, Ayyalusamy Ramamoorthy, and Subramanian Vivekanandan

Subjects
chemistry.chemical_classification, Nitrogen Isotopes, Globular protein, Relaxation (NMR), Heme, Nuclear magnetic resonance spectroscopy, Ferric Compounds, Article, Surfaces, Coatings and Films, Turn (biochemistry), chemistry.chemical_compound, Crystallography, Cytochromes b5, chemistry, Membrane protein, Materials Chemistry, Animals, Rabbits, Physical and Theoretical Chemistry, Anisotropy, Nuclear Magnetic Resonance, Biomolecular, Protein secondary structure
Abstract

Chemical shift anisotropy (CSA) tensors are essential in the structural and dynamic studies of proteins using NMR spectroscopy. Results from relaxation studies in biomolecular solution and solid-state NMR experiments on aligned samples are routinely interpreted using well-characterized CSA tensors determined from model compounds. Since CSA tensors, particularly the (15)N CSA, highly depend on a number of parameters including secondary structure, electrostatic interaction, and the amino acid sequence, there is a need for accurately determined CSA tensors from proteins. In this study, we report the backbone amide-(15)N CSA tensors for a 16.7-kDa membrane-bound and paramagnetic-heme containing protein, rabbit Cytochrome b(5) (cytb(5)), determined using the (15)N CSA/(15)N-(1)H dipolar transverse cross-correlation rates. The mean values of (15)N CSA determined for residues in helical, sheet, and turn regions are -187.9, -166.0, and -161.1 ppm, respectively, with an overall average value of -171.7 ppm. While the average CSA value determined from this study is in good agreement with previous solution NMR experiments on small globular proteins, the CSA value determined for residues in helical conformation is slightly larger, which may be attributed to the paramagnetic effect from Fe(III) of the heme unit in cytb(5). However, like in previous solution NMR studies, the CSA values reported in this study are larger than the values measured from solid-state NMR experiments. We believe that the CSA parameters reported in this study will be useful in determining the structure, dynamics, and orientation of proteins, including membrane proteins, using NMR spectroscopy.

Published
2012

12. Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist

Author

Brian Safina, Honorio Sampang, Bobby Brillantes, Christopher M. Koth, Hoangdung Ho, Shivani Ahuja, Sophia Lin, Christoph Martin Dehnhardt, Krista K. Bowman, Michael Edward Grimwood, Ping Wu, Melissa A. Starovasnik, David H. Hackos, Christine Tam, J. P. Johnson, Charles J. Cohen, Zhiwei Xie, Jian Payandeh, Yvonne Franke, Kuldip Khakh, Mary Coons, Kevin R Clark, Jun Li, Susmith Mukund, Elaine Chang, Jean-Christophe Andrez, Stephanie Shriver, Daniel F. Ortwine, Kyle Mortara, Clint Young, Alberto Estevez, Henry Verschoof, Thilo Focken, Daniel P. Sutherlin, and Lunbin Deng

Subjects
Models, Molecular, Gene isoform, Stereochemistry, DNA Mutational Analysis, Molecular Sequence Data, Gating, Crystallography, X-Ray, Protein Engineering, Protein Structure, Secondary, Cell membrane, Protein structure, Thiadiazoles, medicine, Humans, Protein Isoforms, Amino Acid Sequence, Receptor, Sulfonamides, Multidisciplinary, Chemistry, Cell Membrane, NAV1.7 Voltage-Gated Sodium Channel, Pain Perception, Small molecule, Protein Structure, Tertiary, medicine.anatomical_structure, Helix, Biophysics, Crystallization, Sodium Channel Blockers
Abstract

Voltage-gated sodium (Nav) channels propagate action potentials in excitable cells. Accordingly, Nav channels are therapeutic targets for many cardiovascular and neurological disorders. Selective inhibitors have been challenging to design because the nine mammalian Nav channel isoforms share high sequence identity and remain recalcitrant to high-resolution structural studies. Targeting the human Nav1.7 channel involved in pain perception, we present a protein-engineering strategy that has allowed us to determine crystal structures of a novel receptor site in complex with isoform-selective antagonists. GX-936 and related inhibitors bind to the activated state of voltage-sensor domain IV (VSD4), where their anionic aryl sulfonamide warhead engages the fourth arginine gating charge on the S4 helix. By opposing VSD4 deactivation, these compounds inhibit Nav1.7 through a voltage-sensor trapping mechanism, likely by stabilizing inactivated states of the channel. Residues from the S2 and S3 helices are key determinants of isoform selectivity, and bound phospholipids implicate the membrane as a modulator of channel function and pharmacology. Our results help to elucidate the molecular basis of voltage sensing and establish structural blueprints to design selective Nav channel antagonists.

Published
2015

13. Structure and function of G protein-coupled receptors using NMR spectroscopy

Author

Shivani Ahuja, Steven O. Smith, Markus Eilers, Sina Erfani, and Joseph A. Goncalves

Subjects
Models, Molecular, Rhodopsin, Nuclear and High Energy Physics, biology, Protein Conformation, Chemistry, Class C GPCR, Biochemistry, Article, Rhodopsin-like receptors, Receptors, G-Protein-Coupled, Analytical Chemistry, Transmembrane domain, Metabotropic glutamate receptor, Heterotrimeric G protein, Biophysics, biology.protein, Animals, Humans, Receptor, Nuclear Magnetic Resonance, Biomolecular, Spectroscopy, G protein-coupled receptor
Abstract

Nathans and Hogness [1] cloned the gene for the visual pigment rhodopsin in 1983, and found that the receptor contained seven hydrophobic membrane-spanning helices. At roughly the same time, the paradigm in the visual receptor field that rhodopsin functions as a light-activated Ca2+ channel was being overturned in favor of a competing model that rhodopsin is responsible for activating a heterotrimeric G-protein [2]. In 1986, a landmark paper by Strader, Lefkowitz and co-workers [3] reported the sequence of the β2-adrenergic receptor. They recognized that the β2-adrenergic receptor shares significant sequence homology with rhodopsin, including seven transmembrane (TM) segments. They proposed that the amine ligands of the adrenergic receptors intercalate into the TM helices and trigger receptor activation in the same manner as the retinal in rhodopsin. Because the receptors of the adenylate cyclase system were known to activate G-proteins [2,4,5], the similarity between the β2-adrenergic receptor and rhodopsin provided the first hint of the existence of a large G protein-coupled receptor (GPCR) family. Early structural work in the emerging GPCR field was guided by two pioneering studies. In 1993, Schertler, Villa and Henderson [6] reported an electron density projection map based on cryo-EM images of rhodopsin that showed the seven-helix architecture is distinctly different from that of bacteriorhodopsin, which had been a favored template for modeling GPCRs. In 1996, Hubbell and Khorana [7] used site-directed spin labeling in combination with EPR spectroscopy to reveal that activation is mediated by rigid body rotation of the TM helices. A breakthrough in the GPCR field came in 2000 with the determination of the rhodopsin crystal structure [8] (Fig. 1). The structure was solved of the dark, inactive conformation of the protein. The structure of the active state, however, has been more elusive. When illuminated, the crystals of rhodopsin crack and dissolve [9], presumably due to rigid body helix motions that accompany receptor activation. In 2007, the crystal structure of the β2-adrenergic receptor was solved with the inverse agonist carazolol bound in the active site [10]. The structure of this first ligand-activated GPCR confirmed that the overall seven-transmembrane helix architecture is similar to that of rhodopsin. Together the rhodopsin and β2-adrenergic receptor structures provide a high-resolution framework for understanding the structural features that are responsible for locking these receptors in the off conformation, and a starting point for investigating the mechanism of receptor activation. Fig. 1 Crystal structure of rhodopsin. The first crystal structure of a GPCR was obtained in 2000 by Palczewski and Okada [8]. Views of rhodopsin spanning the membrane bilayer (a) and from the extracellular (or intradiscal) surface of the membrane (b) show the ... In this review, we describe the progress that has been made using NMR spectroscopy to characterize the structure and dynamics of GPCRs in membrane environments. NMR methods have been used extensively to establish the structural changes occurring upon the activation of rhodopsin, as well as several ligand-activated receptors. We describe below the importance of these receptors in terms of their cell biology and pharmacology, and then outline the role that NMR can play in answering questions of structure and function. 1.1 Cell biology The 7-transmembrane helix GPCRs have evolved to recognize and transduce signals as diverse as light, Ca2+, small organic molecules and proteins. These receptors are found in both vertebrates and invertebrates, and are typically divided into six classes (Class A–F) based on sequence homology and functional similarity [11–13]. However, the classification is still open to debate. For example, on the basis of phylogeny, the human GPCRs have been divided into five families (Rhodopsin-like, Secretin, Adhesion, Glutamate, and Frizzled/Taste2) [14]. In this scheme, the Class A receptors correspond to the Rhodopsin-like family, but the Class B receptors are divided into the Secretin and Adhesion families. Nevertheless, in all classification schemes proposed to date, the lack of homology between classes or families suggests that nature has converged on the same seven transmembrane helix framework multiple times. The Class A (Rhodopsin-like family) receptors respond to the presence of diverse stimuli ranging from light absorption to the binding of various ligands, which include small molecule amines and hormones. Class B (Secretin and Adhesion families) receptors are activated by peptides of the glucagon hormone family [15,16]. The Class C (Glutamate family) GPCRs are comprised of the metabotropic glutamate receptors. These receptors are characterized by a large N-terminal ligand binding domain [17], which appears to be structurally homologous to the amino terminal domain of the ligand-gated ionotropic glutamate receptors in postsynaptic neuronal membranes [18]. Pheromones (e.g. α-factor) secreted by Saccharomyces cerevisiae bind to Class D GPCRs (e.g. STE2) during the mating process. Similar mechanisms are involved in the mating of several fungi [19]. Class E receptors have been implicated in the chemotactic migration of slime mold and can potentially be exploited as antifungal targets [20,21]. Class F (Frizzled/smoothened/taste2 family) contains receptors in the Wnt signaling pathway [14], which perform indispensable roles in embryonic development [22]. The Class A receptors are by far the most populated class of GPCRs. In the GPCR database there are over 20,000 Class A sequences (http://www.gpcr.org/). In humans, 952 of 1061 GPCRs identified in the human genome are in Class A. Of the 952 human Class A receptors, most (509) are olfactory receptors. The remaining Class A GPCRs are subdivided into 18 subfamilies including the well studied visual and small molecule amine receptors, as well as hormone and peptide receptors. Despite the breadth of this group, there exists a degree of sequence conservation among these receptors. Furthermore, the Class A receptors share similar intracellular proteins (e.g. protein kinases, arrestins) that mediate receptor desensitization.

Published
2010

14. Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils

Author

Steven O. Smith, Mahiuddin Ahmed, James I. Elliott, Shivani Ahuja, Takeshi Sato, Darryl Aucoin, William E. Van Nostrand, Judianne Davis, and Saburo Aimoto

Subjects
Models, Molecular, Cell Survival, Amyloid beta, Molecular Sequence Data, Peptide, macromolecular substances, 010402 general chemistry, Fibril, 01 natural sciences, Protein Structure, Secondary, Article, Turn (biochemistry), Mice, 03 medical and health sciences, Protein structure, Alzheimer Disease, Structural Biology, Animals, Amino Acid Sequence, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, Peptide sequence, Cells, Cultured, 030304 developmental biology, Neurons, chemistry.chemical_classification, 0303 health sciences, Amyloid beta-Peptides, biology, Chemistry, Nuclear magnetic resonance spectroscopy, Peptide Fragments, 0104 chemical sciences, Cold Temperature, Crystallography, Polymerization, biology.protein, Salts, Protein Multimerization
Abstract

The amyloid-beta(1-42) (Abeta42) peptide rapidly aggregates to form oligomers, protofibils and fibrils en route to the deposition of amyloid plaques associated with Alzheimer's disease. We show that low-temperature and low-salt conditions can stabilize disc-shaped oligomers (pentamers) that are substantially more toxic to mouse cortical neurons than protofibrils and fibrils. We find that these neurotoxic oligomers do not have the beta-sheet structure characteristic of fibrils. Rather, the oligomers are composed of loosely aggregated strands whose C termini are protected from solvent exchange and which have a turn conformation, placing Phe19 in contact with Leu34. On the basis of NMR spectroscopy, we show that the structural conversion of Abeta42 oligomers to fibrils involves the association of these loosely aggregated strands into beta-sheets whose individual beta-strands polymerize in a parallel, in-register orientation and are staggered at an intermonomer contact between Gln15 and Gly37.

Published
2010

15. 6-s-cis Conformation and Polar Binding Pocket of the Retinal Chromophore in the Photoactivated State of Rhodopsin

Author

Mordechai Sheves, Martine Ziliox, Thomas P. Sakmar, Elsa C. Y. Yan, Markus Eilers, Shivani Ahuja, Amiram Hirshfeld, and Steven O. Smith

Subjects
Models, Molecular, Steric effects, Rhodopsin, Magnetic Resonance Spectroscopy, genetic structures, Stereochemistry, Photochemistry, Biochemistry, Article, Catalysis, Cell Line, chemistry.chemical_compound, Colloid and Surface Chemistry, Magic angle spinning, Humans, Binding Sites, Schiff base, Molecular Structure, biology, Chemical shift, Retinal, General Chemistry, Chromophore, Photochemical Processes, Protein Structure, Tertiary, chemistry, Mutation, Retinaldehyde, biology.protein
Abstract

The visual pigment rhodopsin is unique among the G protein-coupled receptors in having an 11-cis retinal chromophore covalently bound to the protein through a protonated Schiff base linkage. The chromophore locks the visual receptor in an inactive conformation through specific steric and electrostatic interactions. This efficient inverse agonist is rapidly converted to an agonist, the unprotonated Schiff base of all-trans retinal, upon light activation. Here, we use magic angle spinning NMR spectroscopy to obtain the (13)C chemical shifts (C5-C20) of the all-trans retinylidene chromophore and the (15)N chemical shift of the Schiff base nitrogen in the active metarhodopsin II intermediate. The retinal chemical shifts are sensitive to the conformation of the chromophore and its molecular interactions within the protein-binding site. Comparison of the retinal chemical shifts in metarhodopsin II with those of retinal model compounds reveals that the Schiff base environment is polar. In particular, the (13)C15 and (15)Nepsilon chemical shifts indicate that the C horizontal lineN bond is highly polarized in a manner that would facilitate Schiff base hydrolysis. We show that a strong perturbation of the retinal (13)C12 chemical shift observed in rhodopsin is reduced in wild-type metarhodopsin II and in the E181Q mutant of rhodopsin. On the basis of the T(1) relaxation time of the retinal (13)C18 methyl group and the conjugated retinal (13)C5 and (13)C8 chemical shifts, we have determined that the conformation of the retinal C6-C7 single bond connecting the beta-ionone ring and the retinylidene chain is 6-s-cis in both the inactive and the active states of rhodopsin. These results are discussed within the general framework of ligand-activated G protein-coupled receptors.

Published
2009

16. Multiple Switches in G Protein-Coupled Receptor Activation

Author

Shivani Ahuja and Steven O. Smith

Subjects
Rhodopsin, Opsin, Magnetic Resonance Spectroscopy, Drug Inverse Agonism, Protein Conformation, Stereochemistry, Ligands, Toxicology, Receptors, G-Protein-Coupled, Protein structure, Animals, Humans, Receptor, G protein-coupled receptor, Pharmacology, chemistry.chemical_classification, Opsins, biology, Nuclear magnetic resonance spectroscopy, Amino acid, Transmembrane domain, chemistry, Biophysics, biology.protein, Cattle, Crystallization
Abstract

The activation mechanism of G protein-coupled receptors has presented a puzzle that finally may be close to solution. These receptors have a relatively simple architecture consisting of seven transmembrane helices that contain just a handful of highly conserved amino acids, yet they respond to light and a range of chemically diverse ligands. Recent NMR structural studies on the active metarhodopsin II intermediate of the visual receptor rhodopsin, along with the recent crystal structure of the apoprotein opsin, have revealed multiple structural elements or 'switches' that must be simultaneously triggered to achieve full activation. The confluence of several required structural changes is an example of "coincidence counting", which is often used by nature to regulate biological processes. In ligand-activated G protein-coupled receptors, the presence of multiple switches may provide an explanation for the differences between full, partial and inverse agonists.

Published
2009

17. Location of the Retinal Chromophore in the Activated State of Rhodopsin

Author

Martine Ziliox, Steven O. Smith, Markus Eilers, Amiram Hirshfeld, Shivani Ahuja, H. Gobind Khorana, Evan Crocker, Philip J. Reeves, Natalie Syrett, Viktor Hornak, and Mordechai Sheves

Subjects
Rhodopsin, Magnetic Resonance Spectroscopy, Protein Conformation, Stereochemistry, Retinal binding, Molecular Conformation, Polyenes, Biochemistry, Retina, Cell Line, Receptors, G-Protein-Coupled, chemistry.chemical_compound, Protein structure, Humans, Binding site, Molecular Biology, Schiff Bases, Binding Sites, biology, Chemistry, Mechanisms of Signal Transduction, Retinal, Cell Biology, Rod Cell Outer Segment, Chromophore, Transmembrane domain, biology.protein
Abstract

Rhodopsin is a highly specialized G protein-coupled receptor (GPCR) that is activated by the rapid photochemical isomerization of its covalently bound 11-cis-retinal chromophore. Using two-dimensional solid-state NMR spectroscopy, we defined the position of the retinal in the active metarhodopsin II intermediate. Distance constraints were obtained between amino acids in the retinal binding site and specific (13)C-labeled sites located on the beta-ionone ring, polyene chain, and Schiff base end of the retinal. We show that the retinal C20 methyl group rotates toward the second extracellular loop (EL2), which forms a cap on the retinal binding site in the inactive receptor. Despite the trajectory of the methyl group, we observed an increase in the C20-Gly(188) (EL2) distance consistent with an increase in separation between the retinal and EL2 upon activation. NMR distance constraints showed that the beta-ionone ring moves to a position between Met(207) and Phe(208) on transmembrane helix H5. Movement of the ring toward H5 was also reflected in increased separation between the Cepsilon carbons of Lys(296) (H7) and Met(44) (H1) and between Gly(121) (H3) and the retinal C18 methyl group. Helix-helix interactions involving the H3-H5 and H4-H5 interfaces were also found to change in the formation of metarhodopsin II reflecting increased retinal-protein interactions in the region of Glu(122) (H3) and His(211) (H5). We discuss the location of the retinal in metarhodopsin II and its interaction with sequence motifs, which are highly conserved across the pharmaceutically important class A GPCR family, with respect to the mechanism of receptor activation.

Published
2009

18. Insights into the Role of Substrates on the Interaction between Cytochrome b5 and Cytochrome P450 2B4 by NMR

Author

Rui Huang, Ayyalusamy Ramamoorthy, Lucy Waskell, Meng Zhang, Shivani Ahuja, Sang Choul Im, and Stéphanie V. Le Clair

Subjects
Models, Molecular, Protein Conformation, Population, Plasma protein binding, Sodium Chloride, environment and public health, Article, Substrate Specificity, Protein structure, Cytochrome b5, Cytochrome P450 Family 2, education, Nuclear Magnetic Resonance, Biomolecular, education.field_of_study, Multidisciplinary, biology, Chemistry, Osmolar Concentration, Substrate (chemistry), Cytochrome P450, enzymes and coenzymes (carbohydrates), Cytochromes b5, Catalytic cycle, Biochemistry, Ionic strength, embryonic structures, cardiovascular system, Biophysics, biology.protein, Aryl Hydrocarbon Hydroxylases, Protein Binding
Abstract

Mammalian cytochrome b5 (cyt b5) is a membrane-bound protein capable of donating an electron to cytochrome P450 (P450) in the P450 catalytic cycle. The interaction between cyt b5 and P450 has been reported to be affected by the substrates of P450; however, the mechanism of substrate modulation on the cyt b5-P450 complex formation is still unknown. In this study, the complexes between full-length rabbit cyt b5 and full-length substrate-free/substrate-bound cytochrome P450 2B4 (CYP2B4) are investigated using NMR techniques. Our findings reveal that the population of complexes is ionic strength dependent, implying the importance of electrostatic interactions in the complex formation process. The observation that the cyt b5-substrate-bound CYP2B4 complex shows a weaker dependence on ionic strength than the cyt b5-substrate-free CYP2B4 complex suggests the presence of a larger fraction of steoreospecific complexes when CYP2B4 is substrate-bound. These results suggest that a CYP2B4 substrate likely promotes specific interactions between cyt b5 and CYP2B4. Residues D65, V66, T70, D71 and A72 are found to be involved in specific interactions between the two proteins due to their weak response to ionic strength change. These findings provide insights into the mechanism underlying substrate modulation on the cyt b5-P450 complexation process.

Published
2015

19. Probing color coherence effects in pp collisions at $$\sqrt{s}=7\,\text {TeV} $$ s = 7 TeV

Author

Ben Bylsma, A. Barker, Jing Wang, Ulla Gebbert, J. Karancsi, Lorenzo Foà, J. Smith, Matthew Chadwick, M. W. Arenton, R. Horisberger, Andrew Levin, C. Goetzmann, L. M. Cremaldi, D. Carlsmith, Jose M Hernandez, R. Stringer, M. Konecki, K. Theofilatos, M. Sharma, P. Jindal, R. Rahmat, B. Kreis, I. Golutvin, A. Montanari, S. Khalid, Hans J. Vogel, Sridhara Dasu, Emilio Meschi, Evangelos Paradas, R. E. Hughes, Pierre Piroué, N. De Filippis, Jean-Louis Faure, M. Choi, S. Albergo, C. Amsler, Dooyeon Gyun, S. Kailas, H. K. Wöhri, D. Ferencek, S. Costantini, A. York, P. Ronchese, Anastasia Grebenyuk, An Vorobyev, S. Bitioukov, A. Léonard, Hyangkyu Park, Douglas Wright, Giacomo Fedi, K. Harder, Daniele Pedrini, J. Pela, C. Dozen, L. Teodorescu, D. Krücker, Valerie Halyo, N. Eggert, A. Mestvirishvili, D. Pitzl, Caroline Collard, I. Marfin, G. Schott, T. Scarborough, M. Grimes, R. Khurana, Carsten Heidemann, Costas Foudas, A. Y. Rodríguez-Marrero, Philippe Gras, S. Nourbakhsh, A. A. Abdelalim, Melody A. Swartz, V. Karimäki, Devdatta Majumder, Benjamin Michlin, B. Snook, B. Dahmes, D. Hits, Anna Cimmino, J. Yelton, M. Chamizo Llatas, Mauro Emanuele Dinardo, I. C. Park, Stephen Mrenna, A. Ruiz-Jimeno, N. Cripps, F. J.M. Geurts, P. Zotto, F. Blekman, V. Zhukov, Christof Roland, T. Du Pree, W. De Boer, Anita Topkar, Y. Kuessel, B. Rahbaran, Alberto Potenza, S. Rappoccio, James John Brooke, A. Spiridonov, T. Tuuva, Raffaello D'Alessandro, B. Casal, Y. Guo, Slawek Tkaczyk, K. Hoepfner, S. Liang, D. J. A. Cockerill, J. Lazo-Flores, F. Glege, Wolfgang Treberer-Treberspurg, J. Alimena, David Cutts, D. Cline, P. Maksimovic, H. Wolfe, Eric Clément, Achim Stahl, Myriam Grunewald, A. Uzunian, Fabrizio Gasparini, S. Cihangir, J. Santaolalla, D. Duggan, Ignazio Lazzizzera, Marco Zanetti, Gulsen Onengut, Viktor Matveev, Gian Mario Bilei, Meenakshi Narain, Gonzalo Gomez, M. Mohammadi Najafabadi, A. Petrukhin, J. Marrouche, Alessandro Thea, Sunil Somalwar, Marc Dejardin, V. Stolin, E. Karavakis, M. S. Soares, F. Meijers, Mohamed Mahmoud, E. Calvo, P. Fabbricatore, Robyn Lucas, J. E. Ramirez Vargas, Philippe Miné, Santiago Folgueras, George Alverson, Polina Otiougova, M. Chasco, G. A. Pierro, W. Andrews, Nazar Bartosik, N. Wardle, Manfred Paulini, Victor Krychkine, Pierluigi Bortignon, C. O'Brien, W. Kiesenhofer, S. K. Nam, Yu Andreev, Antony Adair, P. Siegrist, S. Sumowidagdo, L. Perrozzi, Andrey Belyaev, S. Bilmis, K. Petridis, K. Kadija, Pedro Silva, M. Bellato, Willi Bertl, A. Rosowsky, Nicola Cavallo, N. Almeida, Gui Nyun Kim, P. Kreuzer, P. Luukka, M. Zielinski, Marco Meschini, Ashok Kumar, S. Malvezzi, S. Kesisoglou, M. Maggi, A. Juodagalvis, Stefano Mersi, Regina Demina, F. Nguyen, M. Besancon, J. Fernandez Menendez, T. Khurshid, Stephen Wimpenny, Yanjun Tu, D. M. Morse, Atul Gurtu, P. Turner, Sara Fiorendi, C. Albajar, J. R. Komaragiri, A. Calamba, Clara Jorda, M. Abbrescia, J. Sammet, I. Asin, Lorenzo Uplegger, William T. Ford, T. Tabarelli de Fatis, C.W. Fabjan, B. P. Padley, Ilina Vasileva Akin, L. Lusito, C. H. Jiang, Marvin Johnson, D. Treille, V. Rekovic, Z. L. Trocsanyi, D. Lazic, J. Velkovska, J. Piedra Gomez, Wolfram Erdmann, Nicolo Cartiglia, Stefano Colafranceschi, Harold Nguyen, D. Eckstein, Nasuf Sonmez, Hannsjoerg Artur Weber, Gordon H. Hanson, J. R. Vlimant, J. Sibille, Maciej Górski, P. Lobelle Pardo, Andreas Kornmayer, N. Leonardo, L. Gouskos, S. Ozkorucuklu, Gail Davies, P. Checchia, A. Kayis Topaksu, V. Perelygin, Venkatesh Veeraraghavan, M. Kadastik, Th Muller, E. Kwon, S. Vavilov, K. Hatakeyama, Dimitri Bourilkov, S. Carrillo Moreno, D. Hidas, K. Klapoetke, M. Vidal Marono, H. Flacher, S. Jabeen, Atanu Modak, J. Hugon, Junghwan Goh, Livio Fanò, M. Aldaya Martin, Lucie Gauthier, A. C. Le Bihan, S. Semenov, G. Eckerlin, Zhenwei Yang, F. M. Stober, Andrei Gritsan, G. Zito, T. Christiansen, P. Lawson, Paolo Gunnellini, Michael Walker, P. Markowitz, T. Dorigo, I. Vorobiev, S. Linn, James Alexander, Vasundhara Chetluru, Lukasz Kreczko, Claudio Campagnari, A. Quintario Olmeda, M. Vergili, B. Gomber, W. Dominik, Thomas Kress, J. Chasserat, Christopher Neu, Z. Staykova, Batool Safarzadeh, Yongsun Kim, Lev Dudko, Y. Roh, P. Raics, J. Haas, M. Rodenburg, L. Quertenmont, Wei Xie, G. Breto, A. Branca, Y. D. Oh, Hasan Ogul, Emine Gurpinar, Klaus Freudenreich, D. Marlow, W. Lohmann, Sergio Cittolin, Julien Caudron, Jared Sturdy, D. Mason, M. A. Buchmann, E. Friis, D. Toback, Emanuele Usai, C. Park, Rajat Gupta, A. F. Barfuss, G. Georgiou, Silvia Taroni, N. Heracleous, Michal Bluj, P. Vischia, Andrey Marinov, Karl Gill, V. Azzolini, W. To, Filip Moortgat, C. Willmott, Joshua Bendavid, Manuel Patrice Geisler, N. Mirman, H. Snoek, F. Romeo, M. Marone, N. Wickramage, A. Sakharov, Guofan Hu, Alexander Toropin, Hwi Dong Yoo, M. Selvaggi, K. Ocalan, D. Horton, V. Knünz, L. Perchalla, Aram Apyan, E. Avdeeva, F. Thyssen, Yuan Chao, John Perry Cumalat, E. Berry, Valentin Sulimov, B. Bilin, Oliver Pooth, R. Schmidt, A. De Cosa, Jan Steggemann, Fiorenza Micheli, Thomas Weiler, Paolo Vitulo, Jay Roberts, Cristina Ferro, A. Zhokin, Alain Martelli, P. Spagnolo, Andrew R. Tapper, P. Paganini, M. Park, A. Nowack, Yuri Gershtein, Debarun Dutta, S. Paktinat Mehdiabadi, Leander Litov, Joerg Behr, M. Olschewski, Tomasz Frueboes, K. Ozdemir, L. Barbone, A. Ghezzi, J. Anderson, B. Calvert, A. Pozdnyakov, H. Mendez, Efstathios Stiliaris, Michael Seidel, Gianluca Petrillo, N. Golubev, Ivan Glushkov, A. Meyer, Sven Dildick, Frank Hartmann, D. Renker, Gouranga Kole, Andreas Hinzmann, Vasile Mihai Ghete, T. Rovelli, S. Girgis, W. A. Khan, Matt J. Jarvis, Z. Antunovic, Shivani Ahuja, S. Petrushanko, R. Magaña Villalba, V. Brigljevic, Olga Novgorodova, M. Friedl, Pushpalatha C Bhat, N. Beliy, F. Ligabue, J. Luetic, Ivan Amos Cali, Ilya Osipenkov, Ian Macneill, Norbert Neumeister, V. Golovtsov, M. Calderon De La Barca Sanchez, C. Mariotti, C. Seez, R. Carlin, D. Baumgartel, D. Piparo, Chris Sander, S. Xie, K. Deiters, S. Gollapinni, Thomas Hauth, C. Botta, S. Sanders, Philip H Butler, Daniel Berry, Sunita Chauhan, Paul Edmund Karchin, Daijin Kim, C. Fernandez Bedoya, G. G. Da Silveira, H. Xiao, M. Hildreth, Arshad Saleem Bhatti, Leonardo Benucci, Claire Shepherd-Themistocleous, Benoit Roland, G. Ryu, I. Puljak, Robert Cousins, J. Krolikowski, S. Goy Lopez, Enrico Robutti, George Stephans, A. Ferapontov, Suzan Basegmez, S. M. Etesami, P. Capiluppi, S. Morovic, Eric Takasugi, Isabell-Alissandra Melzer-Pellmann, W-S Hou, C. Cowden, J. Rodrigues Antunes, T. Peltola, Joao Seixas, Francisco Matorras, Nicola Pacifico, Sergio P Ratti, A. Racz, Wesley H Smith, M. Planer, I. Gonzalez Caballero, Davide Piccolo, T. Pearson, Vincenzo Monaco, H. Nogima, N. Amapane, Vitaly Smirnov, Dragos Velicanu, A. Messineo, C-E Wulz, L. Levchuk, M. Stein, Eija Tuominen, C. La Licata, Luigi Fiore, Roberval Walsh, W. Ferguson, N. Tambe, Akram Khan, M. Gallinaro, G. Mitselmakher, C. Martinez Rivero, D. Acosta, A. K. Sanchez, Oliver Gutsche, V. Palichik, Terence Libeiro, R. Plestina, T. Camporesi, M. Merola, M. H.G. Souza, James Zabel, H. Sakulin, Otilia Militaru, Sebastian Thüer, Colin Bernet, Nadia Pastrone, Fuqiang Wang, A. Ershov, Miroslav Finger, D. Giordano, M. Luk, N. Hörmann, Johannes Haller, M. Pimiä, Andrey Popov, Ming Yang, H. Geenen, Dave M Newbold, C. Calabria, D. Del Re, Peicho Petkov, Achille Petrilli, Helena Malbouisson, B. Gomez Moreno, Kajari Mazumdar, C. Kottachchi Kankanamge Don, Lawrence Sulak, B. Blumenfeld, Alyson E. Santoro, G. Garcia, A. Lanaro, W. Adam, A. Vorobyev, Austin Ball, U. E. Surat, E. Eskut, Manuel Aguilar-Benitez, Vanessa Gaultney, C. Justus, M. Merschmeyer, J. Berger, Y. Eshaq, M. Verzetti, Stefano Marcellini, M. Azarkin, G. P. Van Onsem, J. Incandela, P. Janot, A. Gilbert, Marcus Hohlmann, N. Lychkovskaya, Giovanna Selvaggi, V. Krutelyov, S. Boutle, M. Yalvac, T. Speer, D. Troendle, Bartolomeo Marangelli, D. Lincoln, Jose Chinellato, H. B. Newman, A. Baden, A. J. Zsigmond, Jessica Shiu, L. Pape, Quentin Ingram, Dmytro Kovalskyi, J.-P. Merlo, J. Butt, M. Searle, Paul Dauncey, Geoffrey Smith, J. N. Butler, A. Garcia-Bellido, Christopher Tully, A. Sobol, S. Naumann-Emme, U. Husemann, P. Verdier, Guido Tonelli, A. Mussgiller, M. Müntel, Christoph Paus, Peter Thomassen, Wolfgang Waltenberger, Nikolai Skatchkov, Piergiulio Lenzi, Y. Weng, Rosamaria Venditti, N. Valls, N. Shumeiko, P. Hebda, C. Hartl, N. Marinelli, Willard Johns, S. S. Yu, C. Vander Velde, X. Quan, Bożena Boimska, Kerem Cankocak, E. Gallo, J. Bochenek, Peter E. Schlein, L. Spiegel, N. Colino, S. Khalatyan, H. A. Weber, S. Schnetzer, F. Pauss, G. Auzinger, J. Varela, C. A. Carrillo Montoya, V. E. Bazterra, H. Gamsizkan, A. Delgado Peris, Ilknur Hos, S. Ganjour, T. Medvedeva, G. Flucke, K. Krajczar, M. Lethuillier, Abdollah Mohammadi, W. Martin, Hamish Silverwood, M. Cardaci, T. Aziz, J. Hegeman, Karl Matthew Ecklund, J. D'Hondt, Ignas Grigelionis, Burin Asavapibhop, Roberta Ferretti, Pamela E. Harris, Giuseppe Bagliesi, J. Erö, Jan Olzem, J. Salfeld-Nebgen, Lindsey Gray, J. R. Smith, S. Di Guida, B. Stieger, S. Stoynev, Sa. Jain, Jue Chen, M. Menichelli, Ta-Yung Ling, Christian Barth, Daniele Fasanella, R. Y. Zhu, Simone Paoletti, Paolo Lariccia, M. Cepeda, R. Conway, P. Van Mulders, James A. Ellison, P. Juillot, Gagan Bihari Mohanty, Jeffrey Richman, Gilvan Alves, T. Aliev, M. Gosselink, David Wood, Pavel Sorokin, Salvatore My, Niladri Sen, Pascal Vanlaer, Luciano Barone, Z. Hatherell, I. J. Cabrillo, J. Klukas, S. Tuo, A. Dabrowski, G. Franzoni, J. Konigsberg, Nikola Godinovic, Altan Cakir, Tomislav Seva, N. Dhingra, Torben Schum, S. Hewamanage, Christina Urscheler, V. I. Martinez Outschoorn, Helena Bialkowska, Erhan Gülmez, Aurelijus Rinkevicius, M. Kress, Jerry Goldstein, Erik Butz, P. Rumerio, M. Pioppi, Tai Sakuma, M. Ivova Rikova, Sunghyun Chang, V. 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Ivanov, Jorge Luis Rodriguez, Manuk Zubin Mehta, R. S. Höing, Sarah Catherine Eno, David Colling, Monika Grothe, A. Lath, Brian Dorney, M. De Mattia, Z. Szillasi, B. Pollack, Mariarosaria D'Alfonso, Mario Galanti, Joschka Lingemann, F. Raupach, J. Molnar, R. Klanner, Zheng Wang, G. Bauer, A. Pfeiffer, E. Tuovinen, A. Fanfani, A. Kyriakis, Y. W. Chang, M. Plagge, Maxim Goncharov, I. Ross, Richard D Field, Marco Pieri, R. Redjimi, Francesco Costanza, S. Chatrchyan, N. Tosi, T. Ferguson, Ian R Tomalin, L. Martini, P. Kurt, T. R. Fernandez Perez Tomei, A. C. Marini, M. Deniz, Michael Schmitt, R. P. Kenny, R. R. Betts, H. S. Chen, D. Bonacorsi, V. Epshteyn, Emmanuel Olaiya, Alexander Schmidt, Panos A Razis, R. Bellan, I. Azhgirey, Songkyo Lee, Nadir Daci, Lei Zhang, S. I. Cooper, H. Seo, M. I. Josa, K. Klein, Adrian Perieanu, N. Mccoll, R. N.C. Gray, F. Ratnikov, Alessandro Degano, Benjamin Henry Hooberman, Umesh Joshi, R. Kroeger, John Rander, C. Silkworth, Leonardo Sala, F. De Guio, D. Lopes Pegna, Sanjay Padhi, R. Houtz, S. Shalhout, P. Adzic, O. Bondu, Mohsen Khakzad, M. Chen, D. Creanza, Chris Lucas, Matthew Hollingsworth, Edouard Boos, Jose Flix, A. P. Singh, G. Hellwig, M. Gardner, A. Kalogeropoulos, U. Heintz, Ilya Kravchenko, Christopher Palmer, Ezio Torassa, R. Paramatti, Igor Dremin, W. Haj Ahmad, Balazs Ujvari, R. Ruchti, Abideh Jafari, G. H. Hammad, W. Wu, J. E. Cole, Francesca Cavallo, M. Ata, A. Dominguez, A. Markina, W. D. Zeuner, A. Tsirou, Y. J. Lei, E. Sexton-Kennedy, B. Rutherford, L. Masetti, M. Vander Donckt, A. Pashenkov, Sue Ann Koay, Y. M. Tzeng, A. Graziano, P. Kokkas, C. Autermann, Roberto Rossin, L. M. Villasenor-Cendejas, E. Salvati, S. Senkin, Aniello Nappi, E. A. Albayrak, Yuri Musienko, M. N. Bakirci, B. R. Drell, Peter Schleper, Zhen Hu, Keith Ulmer, Kerstin M. Stenson, Young-Il Choi, Alexx Perloff, Roman Ryutin, J. G. Acosta, Federica Primavera, A. Bean, P. Klabbers, Wenbo Li, F. Vazquez Valencia, Micah M. 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Breuker, T. Camporesi, G. Cerminara, T. Christiansen, J. A. Coarasa Perez, S. Colafranceschi, M. D’Alfonso, D. d’Enterria, A. Dabrowski, A. David, F. De Guio, A. De Roeck, S. De Visscher, S. Di Guida, M. Dobson, N. Dupont-Sagorin, A. Elliott-Peisert, J. Eugster, G. Franzoni, W. Funk, G. Georgiou, M. Giffel, D. Gigi, K. Gill, D. Giordano, M. Girone, M. Giunta, F. Glege, R. Gomez-Reino Garrido, S. Gowdy, R. Guida, J. Hammer, M. Hansen, P. Harri, C. Hartl, A. Hinzmann, V. Innocente, P. Janot, E. Karavaki, K. Kousouri, K. Krajczar, P. Lecoq, Y.-J. Lee, C. Lourenço, N. Magini, L. Malgeri, M. Mannelli, L. Masetti, F. Meijer, S. Mersi, E. Meschi, R. Moser, M. Mulder, P. Musella, E. Nesvold, L. Orsini, E. Palencia Cortezon, E. Perez, L. Perrozzi, A. Petrilli, A. Pfeiffer, M. Pierini, M. Pimiä, D. Piparo, M. Plagge, L. Quertenmont, A. Racz, W. Reece, G. Rolandi, M. Rovere, H. Sakulin, F. Santanastasio, C. Schäfer, C. Schwick, S. Sekmen, P. Siegrist, P. Silva, M. Simon, P. Sphica, D. Spiga, B. 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M. Kuo, S. W. Li, W. Lin, Y. J. Lu, R. Volpe, S. S. Yu, P. Bartalini, P. Chang, Y. H. Chang, Y. W. Chang, Y. Chao, K. F. Chen, C. Dietz, U. Grundler, W.-S. Hou, Y. Hsiung, K. Y. Kao, Y. J. Lei, R.-S. Lu, D. Majumder, E. Petrakou, X. Shi, J. G. Shiu, Y. M. Tzeng, M. Wang, B. Asavapibhop, N. Suwonjandee, A. Adiguzel, M. N. Bakirci, S. Cerci, C. Dozen, I. Dumanoglu, E. Eskut, S. Girgi, G. Gokbulut, E. Gurpinar, I. Ho, E. E. Kangal, A. Kayis Topaksu, G. Onengut, K. Ozdemir, S. Ozturk, A. Polatoz, K. Sogut, D. Sunar Cerci, B. Tali, H. Topakli, M. Vergili, I. V. Akin, T. Aliev, B. Bilin, S. Bilmi, M. Deniz, H. Gamsizkan, A. M. Guler, G. Karapinar, K. Ocalan, A. Ozpineci, M. Serin, R. Sever, U. E. Surat, M. Yalvac, M. Zeyrek, E. Gülmez, B. Isildak, M. Kaya, O. Kaya, S. Ozkorucuklu, N. Sonmez, H. Bahtiyar, E. Barla, K. Cankocak, Y. O. Günaydin, F. I. Vardarlı, M. Yücel, L. Levchuk, P. Sorokin, J. J. Brooke, E. Clement, D. Cussan, H. Flacher, R. Frazier, J. Goldstein, M. Grime, G. P. Heath, H. F. Heath, L. Kreczko, C. Luca, Z. Meng, S. Metson, D. M. Newbold, K. Nirunpong, S. Paramesvaran, A. Poll, S. Senkin, V. J. Smith, T. William, K. W. Bell, A. Belyaev, C. Brew, R. M. Brown, D. J. A. Cockerill, J. A. Coughlan, K. Harder, S. Harper, J. Ilic, E. Olaiya, D. Petyt, B. C. Radburn-Smith, C. H. Shepherd-Themistocleou, I. R. Tomalin, W. J. Womersley, R. Bainbridge, O. Buchmuller, D. Burton, D. Colling, N. Cripp, M. Cutajar, P. Dauncey, G. Davie, M. Della Negra, W. Ferguson, J. Fulcher, D. Futyan, A. Gilbert, A. Guneratne Bryer, G. Hall, Z. Hatherell, J. Hay, G. Ile, M. Jarvi, G. Karapostoli, M. Kenzie, R. Lane, R. Luca, L. Lyon, A.-M. Magnan, J. Marrouche, B. Mathia, R. Nandi, J. Nash, A. Nikitenko, J. Pela, M. Pesaresi, K. Petridi, M. Pioppi, D. M. Raymond, S. Rogerson, A. Rose, C. Seez, P. Sharp, A. Sparrow, A. Tapper, M. Vazquez Acosta, T. Virdee, S. Wakefield, N. Wardle, M. Chadwick, J. E. Cole, P. R. Hobson, A. Khan, P. Kyberd, D. Leggat, D. Leslie, W. Martin, I. D. Reid, P. Symond, L. Teodorescu, M. Turner, J. Dittmann, K. Hatakeyama, A. Kasmi, H. Liu, T. Scarborough, O. Charaf, S. I. Cooper, C. Henderson, P. Rumerio, A. Avetisyan, T. Bose, C. Fantasia, A. Heister, P. Lawson, D. Lazic, J. Rohlf, D. Sperka, J. St. John, L. Sulak, J. Alimena, G. Christopher, D. Cutt, Z. Demiragli, A. Ferapontov, A. Garabedian, U. Heintz, S. Jabeen, G. Kukartsev, E. Laird, G. Landsberg, M. Luk, M. Narain, M. Segala, T. Sinthuprasith, T. Speer, R. Breedon, G. Breto, M. Calderon De La Barca Sanchez, S. Chauhan, M. Chertok, J. Conway, R. Conway, P. T. Cox, R. Erbacher, M. Gardner, R. Houtz, W. Ko, A. Kopecky, R. Lander, T. Miceli, D. Pellett, J. Pilot, F. Ricci-Tam, B. Rutherford, M. Searle, S. Shalhout, J. Smith, M. Squire, M. Tripathi, S. Wilbur, R. Yohay, D. Cline, R. Cousin, S. Erhan, P. Everaert, C. Farrell, M. Felcini, J. Hauser, M. Ignatenko, C. Jarvi, G. Rakne, P. Schlein, E. Takasugi, P. Traczyk, V. Valuev, J. Babb, R. Clare, J. Ellison, J. W. Gary, G. Hanson, J. Heilman, P. Jandir, O. R. Long, A. Luthra, M. Malberti, H. Nguyen, A. Shriniva, J. Sturdy, S. Sumowidagdo, R. Wilken, S. Wimpenny, W. Andrew, J. G. Branson, G. B. Cerati, S. Cittolin, D. Evan, A. Holzner, R. Kelley, M. Lebourgeoi, J. Lett, I. Macneill, S. Padhi, C. Palmer, G. Petrucciani, M. Pieri, M. Sani, S. Simon, E. Sudano, M. Tadel, Y. Tu, A. Vartak, S. Wasserbaech, F. Würthwein, A. Yagil, J. Yoo, D. Barge, C. Campagnari, T. Danielson, K. Flower, P. Geffert, C. George, F. Golf, J. Incandela, C. Justu, D. Kovalskyi, V. Krutelyov, R. Magaña Villalba, N. Mccoll, V. Pavlunin, J. Richman, R. Rossin, D. Stuart, W. To, C. West, A. Apresyan, A. Bornheim, J. Bunn, Y. Chen, E. Di Marco, J. Duarte, D. Kcira, Y. Ma, A. Mott, H. B. Newman, C. Pena, C. Rogan, M. Spiropulu, V. Timciuc, J. Veverka, R. Wilkinson, S. Xie, R. Y. Zhu, V. Azzolini, A. Calamba, R. Carroll, T. Ferguson, Y. Iiyama, D. W. Jang, Y. F. Liu, M. Paulini, J. Ru, H. Vogel, I. Vorobiev, J. P. Cumalat, B. R. Drell, W. T. Ford, A. Gaz, E. Luiggi Lopez, U. Nauenberg, J. G. Smith, K. Stenson, K. A. Ulmer, S. R. Wagner, J. Alexander, A. Chatterjee, N. Eggert, L. K. Gibbon, W. Hopkin, A. Khukhunaishvili, B. Krei, N. Mirman, G. Nicolas Kaufman, J. R. Patterson, A. Ryd, E. Salvati, W. Sun, W. D. Teo, J. Thom, J. Thompson, J. Tucker, Y. Weng, L. Winstrom, P. Wittich, D. Winn, S. Abdullin, M. Albrow, J. Anderson, G. Apollinari, L. A. T. Bauerdick, A. Beretva, J. Berryhill, P. C. Bhat, K. Burkett, J. N. Butler, V. Chetluru, H. W. K. Cheung, F. Chlebana, S. Cihangir, V. D. Elvira, I. Fisk, J. Freeman, Y. Gao, E. Gottschalk, L. Gray, D. Green, O. Gutsche, D. Hare, R. M. Harri, J. Hirschauer, B. Hooberman, S. Jindariani, M. Johnson, U. Joshi, K. Kaadze, B. Klima, S. Kunori, S. Kwan, J. Linacre, D. Lincoln, R. Lipton, J. Lykken, K. Maeshima, J. M. Marraffino, V. I. Martinez Outschoorn, S. Maruyama, D. Mason, P. McBride, K. Mishra, S. Mrenna, Y. Musienko, C. Newman-Holme, V. O’Dell, O. Prokofyev, N. Ratnikova, E. Sexton-Kennedy, S. Sharma, W. J. Spalding, L. Spiegel, L. Taylor, S. Tkaczyk, N. V. Tran, L. Uplegger, E. W. Vaandering, R. Vidal, J. Whitmore, W. Wu, F. Yang, J. C. Yun, D. Acosta, P. Avery, D. Bourilkov, M. Chen, T. Cheng, S. Da, M. De Gruttola, G. P. Di Giovanni, D. Dobur, A. Drozdetskiy, R. D. Field, M. Fisher, Y. Fu, I. K. Furic, J. Hugon, B. Kim, J. Konigsberg, A. Korytov, A. Kropivnitskaya, T. Kypreo, J. F. Low, K. Matchev, P. Milenovic, G. Mitselmakher, L. Muniz, R. Remington, A. Rinkeviciu, N. Skhirtladze, M. Snowball, J. Yelton, M. Zakaria, V. Gaultney, S. Hewamanage, S. Linn, P. Markowitz, G. Martinez, J. L. Rodriguez, T. Adam, A. Askew, J. Bochenek, J. Chen, B. Diamond, J. Haa, S. Hagopian, V. Hagopian, K. F. Johnson, H. Prosper, V. Veeraraghavan, M. Weinberg, M. M. Baarmand, B. Dorney, M. Hohlmann, H. Kalakhety, F. Yumiceva, M. R. Adam, L. Apanasevich, V. E. Bazterra, R. R. Bett, I. Bucinskaite, J. Callner, R. Cavanaugh, O. Evdokimov, L. Gauthier, C. E. Gerber, D. J. Hofman, S. Khalatyan, P. Kurt, F. Lacroix, D. H. Moon, C. O’Brien, C. Silkworth, D. Strom, P. Turner, N. Varela, U. Akgun, E. A. Albayrak, B. Bilki, W. Clarida, K. Dilsiz, F. Duru, S. Griffith, J.-P. Merlo, H. Mermerkaya, A. Mestvirishvili, A. Moeller, J. Nachtman, C. R. Newsom, H. Ogul, Y. Onel, F. Ozok, S. Sen, P. Tan, E. Tira, J. Wetzel, T. Yetkin, K. Yi, B. A. Barnett, B. Blumenfeld, S. Bolognesi, G. Giurgiu, A. V. Gritsan, G. Hu, P. Maksimovic, C. Martin, M. Swartz, A. Whitbeck, P. Baringer, A. Bean, G. Benelli, R. P. Kenny, M. Murray, D. Noonan, S. Sander, R. Stringer, J. S. Wood, A. F. Barfu, I. Chakaberia, A. Ivanov, S. Khalil, M. Makouski, Y. Maravin, L. K. Saini, S. Shrestha, I. Svintradze, J. Gronberg, D. Lange, F. Rebassoo, D. Wright, A. Baden, B. Calvert, S. C. Eno, J. A. Gomez, N. J. Hadley, R. G. Kellogg, T. Kolberg, Y. Lu, M. Marionneau, A. C. Mignerey, K. Pedro, A. Peterman, A. Skuja, J. Temple, M. B. Tonje, S. C. Tonwar, A. Apyan, G. Bauer, W. Busza, I. A. Cali, M. Chan, L. Di Matteo, V. Dutta, G. Gomez Ceballo, M. Goncharov, D. Gulhan, Y. Kim, M. Klute, Y. S. Lai, A. Levin, P. D. Luckey, T. Ma, S. Nahn, C. Pau, D. Ralph, C. Roland, G. Roland, G. S. F. Stephan, F. Stöckli, K. Sumorok, D. Velicanu, R. Wolf, B. Wyslouch, M. Yang, Y. Yilmaz, A. S. Yoon, M. Zanetti, V. Zhukova, B. Dahme, A. De Benedetti, A. Gude, J. Haupt, S. C. Kao, K. Klapoetke, Y. Kubota, J. Man, N. Pastika, R. Rusack, M. Sasseville, A. Singovsky, N. Tambe, J. Turkewitz, J. G. Acosta, L. M. Cremaldi, R. Kroeger, S. Olivero, L. Perera, R. Rahmat, D. A. Sander, D. Summer, E. Avdeeva, K. Bloom, S. Bose, D. R. Clae, A. Dominguez, M. Ead, R. Gonzalez Suarez, J. Keller, I. Kravchenko, J. Lazo-Flore, S. Malik, F. Meier, G. R. Snow, J. Dolen, A. Godshalk, I. Iashvili, S. Jain, A. Kharchilava, S. Rappoccio, Z. Wan, G. Alverson, E. Barberi, D. Baumgartel, M. Chasco, J. Haley, A. Massironi, D. Nash, T. Orimoto, D. Trocino, D. Wood, J. Zhang, A. Anastassov, K. A. Hahn, A. Kubik, L. Lusito, N. Mucia, N. Odell, B. Pollack, A. Pozdnyakov, M. Schmitt, S. Stoynev, K. Sung, M. Velasco, S. Won, D. Berry, A. Brinkerhoff, K. M. Chan, M. Hildreth, C. Jessop, D. J. Karmgard, J. Kolb, K. Lannon, W. Luo, S. Lynch, N. Marinelli, D. M. Morse, T. Pearson, M. Planer, R. Ruchti, J. Slaunwhite, N. Vall, M. Wayne, M. Wolf, L. Antonelli, B. Bylsma, L. S. Durkin, C. Hill, R. Hughe, K. Kotov, T. Y. Ling, D. Puigh, M. Rodenburg, G. Smith, C. Vuosalo, B. L. Winer, H. Wolfe, E. Berry, P. Elmer, V. Halyo, P. Hebda, J. Hegeman, A. Hunt, P. Jindal, S. A. Koay, P. Lujan, D. Marlow, T. Medvedeva, M. Mooney, J. Olsen, P. Piroué, X. Quan, A. Raval, H. Saka, D. Stickland, C. Tully, J. S. Werner, S. C. Zenz, A. Zuranski, E. Brownson, A. Lopez, H. Mendez, J. E. Ramirez Varga, E. Alagoz, D. Benedetti, G. Bolla, D. Bortoletto, M. De Mattia, A. Everett, Z. Hu, M. Jone, K. Jung, O. Koybasi, M. Kre, N. Leonardo, D. Lopes Pegna, V. Maroussov, P. Merkel, D. H. Miller, N. Neumeister, I. Shipsey, D. Silver, A. Svyatkovskiy, F. Wang, W. Xie, L. Xu, H. D. Yoo, J. Zablocki, Y. Zheng, N. Parashar, A. Adair, B. Akgun, K. M. Ecklund, F. J. M. Geurt, B. Michlin, B. P. Padley, R. Redjimi, J. Robert, J. Zabel, B. Betchart, A. Bodek, R. Covarelli, P. de Barbaro, R. Demina, Y. Eshaq, T. Ferbel, A. Garcia-Bellido, P. Goldenzweig, J. Han, A. Harel, D. C. Miner, G. Petrillo, D. Vishnevskiy, M. Zielinski, A. Bhatti, R. Ciesielski, L. Demortier, K. Gouliano, G. Lungu, C. Mesropian, S. Arora, A. Barker, J. P. Chou, C. Contreras-Campana, E. Contreras-Campana, D. Duggan, D. Ferencek, Y. Gershtein, R. Gray, E. Halkiadaki, D. Hida, A. Lath, S. Panwalkar, M. Park, R. Patel, V. Rekovic, J. Roble, S. Salur, S. Schnetzer, C. Seitz, S. Somalwar, R. Stone, S. Thoma, P. Thomassen, M. Walker, G. Cerizza, M. Hollingsworth, K. Rose, S. Spanier, Z. C. Yang, A. York, O. Bouhali, R. Eusebi, W. Flanagan, J. Gilmore, T. Kamon, V. Khotilovich, R. Montalvo, I. Osipenkov, Y. Pakhotin, A. Perloff, J. Roe, A. Safonov, T. Sakuma, I. Suarez, A. Tatarinov, D. Toback, N. Akchurin, C. Cowden, J. Damgov, C. Dragoiu, P. R. Dudero, K. Kovitanggoon, S. W. Lee, T. Libeiro, I. Volobouev, E. Appelt, A. G. Delannoy, S. Greene, A. Gurrola, W. John, C. Maguire, A. Melo, M. Sharma, P. Sheldon, B. Snook, S. Tuo, J. Velkovska, M. W. Arenton, S. Boutle, B. Cox, B. Franci, J. Goodell, R. Hirosky, A. Ledovskoy, C. Lin, C. Neu, J. Wood, S. Gollapinni, R. Harr, P. E. Karchin, C. Kottachchi Kankanamge Don, P. Lamichhane, A. Sakharov, D. A. Belknap, L. Borrello, D. Carlsmith, M. Cepeda, S. Dasu, S. Duric, E. Frii, M. Grothe, R. Hall-Wilton, M. Herndon, A. Hervé, P. Klabber, J. Kluka, A. Lanaro, R. Lovele, A. Mohapatra, I. Ojalvo, T. Perry, G. A. Pierro, G. Polese, I. Ro, T. Sarangi, A. Savin, W. H. Smith, and J. Swanson

Subjects
Physics, Particle physics, Large Hadron Collider, Physics and Astronomy (miscellaneous), 010308 nuclear & particles physics, CMS, Astrophysics::High Energy Astrophysical Phenomena, Detector, Monte Carlo method, Inverse, Radiation, 01 natural sciences, HEP, Gluon, 0103 physical sciences, Transverse momentum, High Energy Physics::Experiment, LHC, 010306 general physics, Engineering (miscellaneous), Coherence (physics)
Abstract

A study of color coherence effects in pp collisions at a center-of-mass energy of 7 TeV is presented. The data used in the analysis were collected in 2010 with the CMS detector at the LHC and correspond to an integrated luminosity of 36 inverse picobarns. Events are selected that contain at least three jets and where the two jets with the largest transverse momentum exhibit a back-to-back topology. The measured angular correlation between the second- and third-leading jet is shown to be sensitive to color coherence effects, and is compared to the predictions of Monte Carlo models with various implementations of color coherence. None of the models describe the data satisfactorily.

Published
2014

20. Probing the Transmembrane Structure and Topology of Microsomal Cytochrome-P450 by Solid-State NMR on Temperature-Resistant Bicelles

Author

Lucy Waskell, Kazutoshi Yamamoto, Melissa Gildenberg, Sang Choul Im, Paige Pearcy, Shivani Ahuja, and Ayyalusamy Ramamoorthy

Subjects
0303 health sciences, Magnetic Resonance Spectroscopy, Multidisciplinary, Chemistry, Lipid Bilayers, Peripheral membrane protein, Nuclear magnetic resonance spectroscopy, Model lipid bilayer, 010402 general chemistry, 01 natural sciences, Article, Transmembrane protein, Specimen Handling, 0104 chemical sciences, 03 medical and health sciences, Membrane, Cytochrome P-450 Enzyme System, Biochemistry, Solid-state nuclear magnetic resonance, Membrane protein, Microsomes, Liver, Biophysics, Humans, Lipid bilayer, 030304 developmental biology
Abstract

Though the importance of high-resolution structure and dynamics of membrane proteins has been well recognized, optimizing sample conditions to retain the native-like folding and function of membrane proteins for Nuclear Magnetic Resonance (NMR) or X-ray measurements has been a major challenge. While bicelles have been shown to stabilize the function of membrane proteins and are increasingly utilized as model membranes, the loss of their magnetic-alignment at low temperatures makes them unsuitable to study heat-sensitive membrane proteins like cytochrome-P450 and protein-protein complexes. In this study, we report temperature resistant bicelles that can magnetically-align for a broad range of temperatures and demonstrate their advantages in the structural studies of full-length microsomal cytochrome-P450 and cytochrome-b5 by solid-state NMR spectroscopy. Our results reveal that the N-terminal region of rabbit cytochrome-P4502B4, that is usually cleaved off to obtain crystal structures, is helical and has a transmembrane orientation with ~17° tilt from the lipid bilayer normal.

Published
2013

21. ¹H, ¹³C and ¹⁵N resonance assignments for the full-length mammalian cytochrome b₅ in a membrane environment

Author

Subramanian, Vivekanandan, Shivani, Ahuja, Sang-Choul, Im, Lucy, Waskell, and Ayyalusamy, Ramamoorthy

Subjects
Cytochromes b5, Phosphorylcholine, Cell Membrane, Animals, Rabbits, Nuclear Magnetic Resonance, Biomolecular, Micelles, Article
Abstract

Microsomal cytochrome b5 plays a key role in the oxidation of a variety of exogenous and endogenous compounds, including drugs, fatty acids, cholesterol and steroid hormones. To better understand its functional properties in a membrane mimic environment, we carried out high-resolution solution NMR studies. Here we report resonance assignments for full-length rabbit cytochrome b5 embedded in DPC (dodecylphosphocholine) micelles.

Published
2013

22. Structural Transitions of Transmembrane Helix 6 in the Formation of Metarhodopsin I

Author

Markus Eilers, Joseph A. Goncalves, Colleen Kirkup, Steven O. Smith, Carlos Simmerling, Shivani Ahuja, Philip J. Reeves, Mordechai Sheves, and Amiram Hirshfeld

Subjects
Rhodopsin, Magnetic Resonance Spectroscopy, genetic structures, Photoisomerization, Molecular Dynamics Simulation, Article, Protein Structure, Secondary, chemistry.chemical_compound, Isomerism, Materials Chemistry, Humans, Physical and Theoretical Chemistry, Carbon Isotopes, Binding Sites, biology, Nitrogen Isotopes, Chemistry, Retinal, Nuclear magnetic resonance spectroscopy, META II, Recombinant Proteins, Surfaces, Coatings and Films, Transmembrane domain, Crystallography, Dark state, HEK293 Cells, biology.protein, Salt bridge, sense organs
Abstract

Absorption of light by the visual pigment rhodopsin triggers a rapid cis-trans photoisomerization of its retinal chromophore and a series of conformational changes in both the retinal and protein. The largest structural change is an outward tilt of transmembrane helix H6 that increases the separation of the intracellular ends of H6 and H3 and opens up the G-protein binding site. In the dark state of rhodopsin, Glu247 at the intracellular end of H6 forms a salt bridge with Arg135 on H3 to tether H6 in an inactive conformation. The Arg135-Glu247 interaction is broken in the active state of the receptor, and Arg135 is then stabilized by interactions with Tyr223, Met257, and Tyr306 on helices H5, H6, and H7, respectively. To address the mechanism of H6 motion, solid-state NMR measurements are undertaken of Metarhodopsin I (Meta I), the intermediate preceding the active Metarhodopsin II (Meta II) state of the receptor. (13)C NMR dipolar recoupling measurements reveal an interhelical contact of (13)Cζ-Arg135 with (13)Cε-Met257 in Meta I but not with (13)Cζ-Tyr223 or (13)Cζ-Tyr306. These observations suggest that helix H6 has rotated in the formation of Meta I but that structural changes involving helices H5 and H7 have not yet occurred. Together, our results provide insights into the sequence of events leading up to the outward motion of H6, a hallmark of G protein-coupled receptor activation.

Published
2012

23. Partial Transmit Sequence with Convolutional codes for reducing the PAPR of the OFDM signal

Author

Pawan Sharma, Pallavi Hajela, Shivani Ahuja, and Seema Verma

Subjects
Computer science, Convolutional code, Orthogonal frequency-division multiplexing, business.industry, Power ratio, Real-time computing, Broadband, Bpsk modulation, Wireless, business, Algorithm, Phase-shift keying, Coding (social sciences)
Abstract

Orthogonal Frequency Division Multiplexing (OFDM) is a promising broadband technique. The drawback of high peak to average power ratio (PAPR) can outweigh all the potential benefits of OFDM. In this paper, the problem has been dealt by using Partial Transmit Sequence (PTS) along with Convolutional codes, a type of error correcting codes. PTS is a proven technique to reduce the PAPR in OFDM systems. It achieves considerable PAPR reduction without distortion; however the conventional PTS technique requires an exhaustive searching over all the combinations of the given phase factors. By considering the example of OFDM, with BPSK modulation, simulation results show that the combination of PTS and convolution coding performs well in reducing PAPR.

Published
2011

24. Highly conserved tyrosine stabilizes the active state of rhodopsin

Author

Steven O. Smith, Chikwado A. Opefi, Kieron South, Ekaterina Zaitseva, Joseph A. Goncalves, Shivani Ahuja, Philip J. Reeves, Reiner Vogel, and Markus Eilers

Subjects
Opsin, Rhodopsin, Magnetic Resonance Spectroscopy, Stereochemistry, Protein Conformation, education, Biology, Crystallography, X-Ray, Protein Structure, Secondary, Structure-Activity Relationship, Protein structure, Animals, Humans, Conserved Sequence, Multidisciplinary, Alanine, Protein Stability, Nuclear magnetic resonance spectroscopy, Chromophore, Biological Sciences, META II, Transmembrane domain, HEK293 Cells, Amino Acid Substitution, Helix, Mutation, biology.protein, Tyrosine, Cattle, Mutant Proteins, Ion Channel Gating, Signal Transduction
Abstract

Light-induced isomerization of the 11- cis- retinal chromophore in the visual pigment rhodopsin triggers displacement of the second extracellular loop (EL2) and motion of transmembrane helices H5, H6, and H7 leading to the active intermediate metarhodopsin II (Meta II). We describe solid-state NMR measurements of rhodopsin and Meta II that target the molecular contacts in the region of the ionic lock involving these three helices. We show that a contact between Arg135 3.50 and Met257 6.40 forms in Meta II, consistent with the outward rotation of H6 and breaking of the dark-state Glu134 3.49 -Arg135 3.50 -Glu247 6.30 ionic lock. We also show that Tyr223 5.58 and Tyr306 7.53 form molecular contacts with Met257 6.40 . Together these results reveal that the crystal structure of opsin in the region of the ionic lock reflects the active state of the receptor. We further demonstrate that Tyr223 5.58 and Ala132 3.47 in Meta II stabilize helix H5 in an active orientation. Mutation of Tyr223 5.58 to phenylalanine or mutation of Ala132 3.47 to leucine decreases the lifetime of the Meta II intermediate. Furthermore, the Y223F mutation is coupled to structural changes in EL2. In contrast, mutation of Tyr306 7.53 to phenylalanine shows only a moderate influence on the Meta II lifetime and is not coupled to EL2.

Published
2010

25. Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints

Author

Mordechai Sheves, Markus Eilers, Philip J. Reeves, Joseph A. Goncalves, Shivani Ahuja, Steven O. Smith, and Viktor Hornak

Subjects
Models, Molecular, Rhodopsin, Photoisomerization, genetic structures, Light, Protein Conformation, Protein Data Bank (RCSB PDB), Molecular Dynamics Simulation, Article, Molecular dynamics, Protein structure, Structural Biology, Animals, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular, biology, Chemistry, META II, Protein Structure, Tertiary, Transmembrane domain, Crystallography, Solid-state nuclear magnetic resonance, biology.protein, Biophysics, Cattle, sense organs
Abstract

Structural restraints provided by solid-state NMR measurements of the metarhodopsin II intermediate are combined with molecular dynamics simulations to help visualize structural changes in the light activation of rhodopsin. Since the timescale for the formation of the metarhodopsin II intermediate (> 1 ms) is beyond that readily accessible by molecular dynamics, we use NMR distance restraints derived from 13 C dipolar recoupling measurements to guide the simulations. The simulations yield a working model for how photoisomerization of the 11- cis retinylidene chromophore bound within the interior of rhodopsin is coupled to transmembrane helix motion and receptor activation. The mechanism of activation that emerges is that multiple switches on the extracellular (or intradiscal) side of rhodopsin trigger structural changes that converge to disrupt the ionic lock between helices H3 and H6 on the intracellular side of the receptor.

Published
2009

26. Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation

Author

Shivani Ahuja, Thomas P. Sakmar, Amiram Hirshfeld, Steven O. Smith, Elsa C. Y. Yan, Markus Eilers, Martine Ziliox, Viktor Hornak, Mordechai Sheves, Joseph A. Goncalves, Philip J. Reeves, and Natalie Syrett

Subjects
Models, Molecular, Rhodopsin, Light, Stereochemistry, Plasma protein binding, Crystal structure, Article, Cell Line, 03 medical and health sciences, Structural Biology, Extracellular, Animals, Humans, Receptor, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, 0303 health sciences, biology, Chemistry, 030302 biochemistry & molecular biology, Loop (topology), Retinaldehyde, Helix, biology.protein, Cattle, sense organs, Protein Binding
Abstract

The second extracellular loop (EL2) of rhodopsin forms a cap over the binding site of its photoreactive 11-cis retinylidene chromophore. A crucial question has been whether EL2 forms a reversible gate that opens upon activation or acts as a rigid barrier. Distance measurements using solid-state (13)C NMR spectroscopy between the retinal chromophore and the beta4 strand of EL2 show that the loop is displaced from the retinal binding site upon activation, and there is a rearrangement in the hydrogen-bonding networks connecting EL2 with the extracellular ends of transmembrane helices H4, H5 and H6. NMR measurements further reveal that structural changes in EL2 are coupled to the motion of helix H5 and breaking of the ionic lock that regulates activation. These results provide a comprehensive view of how retinal isomerization triggers helix motion and activation in this prototypical G protein-coupled receptor.

Published
2008

27. Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin

Author

Steven O. Smith, Amiram Hirshfeld, Mordechai Sheves, Shivani Ahuja, Viktor Hornak, Evan Crocker, and Markus Eilers

Subjects
Models, Molecular, Rhodopsin, Binding Sites, biology, Tryptophan, Retinal, META II, Protein Structure, Secondary, chemistry.chemical_compound, Crystallography, Transmembrane domain, chemistry, Solid-state nuclear magnetic resonance, Structural Biology, Magic angle spinning, biology.protein, Retinaldehyde, Animals, Molecular Biology, Isomerization, Nuclear Magnetic Resonance, Biomolecular, G protein-coupled receptor
Abstract

Isomerization of the 11- cis retinal chromophore in the visual pigment rhodopsin is coupled to motion of transmembrane helix H6 and receptor activation. We present solid-state magic angle spinning NMR measurements of rhodopsin and the metarhodopsin II intermediate that support the proposal that interaction of Trp265 6.48 with the retinal chromophore is responsible for stabilizing an inactive conformation in the dark, and that motion of the β-ionone ring allows Trp265 6.48 and transmembrane helix H6 to adopt active conformations in the light. Two-dimensional dipolar-assisted rotational resonance NMR measurements are made between the C19 and C20-methyl groups of the retinal and uniformly 13 C-labeled Trp265 6.48 . The retinal C20–Trp265 6.48 contact present in the dark-state of rhodopsin is lost in metarhodopsin II, and a new contact is formed with the C19 methyl group. We have previously shown that the retinal translates 4–5 A toward H5 in metarhodopsin II. This motion, in conjunction with the Trp–C19 contact, implies that the Trp265 6.48 side-chain moves significantly upon rhodopsin activation. NMR measurements also show that a packing interaction in rhodopsin between Trp265 6.48 and Gly121 3.36 is lost in metarhodopsin II, consistent with H6 motion away from H3. However, a close contact between Gly120 3.35 on H3 and Met86 2.53 on H2 is observed in both rhodopsin and metarhodopsin II, suggesting that H3 does not change orientation significantly upon receptor activation.

Published
2005

28. Correction to 'Cytochrome P450–Cytochrome-b5 Interaction in a Membrane Environment Changes 15N Chemical Shift Anisotropy Tensors'

Author

Ayyalusamy Ramamoorthy, Lucy Waskell, Rui Huang, Shivani Ahuja, Manoj Kumar Pandey, Subramanian Vivekanandan, and Sang Choul Im

Subjects
Membrane, Nuclear magnetic resonance, biology, Chemistry, Chemical physics, Cytochrome b5, Materials Chemistry, biology.protein, Cytochrome P450, Physical and Theoretical Chemistry, Anisotropy, Surfaces, Coatings and Films
Published
2014

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