DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 8,569,057 B2 Wehrman Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) United States Patent (10) Patent No.: US 8,569,057 B2 Wehrman Et Al US008569057B2 (12) United States Patent (10) Patent No.: US 8,569,057 B2 Wehrman et al. (45) Date of Patent: Oct. 29, 2013 (54) MONITORING PROTEIN TRAFFICKING OTHER PUBLICATIONS USING BETA-GALACTOSIDASE REPORTER FRAGMENT COMPLEMENTATION Emr, et al., “Invertase beta-galactosidase hybrid proteins fail to be transported from the endoplasmic reticulum in Saccharomyces (75) Inventors: Thomas S. Wehrman, Mountain View, cerevisiae', Mol. Cell. Biol. 1984, 4(11):2347-2355. CA (US); Daniel Bassoni, Campbell, Drake, et al., “Trafficing of G protein-coupled receptors'. Circ. Research, Sep. 15, 2006, vol. 99, No. 6, pp. 570-582. CA (US); William Raab, San Francisco, International Search Report and Written Opinion, PCT/US 12/ CA (US) 043839, Sep. 7, 2012. Jin, et al. “Disease-associated mutations affect GPR56 protein traf (73) Assignee: DiscoveRx Corporation, Fremont, CA ficking and cell Surface expression'. Human Molecular Genetics, (US) 2007, vol. 16, No. 16, pp. 1972-1985. Mollinari, et al., “Role of EDEM in the release of misfolded (*) Notice: Subject to any disclaimer, the term of this glycoproteins from the calnexin cycle”. Science, vol. 299, Feb. 28. patent is extended or adjusted under 35 2003, pp. 1397-1400. U.S.C. 154(b) by 0 days. Conn, et al., “G protein-coupled receptor trafficking in health and disease: lessons learned to prepare for therapeutic mutant rescue in vivo”. Pharmacological Reviews, vol. 59, No. 3, 2007, pp. 225-250. (21) Appl. No.: 13/531,230 Stephenson, "Structure and trafficking of NMDA and GABA-a receptors'. Biochemical Society Transactions (2006) vol. 34, part 5, (22) Filed: Jun. 22, 2012 pp. 877-881. Petaja-Repo, et al., “Ligands act as pharmacological chaperones and (65) Prior Publication Data increase the efficiency of delta opioid receptor maturation'. The EMBO Journal, vol. 21, No. 7, 2002, pp. 1628-1637. US 2012/0329075A1 Dec. 27, 2012 Lilley, et al. A membrane protein required for dislocation of misfolded proteins from the ER', Nature, vol. 429, Jun. 24, 2004, pp. 834-840. Related U.S. Application Data Li, et al., “Bone morphogenetic protein type II receptor mutations causing protein misfolding inheritable pulmonary arterial hyperten (60) Provisional application No. 61/571,315, filed on Jun. sion”. Proceedings of the American Thoracic Society, vol. 7, 2010, 23, 2011. pp. 395-398. Zeng, et al., “Conserved extracellular cysteine pair in the M3 (51) Int. Cl. muscarinic acetylcholine receptor is essential for proper receptor cell CI2N 5/02 Surface localization but not for G protein coupling'. Journal of (2006.01) Neurochemistry, 72, 1999, pp. 2404-2414. (52) U.S. Cl. Hammer, et al., “A novel enzyme complementation-based assay for USPC .......................................................... 435/375 monitoring G-protein-coupled receptor internalization'. The FASEB (58) Field of Classification Search Journal, vol. 21, Dec. 2007, pp. 3827-3834. None Dong, et al., “Regulation of G protein-coupled receptor export traf See application file for complete search history. ficking, Biochim Biophys Acta., Apr. 2007: 1768(4): 853-870. Primary Examiner — Michael Pak (56) References Cited (74) Attorney, Agent, or Firm — David J. Aston; Peters U.S. PATENT DOCUMENTS Verny, LLP 4,378.428 A 3, 1983 Farina et al. (57) ABSTRACT 4,708,929 A 11, 1987 Henderson 5,037,735 A 8, 1991 Khanna et al. Methods and materials are disclosed for use in an enzyme 5,106,950 A 4, 1992 Farina et al. fragment complementation assay using complementary frag 5,362.625 A 11/1994 Krevolin et al. 5,464,747 A 11/1995 Eisenbeis et al. ments off-galactosidase to study the trafficking of proteins in 5,604,091 A 2f1997 Henderson a cell. Compounds that bind to a target peptide have been 5,643,734 A 7, 1997 Henderson found to affect protein folding and therefore trafficking. 2003/0219848 A1 1 1/2003 Naqvi et al. B-Galactosidase fragments, an enzyme donor (ED) and an 2007/0275397 A1 11/2007 Wehrman et al. 2009/0098588 A1 4/2009 Wehrman et al. enzyme acceptor (EA), are fused to a target peptide and to an 2010.004 1052 A1 2/2010 Feng et al. intracellular compartment protein, wherein the compartment 2010, 0120063 A1 5/2010 Bassoni et al. is involved in intracellular trafficking. Contacting the cell 2010/02O3555 A1 8, 2010 Wehrman et al. 2010/0285451 A1 11/2010 Blau et al. with a compound that binds to the target peptide results in 2011/O130543 A1 6, 2011 Stevens et al. enhanced movement of the protein through the cellular traf ficking pathway comprised of the endoplasmic reticulum, FOREIGN PATENT DOCUMENTS Golgi apparatus, the plasma membrane, endosomes, etc. Using this approach, compounds that bind to a target peptide WO 92.03559 A2 3, 1992 WO 96, 19732 A1 6, 1996 and alter its ability to traffic through the normal cellular WO OO,39348 A1 T 2000 pathway can be readily detected. WO 01 00214 A1 1, 2001 WO 01.60840 A2 8, 2001 8 Claims, 6 Drawing Sheets U.S. Patent Oct. 29, 2013 Sheet 1 of 6 US 8,569,057 B2 PM 4 ProLinkTM / Figure 1 U.S. Patent Oct. 29, 2013 Sheet 2 of 6 US 8,569,057 B2 O. +test compoundA . 202 . i. th a Figure 2 U.S. Patent Oct. 29, 2013 Sheet 3 of 6 US 8,569,057 B2 Ion Channel Trafficking Generating Figure 3 U.S. Patent Oct. 29, 2013 Sheet 4 of 6 US 8,569,057 B2 U2OS Endo-EA ADRB2(W158A)-PK Clone 175OO 15OOO 125OO 1 OOOO 75OO 5OOO 25OO O 10-11 10-10 10-9 10-8 10-7 10-6 10-5 Propanolol (M) Figure 4 U.S. Patent Oct. 29, 2013 Sheet 5 of 6 US 8,569,057 B2 U2OS 5-EAPLC(PH)-Ea KCNH2-PK (mut) 35000 E. Clofilium A Haloperidol V Astemizole 10-11 10-10 10-9 10-8 10-7 10-6 10-5 10-4 Compound (M) Figure 5 U.S. Patent Oct. 29, 2013 Sheet 6 of 6 US 8,569,057 B2 U20S5-EAPLC(PH)-EACHRM4(DC)-PK 60000 LY2033298 50000 A WUO239429 40000 v VU10010 O 4 OXOM 30000 O XanOmeline Oxalate 20000 4-DAMP 10000 109 108 O-7 06 0-5 10-4 103 10-2 Compound (M) Figure 6 US 8,569,057 B2 1. 2 MONITORNG PROTEIN TRAFFICKING LF Jr., 1994 GCRDb: a G-protein-coupled receptor database, USING BETA-GALACTOSIDASE REPORTER Receptors Channels 2 (1): 1-7: Foord S. M. Bonner T I, FRAGMENT COMPLEMENTATION Neubig RR, Rosser EM, Pin JP, Davenport AP Spedding M, Harmar A. J. 2005, International Union of Pharmacology. CROSS-REFERENCE TO RELATED XLVI.G protein-coupled receptor list, Pharmacol Rev 57(2): APPLICATIONS 279-88, InterPro). GPCR's broadly can be grouped into six classes based on sequence homology and functional similar This application claims priority from U.S. Provisional ity, as follows. Patent Application No. 61/571,315 filed on Jun. 23, 2011, which is hereby incorporated by reference. 10 STATEMENT OF GOVERNMENTAL SUPPORT Class A (Rhodopsin-like) Class B (Secretin receptor family) Class C (Metabotropic glutamate?pheromone) None. Class D (Fungal mating pheromone receptors) 15 Class E (Cyclic AMP receptors) REFERENCE TO SEQUENCE LISTING, Class F (Frizzled Smoothened) COMPUTER PROGRAM, OR COMPACT DISK A GPCR adopts a tertiary structure with the seven trans The instant application contains a Sequence Listing which membrane helices which forms a cavity within the plasma has been submitted as an ASCII text file and is hereby incor membrane and the cavity serves as a ligand-binding domain. porated by reference in its entirety. This text file was created Another common structural feature amongst GPCRs is on Jun. 21, 2012, is named “3817 36 1 Seq List.txt and palmitoylation of one or more sites of the C-terminal tail or is 12.412 bytes in size. the intracellular loops which has the effect of targeting the BACKGROUND OF THE INVENTION 25 receptor to cholesterol and sphingolipid-rich microdomains of the plasma membrane called lipid rafts and have a role to 1. Field of the Invention participate in rapid receptor signaling. The present invention relates to the field of assays for Ion channels represent another class of membrane protein measuring the intracellular movement (“trafficking) of pro complexes that play an important function of facilitating the teins containing at least one transmembrane domain, such as 30 diffusion of ions across the biological membranes. They act a cell Surface receptor. as electrical insulators and provide a high conducting, hydro 2. Related Art philic pathway across the hydrophobic interior of the mem Presented below is background information on certain brane. Their mode of action is highly gated and they switch aspects of the present invention as they may relate to technical their confirmations between closed and open States. Depend features referred to in the detailed description, but not neces 35 ing on the chemical and physical modulators that control the sarily described in detail. That is, individual parts or methods gating activity-ion channels can be classified into the follow used in the present invention may be described in greater ing groups: detail in the materials discussed below, which materials may 1. Ligand-gated channels provide further guidance to those skilled in the art for making 2. Voltage-gated channels or using certain aspects of the present invention as claimed. 40 The discussion below should not be construed as an admis 3. Second-messenger gated channels sion as to the relevance of the information to any claims 4. Mechanosensitive channels herein or the prior art effect of the material described. 5. Gap junctions Protein synthesis and its processing are highly regulated There area number of human disorders that can result from events done in a tightly scrutinized and controlled manner at 45 the transcriptional, translational and post-translational levels misfolded/mutated protein ion channels.
Load more

Recommended publications
  • Characterisation of the Α1b-Adrenoceptor by Modeling, Dynamics and Virtual Screening Kapil Jain B.Pharm, M.S.(Pharm.)
    Characterisation of the α1B-Adrenoceptor by Modeling, Dynamics and Virtual Screening Kapil Jain B.Pharm, M.S.(Pharm.) A Thesis submitted for the degree of Master of Philosophy at The University of Queensland in 2018 Institute for Molecular Bioscience 0 Abstract G protein-coupled receptors (GPCRs) are the largest druggable class of proteins yet relatively little is known about the mechanism by which agonist binding induces the conformational changes necessary for G protein activation and intracellular signaling. Recently, the Kobilka group has shown that agonists, neutral antagonists and inverse agonists stabilise distinct extracellular surface (ECS) conformations of the β2-adrenergic receptor (AR) opening up new possibilities for allosteric drug targeting at GPCRs. The goal of this project is to extend these studies to define how the ECS conformation of the α1B-AR changes during agonist binding and develop an understanding of ligand entry and exit mechanisms that may help in the design of specific ligands with higher selectivity, efficacy and longer duration of action. Two parallel approaches were initiated to identify likely functional residues. The role of residues lining the primary binding site were predicted by online web server (Q-Site Finder) while secondary binding sites residues were predicted from molecular dynamics (MD) simulations. Predicted functionally significant residues were mutated and their function was established using FLIPR, radioligand and saturation binding assays. Despite the α1B-AR being pursued as a drug target for over last few decades, few specific agonists and antagonists are known to date. In an attempt to address this gap, we pursued ligand-based approach to find potential new leads.
    [Show full text]
  • Computational Methods for Prediction and Classification of G Protein-Coupled Receptors Khodeza Begum University of Texas at El Paso, [email protected]
    University of Texas at El Paso DigitalCommons@UTEP Open Access Theses & Dissertations 2017-01-01 Computational methods for prediction and classification of G protein-coupled receptors Khodeza Begum University of Texas at El Paso, [email protected] Follow this and additional works at: https://digitalcommons.utep.edu/open_etd Part of the Bioinformatics Commons, Computer Sciences Commons, and the Mathematics Commons Recommended Citation Begum, Khodeza, "Computational methods for prediction and classification of G protein-coupled receptors" (2017). Open Access Theses & Dissertations. 408. https://digitalcommons.utep.edu/open_etd/408 This is brought to you for free and open access by DigitalCommons@UTEP. It has been accepted for inclusion in Open Access Theses & Dissertations by an authorized administrator of DigitalCommons@UTEP. For more information, please contact [email protected]. COMPUTATIONAL METHODS FOR PREDICTION AND CLASSIFICATION OF G PROTEIN-COUPLED RECEPTORS KHODEZA BEGUM Master’s Program in Computational Science APPROVED: Ming-Ying Leung, Ph.D., Chair Rachid Skouta, Ph.D. Xiaogang Su, Ph.D. Charlotte M. Vines, Ph.D. Charles Ambler, Ph.D. Dean of the Graduate School Copyright © by Khodeza Begum 2017 COMPUTATIONAL METHODS FOR PREDICTION AND CLASSIFICATION OF G PROTEIN-COUPLED RECEPTORS by KHODEZA BEGUM, B.S. THESIS Presented to the Faculty of the Graduate School of The University of Texas at El Paso in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE COMPUTATIONAL SCIENCE PROGRAM THE UNIVERSITY OF TEXAS AT EL PASO December 2017 Acknowledgements I would first like to thank my advisor Dr. Ming-Ying Leung for the continuous support and encouragement in my study and thesis.
    [Show full text]
  • Molecular Dissection of G-Protein Coupled Receptor Signaling and Oligomerization
    MOLECULAR DISSECTION OF G-PROTEIN COUPLED RECEPTOR SIGNALING AND OLIGOMERIZATION BY MICHAEL RIZZO A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology December, 2019 Winston-Salem, North Carolina Approved By: Erik C. Johnson, Ph.D. Advisor Wayne E. Pratt, Ph.D. Chair Pat C. Lord, Ph.D. Gloria K. Muday, Ph.D. Ke Zhang, Ph.D. ACKNOWLEDGEMENTS I would first like to thank my advisor, Dr. Erik Johnson, for his support, expertise, and leadership during my time in his lab. Without him, the work herein would not be possible. I would also like to thank the members of my committee, Dr. Gloria Muday, Dr. Ke Zhang, Dr. Wayne Pratt, and Dr. Pat Lord, for their guidance and advice that helped improve the quality of the research presented here. I would also like to thank members of the Johnson lab, both past and present, for being valuable colleagues and friends. I would especially like to thank Dr. Jason Braco, Dr. Jon Fisher, Dr. Jake Saunders, and Becky Perry, all of whom spent a great deal of time offering me advice, proofreading grants and manuscripts, and overall supporting me through the ups and downs of the research process. Finally, I would like to thank my family, both for instilling in me a passion for knowledge and education, and for their continued support. In particular, I would like to thank my wife Emerald – I am forever indebted to you for your support throughout this process, and I will never forget the sacrifices you made to help me get to where I am today.
    [Show full text]
  • Steven, Stacy (2012) the Pharmacology of the 5-HT2A Receptor and the Difficulty Surrounding Single Taret Models
    Steven, Stacy (2012) The pharmacology of the 5-HT2A receptor and the difficulty surrounding single taret models. MSc(R) thesis. http://theses.gla.ac.uk/3636/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] The pharmacology of the 5-HT2A receptor and the difficulty surrounding functional studies with single target models A thesis presented for the degree of Master of Science by research Stacy Steven April 2012 Treatment of many disorders can be frequently problematic due to the relatively non selective nature of many drugs available on the market. Symptoms can be complex and expansive, often leading to symptoms representing other disorders in addition to the primary reason for treatment. In particular mental health disorders fall prey to this situation. Targeting treatment can be difficult due to the implication of receptors in more than one disorder, and more than one receptor in a single disorder. In the instance of GPCRs, receptors such as the serotonin receptors (and in particular the 5-HT2A for the interest of this research) belong to a large family of receptors, the GPCR Class A super family.
    [Show full text]
  • Insights Into Nuclear G-Protein-Coupled Receptors As Therapeutic Targets in Non-Communicable Diseases
    pharmaceuticals Review Insights into Nuclear G-Protein-Coupled Receptors as Therapeutic Targets in Non-Communicable Diseases Salomé Gonçalves-Monteiro 1,2, Rita Ribeiro-Oliveira 1,2, Maria Sofia Vieira-Rocha 1,2, Martin Vojtek 1,2 , Joana B. Sousa 1,2,* and Carmen Diniz 1,2,* 1 Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; [email protected] (S.G.-M.); [email protected] (R.R.-O.); [email protected] (M.S.V.-R.); [email protected] (M.V.) 2 LAQV/REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal * Correspondence: [email protected] (J.B.S.); [email protected] (C.D.) Abstract: G-protein-coupled receptors (GPCRs) comprise a large protein superfamily divided into six classes, rhodopsin-like (A), secretin receptor family (B), metabotropic glutamate (C), fungal mating pheromone receptors (D), cyclic AMP receptors (E) and frizzled (F). Until recently, GPCRs signaling was thought to emanate exclusively from the plasma membrane as a response to extracellular stimuli but several studies have challenged this view demonstrating that GPCRs can be present in intracellular localizations, including in the nuclei. A renewed interest in GPCR receptors’ superfamily emerged and intensive research occurred over recent decades, particularly regarding class A GPCRs, but some class B and C have also been explored. Nuclear GPCRs proved to be functional and capable of triggering identical and/or distinct signaling pathways associated with their counterparts on the cell surface bringing new insights into the relevance of nuclear GPCRs and highlighting the Citation: Gonçalves-Monteiro, S.; nucleus as an autonomous signaling organelle (triggered by GPCRs).
    [Show full text]
  • A REVOLUTION in the PHYSIOLOGY of the LIVING CELL FUTURE ANNUAL MEETINGS of by Gilbert N
    A REVOLUTION IN THE PHYSIOLOGY OF THE LIVING CELL FUTURE ANNUAL MEETINGS OF by Gilbert N. Ling Orig. Ed. 1992 404 pp. $64.50 THE AMERICAN SOCIETY FOR ISBN 0-89464-398-3 CELL BIOLOGY The essence of a major revolution in cell physiology -the first since the cell was recognized as the basic unit of life a century and a half ago - is presented and altemative theories are discussed in this text. Although the conventional mem- brane-pump theory is still being taught, a new theory of the living cell, called the association-induction hypothesis has been proposed. It has successfullywfthstood 1995 twenty-five years of worldwide testing and has already generated an enhancing DC diagnostic tool ofgreat power, magnetic resonance imaging (MRI).This volume is Washington, intended forteachers, students and researchers ofbiology and medicine. December 9-13 i't...a correct basic theory of cell physiology, besides its great intrinsic value in mankind's search forknowledge aboutourselves and the world we live in, willalso play a crucial role in the ultimate conquest of cancer, AIDS, and other incurable 1996 diseases.'-from the Introduction. ASCB Annual Meeting/ on Cell Biology t When ordering please add t".Ling turns cellphysiology upside down. He Sixth International Congress $5.00 first bookl$1.50 each ad- practicallyredefines the cell. He provides com- San Francisco, California ditional book to cover shipping pellingevidencefor headequacyofhis theoryn December 7-11 charges. Foreign shipping costs evidence that cannot fail to impress even the available upon request. most extreme skeptics....'- Gerald H. Pollock, _ Ph.D., Univ. ofWashington.
    [Show full text]
  • Biased Signaling of G Protein Coupled Receptors (Gpcrs): Molecular Determinants of GPCR/Transducer Selectivity and Therapeutic Potential
    Pharmacology & Therapeutics 200 (2019) 148–178 Contents lists available at ScienceDirect Pharmacology & Therapeutics journal homepage: www.elsevier.com/locate/pharmthera Biased signaling of G protein coupled receptors (GPCRs): Molecular determinants of GPCR/transducer selectivity and therapeutic potential Mohammad Seyedabadi a,b, Mohammad Hossein Ghahremani c, Paul R. Albert d,⁎ a Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Iran b Education Development Center, Bushehr University of Medical Sciences, Iran c Department of Toxicology–Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Iran d Ottawa Hospital Research Institute, Neuroscience, University of Ottawa, Canada article info abstract Available online 8 May 2019 G protein coupled receptors (GPCRs) convey signals across membranes via interaction with G proteins. Origi- nally, an individual GPCR was thought to signal through one G protein family, comprising cognate G proteins Keywords: that mediate canonical receptor signaling. However, several deviations from canonical signaling pathways for GPCR GPCRs have been described. It is now clear that GPCRs can engage with multiple G proteins and the line between Gprotein cognate and non-cognate signaling is increasingly blurred. Furthermore, GPCRs couple to non-G protein trans- β-arrestin ducers, including β-arrestins or other scaffold proteins, to initiate additional signaling cascades. Selectivity Biased Signaling Receptor/transducer selectivity is dictated by agonist-induced receptor conformations as well as by collateral fac- Therapeutic Potential tors. In particular, ligands stabilize distinct receptor conformations to preferentially activate certain pathways, designated ‘biased signaling’. In this regard, receptor sequence alignment and mutagenesis have helped to iden- tify key receptor domains for receptor/transducer specificity.
    [Show full text]
  • 2. G-Protein-Coupled Receptors (Gpcrs) 6
    DIPLOMARBEIT / DIPLOMA THESIS Titel der Diplomarbeit / Title of the Diploma Thesis „Odorant receptors“ verfasst von / submitted by Girgis Noser angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Magister der Pharmazie (Mag.pharm.) Wien, 2016 / Vienna, 2016 Studienkennzahl lt. Studienblatt / A 996 449 degree programme code as it appears on the student record sheet: Studienrichtung lt. Studienblatt / Gleichwertigkeit Pharmazie degree programme as it appears on the student record sheet: Betreut von / Supervisor: Univ. Prof. Mag. Dr. G. Buchbauer Contents Acknowledgement III Zusammenfassung IV Abstract V General Introduction in German 1 General Introduction in English 2 1.1 Anatomy of olfactory system 3 1.2 Olfactory Epithelium 4 1.3 The olfactory bulb (OB) 4 1.4 Olfactory sensory neuron cell structure 5 2. G-protein-coupled receptors (GPCRs) 6 2.1 G-Protein-coupled receptors, classification 7 2.2 GPCRs structure. 10 2.3 Bovine Rhodopsin model 11 2.4 GPCRs activation and signaling. 15 2.4.1 Mechanism of signaling formation. 15 2.4.2 G-protein-dependent and independent signaling pathways 18 2.4.3 Terminating the signal 18 2.4.4 Types of ligand according to biological response 18 3. Olfactory receptors (ORs) 19 3.1 ORs genes as the largest gene known superfamily in GPCRs. 19 3.2 ORs genes classification and nomenclature 21 I 3.3 ORs genes distribution 24 3.4 ORs genes expression. 24 3.5 ORs 3D structure. 25 3.6 ORs-odorant interaction. 28 3.7 Signal transduction of olfaction. 30 3.8 Combinatorial coding and olfactory pattern.
    [Show full text]
  • 7Tmrmine: a Web Server for Hierarchical Mining of 7TMR Proteins Guoqing Lu University of Nebraska at Omaha
    University of Nebraska at Omaha DigitalCommons@UNO Biology Faculty Publications Department of Biology 2009 7TMRmine: a Web server for hierarchical mining of 7TMR proteins Guoqing Lu University of Nebraska at Omaha Zhifang Wang University of Nebraska-Lincoln Alan M. Jones University of North Carolina at Chapel Hill Etsuko N. Moriyama University of Nebraska-Lincoln Follow this and additional works at: https://digitalcommons.unomaha.edu/biofacpub Part of the Biology Commons, and the Plant Sciences Commons Recommended Citation Lu, Guoqing; Wang, Zhifang; Jones, Alan M.; and Moriyama, Etsuko N., "7TMRmine: a Web server for hierarchical mining of 7TMR proteins" (2009). Biology Faculty Publications. 11. https://digitalcommons.unomaha.edu/biofacpub/11 This Article is brought to you for free and open access by the Department of Biology at DigitalCommons@UNO. It has been accepted for inclusion in Biology Faculty Publications by an authorized administrator of DigitalCommons@UNO. For more information, please contact [email protected]. BMC Genomics BioMed Central Database Open Access 7TMRmine: a Web server for hierarchical mining of 7TMR proteins Guoqing Lu1,2, Zhifang Wang3, Alan M Jones4,5 and Etsuko N Moriyama*6,7 Address: 1Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA, 2Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA, 3Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0660, USA, 4Departments of Biology, University of
    [Show full text]
  • Production of an Isotopically Labelled G-Protein Coupled Receptor In
    Investigations into the production of integral membrane proteins for solid-state NMR spectroscopy By Rachel Munro A Thesis presented to The University of Guelph In partial fulfillment of requirements for the degree of Master of Science in Biophysics Guelph, Ontario, Canada © Rachel Munro, January, 2016 ABSTRACT Investigations into the production of integral membrane proteins for solid-state NMR spectroscopy Rachel Munro Advisor: Professor L. Brown University of Guelph, 2015 This study seeks to probe the challenges associated with heterologous expression and isotopic labeling of microbial rhodopsins and the GPCR adenosine receptor (2A) (A2aR) through biophysical methods including SSNMR, FTIR and Raman spectroscopy. A2aR was transformed into Pichia pastoris, which has previously been shown to be able to cost-effectively produce isotopically-labelled eukaryotic membrane proteins for SSNMR studies; however poor expression resulted in contamination as detected by both FTIR and SSNMR. Next, for Anabaena sensory rhodopsin (ASR) produced in E. coli, we investigated the effect of a full-length construct on both expression and purification. Finally, we showed that the novel biosynthetic production of an isotopically labelled retinal ligand concurrently with its apoprotein proteorhodopsin in E. coli presents a cost effective alternative to de novo synthesis. By using alternately labeled carbon sources (glycerol) we were able to verify the biosynthetic pathway for retinal and assign several new carbon resonances for proteorhodopsin-bound retinal. Acknowledgements Firstly, I would like to thank my advisor, Dr. Leonid Brown, for his guidance, patience and unwavering support over the last four years. Additional thanks belong to Dr. Vladimir Ladizhansky, for being on my advisory committee and for all his help with NMR.
    [Show full text]
  • Theoretical Modeling and Docking Studies of Silkworm Serotonin
    ics om & B te i ro o P in f f o o Sumathy et al., J Proteomics Bioinform 2012, 5:10 r l m a Journal of a n t r i c u DOI: 10.4172/jpb.1000242 s o J ISSN: 0974-276X Proteomics & Bioinformatics Research Article Article OpenOpen Access Access Theoretical Modeling and Docking Studies of Silkworm Serotonin Receptor Ramasamy Sumathy1, SK Ashwath1 and VK Gopalakrishnan2* 1Bioinformatics centre, Central Sericultural Research and Training Institute, Mysore, Karnataka, India 2Department of Biochemistry and Bioinformatics, Karpagam University, Coimbatore, Tamilnadu, India Abstract The Silkworm serotonin receptor protein is an integral membrane protein which belongs to the largest superfamily of G protein-coupled receptors that communicate signals across the cell membrane through their interaction with heterotrimeric G proteins and regulate many of the physiological processes including the regulation of feeding, aggression, mood, perception, pain, anxiety etc. Despite the importance of serotonin receptor protein its structure have not yet determined experimentally due to difficulty in crystallization. The three-dimensional structure was modelled by the MODELLER program using the template rh1A which has 33% identity. The modelled structure was validated using Procheck and Ramachandran plot. It was found that the percentage of residue lying in the most favoured regions, additionally allowed regions, generously allowed regions, disallowed regions are 93.3%, 6.4%, 0% and 0.3%, respectively and it indicates reasonably good model. The overall Procheck G-factor and overall quality factor of ERRAT graph were 0.04 and 80.759, respectively. The binding site of the serotonin receptor protein was predicted using Q-Sitefinder and the interaction studies carried out with serotonin, agonist and reveals that the seven interaction residues Asp141, Val142, Gln218, Thr227, Ser230, Phe382, Leu405 of serotonin receptor protein interact with the serotonin form three hydrogen bond.
    [Show full text]
  • 1 Differential Signaling and Gene Regulation Among
    Differential Signaling and Gene Regulation Among Three Human EP3 Prostanoid Receptor Isoforms Item Type text; Electronic Dissertation Authors Israel, Davelene Davinah Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 27/09/2021 17:55:54 Link to Item http://hdl.handle.net/10150/196148 1 DIFFERENTIAL SIGNALING AND GENE REGULATION AMONG THREE HUMAN EP3 PROSTANOID RECEPTOR ISOFORMS by Davelene Davinah Israel A Dissertation Submitted to the Faculty of the DEPARTMENT OF PHARMACOLOGY & TOXICOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2008 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Davelene Davinah Israel Entitled: Differential Signaling and Gene Regulation Among Three Human EP3 Prostanoid Receptor Isoforms and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy _________________________________________________ Date: 6/4/08 John W. Regan _________________________________________________ Date: 6/4/08 John W. Bloom _________________________________________________ Date: 6/4/08 W. Daniel Stamer _________________________________________________ Date: 6/4/08 Richard R. Vaillancourt ________________________________________________ Date: Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement.
    [Show full text]