1
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Frommelt F, Ladurner R, Goldmann U, Wolf G, Ingles-Prieto A, Lineiro-Retes E, Gelová Z, Hopp AK, Christodoulaki E, Teoh ST, Leippe P, Santini BL, Rebsamen M, Lindinger S, Serrano I, Onstein S, Klimek C, Barbosa B, Pantielieieva A, Dvorak V, Hannich TJ, Schoenbett J, Sansig G, Mocking TAM, Ooms JF, IJzerman AP, Heitman LH, Sykacek P, Reinhardt J, Müller AC, Wiedmer T, Superti-Furga G. The solute carrier superfamily interactome. Mol Syst Biol 2025:10.1038/s44320-025-00109-1. [PMID: 40355756 DOI: 10.1038/s44320-025-00109-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/28/2025] [Accepted: 04/11/2025] [Indexed: 05/15/2025] Open
Abstract
Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of diverse substrates including nutrients, ions and drugs. There are about 450 different SLCs, residing in a variety of subcellular membranes. Loss-of-function of an unusually high proportion of SLC transporters is genetically associated with a plethora of human diseases, making SLCs a rapidly emerging but challenging drug target class. Knowledge of their protein environment may elucidate the molecular basis for their functional integration with metabolic and cellular pathways and help conceive pharmacological interventions based on modulating proteostatic regulation. We aimed at obtaining a global survey of the SLC-protein interaction landscape and mapped the protein-protein interactions of 396 SLCs by interaction proteomics. We employed a functional assessment based on RNA interference of interactors in combination with measurement of protein stability and localization. As an example, we detail the role of a SLC16A6 phospho-degron and the contributions of PDZ-domain proteins LIN7C and MPP1 to the trafficking of SLC43A2. Overall, our work offers a resource for SLC-protein interactions for the scientific community.
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Affiliation(s)
- Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rene Ladurner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Eva Lineiro-Retes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ann-Katrin Hopp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Shao Thing Teoh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Brianda L Santini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Barbara Barbosa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Anastasiia Pantielieieva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Thomas J Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Julian Schoenbett
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - Gilles Sansig
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - Tamara A M Mocking
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jasper F Ooms
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Peter Sykacek
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Juergen Reinhardt
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
- Fondazione Ri.MED, Palermo, Italy.
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2
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Zhang J, Kriebel CN, Wan Z, Shi M, Glaubitz C, He X. Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. J Chem Theory Comput 2023; 19:7405-7422. [PMID: 37788419 DOI: 10.1021/acs.jctc.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, we developed an accurate and cost-effective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15N and 13C of membrane proteins. The convergence of the AF-QM/MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including cross-protomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15N and 13C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13Cβ chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15N and 13Cα chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.
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Affiliation(s)
- Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clara Nassrin Kriebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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3
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Sahu ID, Lorigan GA. Perspective on the Effect of Membrane Mimetics on Dynamic Properties of Integral Membrane Proteins. J Phys Chem B 2023; 127:3757-3765. [PMID: 37078594 PMCID: PMC11610507 DOI: 10.1021/acs.jpcb.2c07324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Integral membrane proteins are embedded into cell membranes by spanning the width of the lipid bilayer. They play an essential role in important biological functions for the survival of living organisms. Their functions include the transportation of ions and molecules across the cell membrane and initiating signaling pathways. The dynamic behavior of integral membrane proteins is very important for their function. Due to the complex behavior of integral membrane proteins in the cell membrane, studying their structural dynamics using biophysical approaches is challenging. Here, we concisely discuss challenges and recent advances in technical and methodological aspects of biophysical approaches for gleaning dynamic properties of integral membrane proteins to answer pertinent biological questions associated with these proteins.
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Affiliation(s)
- Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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4
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The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses. Int J Mol Sci 2022; 23:ijms232113627. [PMID: 36362412 PMCID: PMC9655316 DOI: 10.3390/ijms232113627] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Transmembrane proteins participate in various physiological activities in plants, including signal transduction, substance transport, and energy conversion. Although more than 20% of gene products are predicted to be transmembrane proteins in the genome era, due to the complexity of transmembrane domains they are difficult to reliably identify in the predicted protein, and they may have different overall three-dimensional structures. Therefore, it is challenging to study their biological function. In this review, we describe the typical structures of transmembrane proteins and their roles in plant growth, development, and stress responses. We propose a model illustrating the roles of transmembrane proteins during plant growth and response to various stresses, which will provide important references for crop breeding.
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5
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Klingler F, Mathias S, Schneider H, Buck T, Raab N, Zeh N, Shieh YW, Pfannstiel J, Otte K. Unveiling the CHO surfaceome: Identification of cell surface proteins reveals cell aggregation-relevant mechanisms. Biotechnol Bioeng 2021; 118:3015-3028. [PMID: 33951178 DOI: 10.1002/bit.27811] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/25/2021] [Indexed: 01/12/2023]
Abstract
Chinese hamster ovary (CHO) suspension cells are the main production hosts for biopharmaceuticals. For the improvement of production processes, it is essential to understand the interaction between CHO cells and their microenvironment. While the cellular membrane is the crucial surface barrier between the inner and outer cell compartments, the subgroup of cell surface proteins (surfaceome) is of particular interest due to its potential to react to external factors and initiate cell communication and interaction pathways. Therefore, the CHO surfaceome was explored for the first time by enriching exposed N-glycosylated membrane proteins before tandem mass spectrometry (MS/MS) analyses, identifying a total of 449 surface proteins, including 34 proteins specific for production cells. Functional annotation and classification located most proteins to the cell surface belonging mainly to the protein classes of receptors, enzymes, and transporters. In addition, adhesion molecules as cadherins, integrins, Ig superfamily and extracellular matrix (ECM) proteins as collagens, laminins, thrombospondin, fibronectin, and tenascin were significantly enriched, which are involved in mechanisms for the formation of cell junctions, cell-cell and cell-ECM adhesion as focal adhesions. As cell adhesion and aggregation counteracts scalable production of biopharmaceuticals, experimental validation confirmed differential expression of integrin β1 (ITGB1) and β3, CD44, laminin, and fibronectin on the surface of aggregation-prone CHO production cells. The subsequent modulation of the central interaction protein ITGB1 by small interfering RNA knockdown substantially counteracted cell aggregation pointing toward novel engineering routes for aggregation reduction in biopharmaceutical production cells and exemplifying the potential of the surfaceome for specified engineering strategies.
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Affiliation(s)
- Florian Klingler
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany.,Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Helga Schneider
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Theresa Buck
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nikolas Zeh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Yu-Wei Shieh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Jens Pfannstiel
- Core Facility Mass Spectrometry, University of Hohenheim, Stuttgart, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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6
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Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Membrane proteins are essential for the survival of living organisms. They are involved in important biological functions including transportation of ions and molecules across the cell membrane and triggering the signaling pathways. They are targets of more than half of the modern medical drugs. Despite their biological significance, information about the structural dynamics of membrane proteins is lagging when compared to that of globular proteins. The major challenges with these systems are low expression yields and lack of appropriate solubilizing medium required for biophysical techniques. Electron paramagnetic resonance (EPR) spectroscopy coupled with site directed spin labeling (SDSL) is a rapidly growing powerful biophysical technique that can be used to obtain pertinent structural and dynamic information on membrane proteins. In this brief review, we will focus on the overview of the widely used EPR approaches and their emerging applications to answer structural and conformational dynamics related questions on important membrane protein systems.
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7
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Ahammad T, Drew DL, Sahu ID, Khan RH, Butcher BJ, Serafin RA, Galende AP, McCarrick RM, Lorigan GA. Conformational Differences Are Observed for the Active and Inactive Forms of Pinholin S 21 Using DEER Spectroscopy. J Phys Chem B 2020; 124:11396-11405. [PMID: 33289567 DOI: 10.1021/acs.jpcb.0c09081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bacteriophages have evolved with an efficient host cell lysis mechanism to terminate the infection cycle and release the new progeny virions at the optimum time, allowing adaptation with the changing host and environment. Among the lytic proteins, holin controls the first and rate-limiting step of host cell lysis by permeabilizing the inner membrane at an allele-specific time known as "holin triggering". Pinholin S21 is a prototype holin of phage Φ21 which makes many nanoscale holes and destroys the proton motive force, which in turn activates the signal anchor release (SAR) endolysin system to degrade the peptidoglycan layer of the host cell and destruction of the outer membrane by the spanin complex. Like many others, phage Φ21 has two holin proteins: active pinholin and antipinholin. The antipinholin form differs only by three extra amino acids at the N-terminus; however, it has a different structural topology and conformation with respect to the membrane. Predefined combinations of active pinholin and antipinholin fine-tune the lysis timing through structural dynamics and conformational changes. Previously, the dynamics and topology of active pinholin and antipinholin were investigated (Ahammad et al. JPCB 2019, 2020) using continuous wave electron paramagnetic resonance (CW-EPR) spectroscopy. However, detailed structural studies and direct comparison of these two forms of pinholin S21 are absent in the literature. In this study, the structural topology and conformations of active pinholin (S2168) and inactive antipinholin (S2168IRS) in DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) proteoliposomes were investigated using the four-pulse double electron-electron resonance (DEER) EPR spectroscopic technique to measure distances between transmembrane domains 1 and 2 (TMD1 and TMD2). Five sets of interlabel distances were measured via DEER spectroscopy for both the active and inactive forms of pinholin S21. Structural models of the active pinholin and inactive antipinholin forms in DMPC proteoliposomes were obtained using the experimental DEER distances coupled with the simulated annealing software package Xplor-NIH. TMD2 of S2168 remains in the lipid bilayer, and TMD1 is partially externalized from the bilayer with some residues located on the surface. However, both TMDs remain incorporated in the lipid bilayer for the inactive S2168IRS form. This study demonstrates, for the first time, clear structural topology and conformational differences between the two forms of pinholin S21. This work will pave the way for further studies of other holin systems using the DEER spectroscopic technique and will give structural insight into these biological clocks in molecular detail.
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Affiliation(s)
- Tanbir Ahammad
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Daniel L Drew
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Rasal H Khan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brandon J Butcher
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rachel A Serafin
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Alberto P Galende
- Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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8
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Ahammad T, Drew DL, Khan RH, Sahu ID, Faul E, Li T, Lorigan GA. Structural Dynamics and Topology of the Inactive Form of S 21 Holin in a Lipid Bilayer Using Continuous-Wave Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2020; 124:5370-5379. [PMID: 32501696 DOI: 10.1021/acs.jpcb.0c03575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacteriophage infection cycle plays a crucial role in recycling the world's biomass. Bacteriophages devise various cell lysis systems to strictly control the length of the infection cycle for an efficient phage life cycle. Phages evolved with lysis protein systems, which can control and fine-tune the length of this infection cycle depending on the host and growing environment. Among these lysis proteins, holin controls the first and rate-limiting step of host cell lysis by permeabilizing the inner membrane at an allele-specific time and concentration hence known as the simplest molecular clock. Pinholin S21 is the holin from phage Φ21, which defines the cell lysis time through a predefined ratio of active pinholin and antipinholin (inactive form of pinholin). Active pinholin and antipinholin fine-tune the lysis timing through structural dynamics and conformational changes. Previously we reported the structural dynamics and topology of active pinholin S2168. Currently, there is no detailed structural study of the antipinholin using biophysical techniques. In this study, the structural dynamics and topology of antipinholin S2168IRS in DMPC proteoliposomes is investigated using electron paramagnetic resonance (EPR) spectroscopic techniques. Continuous-wave (CW) EPR line shape analysis experiments of 35 different R1 side chains of S2168IRS indicated restricted mobility of the transmembrane domains (TMDs), which were predicted to be inside the lipid bilayer when compared to the N- and C-termini R1 side chains. In addition, the R1 accessibility test performed on 24 residues using the CW-EPR power saturation experiment indicated that TMD1 and TMD2 of S2168IRS were incorporated into the lipid bilayer where N- and C-termini were located outside of the lipid bilayer. Based on this study, a tentative model of S2168IRS is proposed where both TMDs remain incorporated into the lipid bilayer and N- and C-termini are located outside of the lipid bilayer. This work will pave the way for the further studies of other holins using biophysical techniques and will give structural insights into these biological clocks in molecular detail.
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Affiliation(s)
- Tanbir Ahammad
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Daniel L Drew
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rasal H Khan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Emily Faul
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Tianyan Li
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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9
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Akdag M, Yunt ZS, Kamacioglu A, Qureshi MH, Akarlar BA, Ozlu N. Proximal Biotinylation-Based Combinatory Approach for Isolating Integral Plasma Membrane Proteins. J Proteome Res 2020; 19:3583-3592. [DOI: 10.1021/acs.jproteome.0c00113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mehmet Akdag
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Zeynep Sabahat Yunt
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Altug Kamacioglu
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | | | - Busra A. Akarlar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
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10
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Zumrut HE, Mallikaratchy PR. Ligand Guided Selection (LIGS) of Artificial Nucleic Acid Ligands against Cell Surface Targets. ACS APPLIED BIO MATERIALS 2019; 3:2545-2552. [PMID: 34013167 DOI: 10.1021/acsabm.9b00938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
With the success of RNA-based therapeutic drugs, the demand has increased for sophisticated nucleic-acid-based targeting agents. Nucleic acid aptamers (NAAs), in this regard, represent a suitable class of molecules with synthetic versatility. Aptamers are composed of single-stranded RNA/DNA/XNA molecules, which can be identified using a method called systematic evolution of ligands by exponential enrichment (SELEX) against any molecule. This Spotlight summarizes the recent introduction of ligand guided selection (LIGS), which will permit the identification of a wide range of functional aptamers against complex targets such as cell surface receptors while maintaining their native functional state. Aptamers identified from LIGS will allow researchers to develop aptamers in biomedicine as low-cost, stable therapeutic agents and diagnostic molecules or biochemical devices.
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Affiliation(s)
- Hasan E Zumrut
- Ph.D. Programs in Chemistry and Biochemistry and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, New York 10016, United States
| | - Prabodhika R Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, New York 10468, United States.,Ph.D. Programs in Chemistry and Biochemistry and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, New York 10016, United States
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11
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Fluorescence-based approaches for monitoring membrane receptor oligomerization. J Biosci 2018. [DOI: 10.1007/s12038-018-9762-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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12
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Sahu ID, Lorigan GA. Site-Directed Spin Labeling EPR for Studying Membrane Proteins. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3248289. [PMID: 29607317 PMCID: PMC5828257 DOI: 10.1155/2018/3248289] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/21/2017] [Indexed: 01/13/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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13
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Batool S, Bhandari S, George S, Okeoma P, Van N, Zümrüt HE, Mallikaratchy P. Engineered Aptamers to Probe Molecular Interactions on the Cell Surface. Biomedicines 2017; 5:biomedicines5030054. [PMID: 28850067 PMCID: PMC5618312 DOI: 10.3390/biomedicines5030054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/01/2017] [Accepted: 08/08/2017] [Indexed: 01/08/2023] Open
Abstract
Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics.
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Affiliation(s)
- Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Sanam Bhandari
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Shanell George
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Precious Okeoma
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Nabeela Van
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Hazan E Zümrüt
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
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14
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Wang Y, Wach JY, Sheehan P, Zhong C, Zhan C, Harris R, Almo SC, Bishop J, Haggarty SJ, Ramek A, Berry KN, O’Herin C, Koehler AN, Hung AW, Young DW. Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β. ACS Med Chem Lett 2016; 7:852-6. [PMID: 27660690 DOI: 10.1021/acsmedchemlett.6b00230] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/14/2016] [Indexed: 11/30/2022] Open
Abstract
Traditional fragment-based drug discovery (FBDD) relies heavily on structural analysis of the hits bound to their targets. Herein, we present a complementary approach based on diversity-oriented synthesis (DOS). A DOS-based fragment collection was able to produce initial hit compounds against the target GSK3β, allow the systematic synthesis of related fragment analogues to explore fragment-level structure-activity relationship, and finally lead to the synthesis of a more potent compound.
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Affiliation(s)
- Yikai Wang
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Jean-Yves Wach
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick Sheehan
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Cheng Zhong
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Chenyang Zhan
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Richard Harris
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Joshua Bishop
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
- Department of Neurology & Psychiatry, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Stephen J. Haggarty
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
- Department of Neurology & Psychiatry, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Alexander Ramek
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Kayla N. Berry
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Conor O’Herin
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Angela N. Koehler
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Alvin W. Hung
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
| | - Damian W. Young
- Chemical
Biology Program, The Broad Institute of Harvard and MIT, 415
Main Street, Cambridge, Massachusetts 02142, United States
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15
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Kuzhelev AA, Shevelev GY, Krumkacheva OA, Tormyshev VM, Pyshnyi DV, Fedin MV, Bagryanskaya EG. Saccharides as Prospective Immobilizers of Nucleic Acids for Room-Temperature Structural EPR Studies. J Phys Chem Lett 2016; 7:2544-8. [PMID: 27320083 PMCID: PMC5453311 DOI: 10.1021/acs.jpclett.6b01024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for structural studies of biomolecules and their complexes. This method, whose applicability has been recently extended to room temperatures, requires immobilization of the studied biosystem to prevent averaging of dipolar couplings; at the same time, the modification of native conformations by immobilization must be avoided. In this work, we provide first demonstration of room-temperature EPR distance measurements in nucleic acids using saccharides trehalose, sucrose, and glucose as immobilizing media. We propose an approach that keeps structural conformation and unity of immobilized double-stranded DNA. Remarkably, room-temperature electron spin dephasing time of triarylmethyl-labeled DNA in trehalose is noticeably longer compared to previously used immobilizers, thus providing a broader range of available distances. Therefore, saccharides, and especially trehalose, can be efficiently used as immobilizers of nucleic acids, mimicking native conditions and allowing wide range of structural EPR studies at room temperatures.
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Affiliation(s)
- Andrey A. Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgiy Yu. Shevelev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olesya A. Krumkacheva
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Victor M. Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Matvey V. Fedin
- International Tomography Center SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G. Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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16
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Abstract
Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
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17
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Lin Y, Wang K, Liu Z, Lin H, Yu L. Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:144-51. [PMID: 26319803 DOI: 10.1016/j.jchromb.2015.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 07/07/2015] [Accepted: 08/14/2015] [Indexed: 01/09/2023]
Abstract
Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and identification of membrane proteins, especially those with high hydrophobicity and multiple TMDs, and thereby displaying more potential for shotgun membrane proteomics.
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Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Lijun Yu
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
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18
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Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS One 2015; 10:e0121513. [PMID: 25837709 PMCID: PMC4383379 DOI: 10.1371/journal.pone.0121513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/03/2015] [Indexed: 01/01/2023] Open
Abstract
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.
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19
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Cabra V, Samsó M. Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction. J Vis Exp 2015:52311. [PMID: 25651412 PMCID: PMC4354528 DOI: 10.3791/52311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level.
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Affiliation(s)
- Vanessa Cabra
- Department of Physiology and Biophysics, Virginia Commonwealth University
| | - Montserrat Samsó
- Department of Physiology and Biophysics, Virginia Commonwealth University;
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20
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Samsó M. 3D Structure of the Dihydropyridine Receptor of Skeletal Muscle. Eur J Transl Myol 2015; 25:4840. [PMID: 26913147 PMCID: PMC4748975 DOI: 10.4081/ejtm.2015.4840] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/16/2014] [Indexed: 11/22/2022] Open
Abstract
Excitation contraction coupling, the rapid and massive Ca2+ release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) mediates the quasi-instantaneous conversion from T-tubule depolarization into Ca2+ release from the sarcoplasmic reticulum (SR). The DHPR has several key modules required for EC coupling: the voltage sensors and II-III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II-III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data.
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Affiliation(s)
- Montserrat Samsó
- Department of Physiology and Biophysics, Virginia Commonwealth University , Richmond, VA, USA
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21
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Lin Y, Lin H, Liu Z, Wang K, Yan Y. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics†. J Sep Sci 2014; 37:3321-9. [DOI: 10.1002/jssc.201400569] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Yujun Yan
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
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22
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Takacs IM, Mot A, Silaghi-Dumitrescu R, Damian G. EPR investigation of libration motion of spin labeled hemerythrin. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Lin X, Parthasarathy K, Surya W, Zhang T, Mu Y, Torres J. A conserved tetrameric interaction of cry toxin helix α3 suggests a functional role for toxin oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1777-84. [PMID: 24657394 DOI: 10.1016/j.bbamem.2014.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/16/2022]
Abstract
Crystal (Cry) toxins are widely used for insect control, but their mechanism of toxicity is still uncertain. These toxins can form lytic pores in vitro, and water soluble tetrameric pre-pore intermediates have been reported. Even the precise oligomeric state of the toxin in membranes, trimeric or tetrameric, is still a debated issue. Based on previous reports, we have assumed that interactions between toxin monomers in solution are at least partly mediated by domain I, and we have analyzed in silico the homo-oligomerization tendencies of the domain I α-helices individually. Using many homologous sequences for each α-helix, our strategy allows selection of evolutionarily conserved interactions. These interactions appeared only in helices α3 and α5, but only α3 produced a suitably oriented or α-helical sample in lipid bilayers, forming homotetramers in C14-betaine, and allowing determination of its rotational orientation in lipid bilayers using site-specific infrared dichroism (SSID). The determined orientation in the tetrameric model is in agreement with only one of the evolutionarily conserved models. In addition mutation R99E, which was found to inhibit oligomerization experimentally, greatly destabilized the tetramer in molecular dynamic simulations. In this model, helix 3 is able to form inter-monomer interactions without significant rearrangements of domain I, which is compatible with the available crystal structure of Cry toxins in solution. The model presented here at least partially explains the reported tetrameric oligomerization of Cry toxins in solution and the inhibition of this oligomerization by a synthetic α3 peptide.
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Affiliation(s)
- Xin Lin
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Krupakar Parthasarathy
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Tong Zhang
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore.
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24
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Murray DT, Hung I, Cross TA. Assignment of oriented sample NMR resonances from a three transmembrane helix protein. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 240:34-44. [PMID: 24509383 PMCID: PMC3980497 DOI: 10.1016/j.jmr.2013.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/21/2013] [Accepted: 12/28/2013] [Indexed: 06/03/2023]
Abstract
Oriented sample solid state NMR techniques have been routinely employed to determine the structures of membrane proteins with one or two transmembrane helices. For larger proteins the technique has been limited by spectral resolution and lack of assignment strategies. Here, a strategy for resonance assignment is devised and applied to a three transmembrane helix protein. Sequence specific assignments for all labeled transmembrane amino acid sites are obtained, which provide a set of orientational restraints and helix orientations in the bilayer. Our experiments expand the utility of solid state NMR in membrane protein structure characterization to three transmembrane helix proteins and represent a straightforward strategy for routinely characterizing multiple transmembrane helix protein structures.
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Affiliation(s)
- D T Murray
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - I Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - T A Cross
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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25
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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26
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Witte K, Kaiser A, Schmidt P, Splith V, Thomas L, Berndt S, Huster D, Beck-Sickinger AG. Oxidative in vitro folding of a cysteine deficient variant of the G protein-coupled neuropeptide Y receptor type 2 improves stability at high concentration. Biol Chem 2014; 394:1045-56. [PMID: 23732681 DOI: 10.1515/hsz-2013-0120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 05/31/2013] [Indexed: 01/28/2023]
Abstract
In vitro folding of G protein-coupled receptors into a detergent environment represents a promising strategy for obtaining sufficient amounts of functional receptor molecules for structural studies. Typically, these preparations exhibit a poor long-term stability especially at the required high protein concentration. Here, we report a protocol for the stabilization of the Escherichia coli-expressed and subsequently folded neuropeptide Y receptor type 2. We identified the free cysteines in the receptor as one major reason for intermolecular protein aggregation. Therefore, six out of the eight cysteine residues were mutated to alanine or serine without any significant loss of functionality of the receptor as demonstrated in cell culture models. Furthermore, the disulfide bond between the remaining two cysteines was irreversibly formed by applying oxidative in vitro folding. Applying this strategy, the stability of the functionally folded Y2 receptor could be increased to 20 days at a concentration of 15 μm in a micelle environment consisting of 1,2-diheptanoyl-sn-glycero-3-phosphocholine and n-dodecyl-ß-D-maltoside.
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Affiliation(s)
- Kristina Witte
- Institute for Medical Physics and Biophysics, Medical Department, Universität Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci 2013; 36:3026-34. [DOI: 10.1002/jssc.201300413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/06/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Kunbo Wang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yujun Yan
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Haiyan Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Bin Peng
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Zhonghua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
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Zhu G, Sun L, Keithley RB, Dovichi NJ. Capillary isoelectric focusing-tandem mass spectrometry and reversed-phase liquid chromatography-tandem mass spectrometry for quantitative proteomic analysis of differentiating PC12 cells by eight-plex isobaric tags for relative and absolute quantification. Anal Chem 2013; 85:7221-9. [PMID: 23822771 DOI: 10.1021/ac4009868] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report the application of capillary isoelectric focusing for quantitative analysis of a complex proteome. Biological duplicates were generated from PC12 cells at days 0, 3, 7, and 12 following treatment with nerve growth factor. These biological duplicates were digested with trypsin, labeled using eight-plex isobaric tags for relative and absolute quantification (iTRAQ) chemistry, and pooled. The pooled peptides were separated into 25 fractions using reversed-phase liquid chromatography (RPLC). Technical duplicates of each fraction were separated by capillary isoelectric focusing (cIEF) using a set of amino acids as ampholytes. The cIEF column was interfaced to an Orbitrap Velos mass spectrometer with an electrokinetically pumped sheath-flow nanospray interface. This HPLC-cIEF-electrospray-tandem mass spectrometry (ESI-MS/MS) approach identified 835 protein groups and produced 2,329 unique peptides IDs. The biological duplicates were analyzed in parallel using conventional strong-cation exchange (SCX)-RPLC-ESI-MS/MS. The iTRAQ peptides were first separated into eight fractions using SCX. Each fraction was then analyzed by RPLC-ESI-MS/MS. The SCX-RPLC approach generated 1,369 protein groups and 3,494 unique peptide IDs. For protein quantitation, 96 and 198 differentially expressed proteins were obtained with RPLC-cIEF and SCX-RPLC, respectively. The combined set identified 231 proteins. Protein expression changes measured by RPLC-cEIF and SCX-RPLC were highly correlated.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Sodium laurate, a novel protease- and mass spectrometry-compatible detergent for mass spectrometry-based membrane proteomics. PLoS One 2013; 8:e59779. [PMID: 23555778 PMCID: PMC3610932 DOI: 10.1371/journal.pone.0059779] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/18/2013] [Indexed: 11/22/2022] Open
Abstract
The hydrophobic nature of most membrane proteins severely complicates their extraction, proteolysis and identification. Although detergents can be used to enhance the solubility of the membrane proteins, it is often difficult for a detergent not only to have a strong ability to extract membrane proteins, but also to be compatible with the subsequent proteolysis and mass spectrometric analysis. In this study, we made evaluation on a novel application of sodium laurate (SL) to the shotgun analysis of membrane proteomes. SL was found not only to lyse the membranes and solubilize membrane proteins as efficiently as SDS, but also to be well compatible with trypsin and chymotrypsin. Furthermore, SL could be efficiently removed by phase transfer method from samples after acidification, thus ensuring not to interfere with the subsequent CapLC-MS/MS analysis of the proteolytic peptides of proteins. When SL was applied to assist the digestion and identification of a standard protein mixture containing bacteriorhodoposin and the proteins in rat liver plasma membrane-enriched fractions, it was found that, compared with other two representative enzyme- and MS-compatible detergents RapiGest SF (RGS) and sodium deoxycholate (SDC), SL exhibited obvious superiority in the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains.
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Langelaan DN, Reddy T, Banks AW, Dellaire G, Dupré DJ, Rainey JK. Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1471-83. [PMID: 23438363 DOI: 10.1016/j.bbamem.2013.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/17/2013] [Accepted: 02/13/2013] [Indexed: 12/20/2022]
Abstract
G-protein coupled receptors (GPCRs) comprise a large family of membrane proteins with rich functional diversity. Signaling through the apelin receptor (AR or APJ) influences the cardiovascular system, central nervous system and glucose regulation. Pathophysiological involvement of apelin has been shown in atherosclerosis, cancer, human immunodeficiency virus-1 (HIV-1) infection and obesity. Here, we present the high-resolution nuclear magnetic resonance (NMR) spectroscopy-based structure of the N-terminus and first transmembrane (TM) segment of AR (residues 1-55, AR55) in dodecylphosphocholine micelles. AR55 consists of two disrupted helices, spanning residues D14-K25 and A29-R55(1.59). Molecular dynamics (MD) simulations of AR built from a hybrid of experimental NMR and homology model-based restraints allowed validation of the AR55 structure in the context of the full-length receptor in a hydrated bilayer. AR55 structural features were functionally probed using mutagenesis in full-length AR through monitoring of apelin-induced extracellular signal-regulated kinase (ERK) phosphorylation in transiently transfected human embryonic kidney (HEK) 293A cells. Residues E20 and D23 form an extracellular anionic face and interact with lipid headgroups during MD simulations in the absence of ligand, producing an ideal binding site for a cationic apelin ligand proximal to the membrane-water interface, lending credence to membrane-catalyzed apelin-AR binding. In the TM region of AR55, N46(1.50) is central to a disruption in helical character. G42(1.46), G45(1.49) and N46(1.50), which are all involved in the TM helical disruption, are essential for proper trafficking of AR. In summary, we introduce a new correlative NMR spectroscopy and computational biochemistry methodology and demonstrate its utility in providing some of the first high-resolution structural information for a peptide-activated GPCR TM domain.
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Affiliation(s)
- David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Simmons KJ, Gotfryd K, Billesbølle CB, Loland CJ, Gether U, Fishwick CWG, Johnson AP. A virtual high-throughput screening approach to the discovery of novel inhibitors of the bacterial leucine transporter, LeuT. Mol Membr Biol 2012; 30:184-94. [PMID: 22908980 DOI: 10.3109/09687688.2012.710341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Membrane proteins are intrinsically involved in both human and pathogen physiology, and are the target of 60% of all marketed drugs. During the past decade, advances in the studies of membrane proteins using X-ray crystallography, electron microscopy and NMR-based techniques led to the elucidation of over 250 unique membrane protein crystal structures. The aim of the European Drug Initiative for Channels and Transporter (EDICT) project is to use the structures of clinically significant membrane proteins for the development of lead molecules. One of the approaches used to achieve this is a virtual high-throughput screening (vHTS) technique initially developed for soluble proteins. This paper describes application of this technique to the discovery of inhibitors of the leucine transporter (LeuT), a member of the neurotransmitter:sodium symporter (NSS) family.
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Promsri S, Ullmann GM, Hannongbua S. Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the N-terminal gp41 fusion mechanism. Biophys Chem 2012; 170:9-16. [DOI: 10.1016/j.bpc.2012.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 06/24/2012] [Accepted: 07/09/2012] [Indexed: 11/26/2022]
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Bosse M, Thomas L, Hassert R, Beck-Sickinger AG, Huster D, Schmidt P. Assessment of a fully active class A G protein-coupled receptor isolated from in vitro folding. Biochemistry 2011; 50:9817-25. [PMID: 21999704 DOI: 10.1021/bi201320e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide a protocol for the preparation of fully active Y2 G protein-coupled receptors (GPCRs). Although a valuable target for pharmaceutical research, information about the structure and dynamics of these molecules remains limited due to the difficulty in obtaining sufficient amounts of homogeneous and fully active receptors for in vitro studies. Recombinant expression of GPCRs as inclusion bodies provides the highest protein yields at lowest costs. But this strategy can only successfully be applied if the subsequent in vitro folding results in a high yield of active receptors and if this fraction can be isolated from the nonactive receptors in a homogeneous form. Here, we followed that strategy to provide large quantities of the human neuropeptide Y receptor type 2 and determined the folding yield before and after ligand affinity chromatography using a radioligand binding assay. Directly after folding, we achieved a proportion of ~25% active receptor. This value could be increased to ~96% using ligand affinity chromatography. Thus, a very homogeneous sample of the Y2 receptor could be prepared that exhibited a K(D) value of 0.1 ± 0.05 nM for the binding of polypeptide Y, which represents one of the natural ligands of the Y2 receptor.
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Affiliation(s)
- Mathias Bosse
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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35
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Langelaan DN, Ngweniform P, Rainey JK. Biophysical characterization of G-protein coupled receptor-peptide ligand binding. Biochem Cell Biol 2011; 89:98-105. [PMID: 21455262 PMCID: PMC3096653 DOI: 10.1139/o10-142] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.
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Affiliation(s)
- David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada
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36
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Berger C, Montag C, Berndt S, Huster D. Optimization of Escherichia coli cultivation methods for high yield neuropeptide Y receptor type 2 production. Protein Expr Purif 2011; 76:25-35. [DOI: 10.1016/j.pep.2010.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/20/2010] [Accepted: 10/27/2010] [Indexed: 12/11/2022]
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Abstract
Intrinsically disordered proteins (IDPs) form a unique protein category characterized by the absence of a well-defined structure and by remarkable conformational flexibility. Electron Paramagnetic Resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) is amongst the most suitable methods to unravel their structure and dynamics. This review summarizes the tremendous methodological developments in the area of SDSL EPR and its applications in protein research. Recent results on the intrinsically disordered Parkinson's disease protein α-synuclein illustrate that the method has gained increasing attention in IDP research. SDSL EPR has now reached a level where broad application in this rapidly advancing field is feasible.
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Affiliation(s)
- Malte Drescher
- Department of Chemistry, University of Konstanz, Konstanz, Germany.
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38
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Tao D, Qiao X, Sun L, Hou C, Gao L, Zhang L, Shan Y, Liang Z, Zhang Y. Development of a highly efficient 2-D system with a serially coupled long column and its application in identification of rat brain integral membrane proteins with ionic liquids-assisted solubilization and digestion. J Proteome Res 2010; 10:732-8. [PMID: 21121671 DOI: 10.1021/pr100893j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two dimensional high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (2D-HPLC-ESI-MS/MS) is one of the most powerful techniques for high resolution, efficiency, and throughput separation and identification of proteomes. For a bottom-up strategy-based proteome analysis, usually multistep salt elution was needed in the first dimension separation by SCX, to simplify the peptides for the further second dimensional separation by RPLC. Here, by using a 30 cm-long serially coupled long column (SCLC) in the second dimension, we reduced the salt steps of SCX from 13 to 5 to shorten the total analysis time. Compared to the commonly applied 2D-HPLC with over 10-step salt elution in SCX and microRPLC with a short column (SC), named as SC-2D, the peak capacity of 2D-HPLC with a SCLC column, named as SCLC-2D, was increased 3.3-folds while the analysis time was increased by only 1.17-folds. Therefore, the time-based protein identification efficiency was ∼55 protein groups/h, nearly 2-fold of that for SC-2D (∼28 protein groups/h). With the further combination of assisted solubilization by ionic liquids and SCLC-2D, 608 integral membrane proteins (IMPs) (27.66% of the total 2198 proteins, FDR < 1%) were identified from rat brain, more than those obtained by the traditional urea method (252 unique IMPs, occupying 17.03% of total 1480 proteins). All of these results demonstrate the promise of the developed technique for large-scale proteome analysis.
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Affiliation(s)
- Dingyin Tao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China
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Sun L, Tao D, Han B, Ma J, Zhu G, Liang Z, Shan Y, Zhang L, Zhang Y. Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics. Anal Bioanal Chem 2010; 399:3387-97. [DOI: 10.1007/s00216-010-4381-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/11/2010] [Accepted: 10/24/2010] [Indexed: 12/25/2022]
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Ahmad S, Singh YH, Paudel Y, Mori T, Sugita Y, Mizuguchi K. Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. BMC Bioinformatics 2010; 11:533. [PMID: 20977780 PMCID: PMC3247134 DOI: 10.1186/1471-2105-11-533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 10/27/2010] [Indexed: 01/04/2023] Open
Abstract
Background Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. However, there is little explanation of why certain residues are predicted in a wrong structural class or with large errors in the absolute values of these features. On the other hand, membrane proteins undergo conformational changes to allow transport as well as ligand binding. These conformational changes often occur via residues that are inherently flexible and hence, predicting fluctuations in residue positions is of great significance. Results We performed a statistical analysis of common patterns among selected one-dimensional equilibrium structural features (ESFs) and developed a method for simultaneously predicting all of these features using an integrated system. Our results show that the prediction performance can be improved if multiple structural features are trained in an integrated model, compared to the current practice of developing individual models. In particular, the performance of the solvent accessibility and bend-angle prediction improved in this way. The well-performing bend-angle prediction can be used to predict helical positions with severe kinks at a modest success rate. Further, we showed that single-chain conformational dynamics, measured by B-factors derived from normal mode analysis, could be predicted from observed and predicted ESFs with good accuracy. A web server was developed (http://tardis.nibio.go.jp/netasa/htmone/) for predicting the one-dimensional ESFs from sequence information and analyzing the differences between the predicted and observed values of the ESFs. Conclusions The prediction performance of the integrated model is significantly better than that of the models performing the task separately for each feature for the solvent accessibility and bend-angle predictions. The predictability of the features also plays a role in determining flexible positions. Although the dynamics studied here concerns local atomic fluctuations, a similar analysis in terms of global structural features will be helpful in predicting large-scale conformational changes, for which work is in progress.
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Affiliation(s)
- Shandar Ahmad
- National Institute of Biomedical Innovation, 7-6-8 Saito-asagi, Ibaraki, Osaka 567 0085, Japan.
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Lin Y, Liu Y, Li J, Zhao Y, He Q, Han W, Chen P, Wang X, Liang S. Evaluation and optimization of removal of an acid-insoluble surfactant for shotgun analysis of membrane proteome. Electrophoresis 2010; 31:2705-2713. [PMID: 20665523 DOI: 10.1002/elps.201000161] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Due to its compatibility with protease activity at high concentration, sodium deoxycholate (SDC) can be used to effectively improve the solubilization and enzymolysis of membrane proteins and has received increasing attention in the field of membrane proteome analysis in recent years. SDC can be removed from digests by means of acidification followed by centrifugation (i.e. acid precipitation, AP) or extraction with ethyl acetate (i.e. phase transfer, PT) so as not to interfere with the downstream analyses like LC-MS/MS. In this study, the two strategies were systematically evaluated, compared and optimized. The results of the study demonstrated that both of the AP and PT strategies led to a certain amount of tryptic peptides being lost, and in PT strategy even more peptides were lost during SDC removal process. However, the lost peptides could be mostly recovered by washing the pellet and solid content produced during AP and PT, respectively. By recovering the lost peptides, the identification efficiency of proteins, especially transmembrane and low abundance ones, was significantly improved. Comparatively, after optimization by recovering the lost peptides, AP strategy was superior to PT strategy because the former not only could achieve the comparable identification efficiency with the latter but also was more economical, safer and easier to operate than the latter.
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Affiliation(s)
- Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
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42
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Neumann S, Fuchs A, Mulkidjanian A, Frishman D. Current status of membrane protein structure classification. Proteins 2010; 78:1760-73. [PMID: 20186977 DOI: 10.1002/prot.22692] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
For over 2 decades, continuous efforts to organize the jungle of available protein structures have been underway. Although a number of discrepancies between different classification approaches for soluble proteins have been reported, the classification of membrane proteins has so far not been comparatively studied because of the limited amount of available structural data. Here, we present an analysis of alpha-helical membrane protein classification in the SCOP and CATH databases. In the current set of 63 alpha-helical membrane protein chains having between 1 and 13 transmembrane helices, we observed a number of differently classified proteins both regarding their domain and fold assignment. The majority of all discrepancies affect single transmembrane helix, two helix hairpin, and four helix bundle domains, while domains with more than five helices are mostly classified consistently between SCOP and CATH. It thus appears that the structural constraints imposed by the lipid bilayer complicate the classification of membrane proteins with only few membrane-spanning regions. This problem seems to be specific for membrane proteins as soluble four helix bundles, not restrained by the membrane, are more consistently classified by SCOP and CATH. Our findings indicate that the structural space of small membrane helix bundles is highly continuous such that even minor differences in individual classification procedures may lead to a significantly different classification. Membrane proteins with few helices and limited structural diversity only seem to be reasonably classifiable if the definition of a fold is adapted to include more fine-grained structural features such as helix-helix interactions and reentrant regions.
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Affiliation(s)
- Sindy Neumann
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, D-85354 Freising, Germany
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Marsico A, Henschel A, Winter C, Tuukkanen A, Vassilev B, Scheubert K, Schroeder M. Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. BMC Bioinformatics 2010; 11:204. [PMID: 20420672 PMCID: PMC2876129 DOI: 10.1186/1471-2105-11-204] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 04/26/2010] [Indexed: 11/23/2022] Open
Abstract
Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94%) appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1) a dimer interface motif found in voltage-gated chloride channels, (2) a proton transfer motif found in heme-copper oxidases, and (3) a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.
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Affiliation(s)
- Annalisa Marsico
- Bioinformatics department, Biotechnology Center TU Dresden, Dresden, Germany
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Schmidt P, Berger C, Scheidt HA, Berndt S, Bunge A, Beck-Sickinger AG, Huster D. A reconstitution protocol for the in vitro folded human G protein-coupled Y2 receptor into lipid environment. Biophys Chem 2010; 150:29-36. [PMID: 20421142 DOI: 10.1016/j.bpc.2010.02.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
Abstract
Although highly resolved crystal structures of G protein-coupled receptors have become available within the last decade, the need for studying these molecules in their natural membrane environment, where the molecules are rather dynamic, has been widely appreciated. Solid-state NMR spectroscopy is an excellent method to study structure and dynamics of membrane proteins in their native lipid environment. We developed a reconstitution protocol for the uniformly (15)N labeled Y(2) receptor into a bicelle-like lipid structure with high yields suitable for NMR studies. Milligram quantities of target protein were expressed in Escherichia coli using an optimized fermentation process in defined medium yielding in over 10mg/L medium of purified Y(2) receptor solubilized in SDS micelles. The structural integrity of the receptor molecules was strongly increased through refolding and subsequent reconstitution into phospholipid membranes. Specific ligand binding to the integrated receptor was determined using radioligand affinity assay. Further, by NMR measurement a dispersion of the (15)N signals comparable to native rhodopsin was shown. The efficiency of the reconstitution could also be inferred from the fact that reasonable (13)C NMR spectra at natural abundance could be acquired.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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Schmidt P, Lindner D, Montag C, Berndt S, Beck-Sickinger AG, Rudolph R, Huster D. Prokaryotic expression, in vitro folding, and molecular pharmacological characterization of the neuropeptide Y receptor type 2. Biotechnol Prog 2010; 25:1732-9. [PMID: 19725122 DOI: 10.1002/btpr.266] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
G protein-coupled receptors (GPCRs) are a class of membrane proteins that represent a major target for pharmacological developments. However, there is still little knowledge about GPCR structure and dynamics since high-level expression and characterization of active GPCRs in vitro is extremely complicated. Here, we describe the recombinant expression and functional folding of the human Y(2) receptor from inclusion bodies of E. coli cultures. Milligram protein quantities were produced using high density fermentation and isolated in a single step purification with a yield of over 20 mg/L culture. Extensive studies were carried out on in vitro refolding and stabilization of the isolated receptor in detergent solution. The specific binding of the ligand, the 36 residue neuropeptide Y (NPY), to the recombinant Y(2) receptors in micellar form was shown by several radioligand affinity assays. In competition experiments, an IC(50) value in low nanomolar range could be determined. Further, a K(D) value of 1.9 nM was determined from a saturation assay, where NPY was titrated to the recombinant Y(2) receptors.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
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A solid-state NMR study of the structure and dynamics of the myristoylated N-terminus of the guanylate cyclase-activating protein-2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:266-74. [DOI: 10.1016/j.bbamem.2009.06.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/16/2009] [Accepted: 06/29/2009] [Indexed: 11/30/2022]
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AFM study of the interaction of cytochrome P450 2C9 with phospholipid bilayers. Chem Phys Lipids 2010; 163:182-9. [DOI: 10.1016/j.chemphyslip.2009.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 08/07/2009] [Accepted: 11/09/2009] [Indexed: 11/18/2022]
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Trusch M, Böhlick A, Hildebrand D, Lichtner B, Bertsch A, Kohlbacher O, Bachmann S, Schlüter H. Application of displacement chromatography for the analysis of a lipid raft proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 878:309-14. [PMID: 20015709 DOI: 10.1016/j.jchromb.2009.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 10/16/2009] [Accepted: 11/20/2009] [Indexed: 10/20/2022]
Abstract
Defining membrane proteomes is fundamental to understand the role of membrane proteins in biological processes and to find new targets for drug development. Usually multidimensional chromatography using step or gradient elution is applied for the separation of tryptic peptides of membrane proteins prior to their mass spectrometric analysis. Displacement chromatography (DC) offers several advantages that are helpful for proteome analysis. However, DC has so far been applied for proteomic investigations only in few cases. In this study we therefore applied DC in a multidimensional LC-MS approach for the separation and identification of membrane proteins located in cholesterol-enriched membrane microdomains (lipid rafts) obtained from rat kidney by density gradient centrifugation. The tryptic peptides were separated on a cation-exchange column in the displacement mode with spermine used as displacer. Fractions obtained from DC were analyzed using an HPLC-chip system coupled to an electrospray-ionization ion-trap mass spectrometer. This procedure yielded more than 400 highly significant peptide spectrum matches and led to the identification of more than 140 reliable protein hits within an established rat kidney lipid raft proteome. The majority of identified proteins were membrane proteins. In sum, our results demonstrate that DC is a suitable alternative to gradient elution separations for the identification of proteins via a multidimensional LC-MS approach.
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Affiliation(s)
- Maria Trusch
- Department of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Campus Forschung, Martinistr. 52, D-20246 Hamburg, Germany.
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Štrancar J, Kavalenka A, Urbančič I, Ljubetič A, Hemminga MA. SDSL-ESR-based protein structure characterization. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:499-511. [DOI: 10.1007/s00249-009-0510-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 06/23/2009] [Indexed: 10/20/2022]
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Vereshaga YA, Volynsky PE, Pustovalova JE, Nolde DE, Arseniev AS, Efremov RG. Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 2009; 69:309-25. [PMID: 17600828 DOI: 10.1002/prot.21555] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BNIP3 is a mitochondrial 19-kDa proapoptotic protein, a member of the Bcl-2 family. It has a single COOH-terminal transmembrane (TM) alpha-helical domain, which is required for membrane targeting, proapoptotic activity, hetero- and homo-dimerization in membrane. The role and the molecular details of association of TM helices of BNIP3 are yet to be established. Here, we present a molecular modeling study of helix interactions in its membrane domain. The approach combines Monte Carlo conformational search in an implicit hydrophobic slab followed by molecular dynamics simulations in a hydrated full-atom lipid bilayer. The former technique was used for exhaustive sampling of the peptides' conformational space and for generation of putative "native-like" structures of the dimer. The latter ones were taken as realistic starting points to assess stability and dynamic behavior of the complex in explicit lipid-water surrounding. As a result, several groups of tightly packed right-handed structures of the dimer were proposed. They have almost similar helix-helix interface, which includes the motif A(176)xxxG(180)xxxG(184) and agrees well with previous mutagenesis data and preliminary NMR analysis. Molecular dynamics simulations of these structures reveal perfect adaptation of most of them to heterogeneous membrane environment. A remarkable feature of the predicted dimeric structures is the occurrence of a cluster of H-bonded histidine 173 and serines 168 and 172 on the helix interface, near the N-terminus. Because of specific polar interactions between the monomers, this part of the dimer has no such dense packing as the C-terminal one, thus allowing penetration of water from the extramembrane side into the membrane interior. We propose that the ionization state of His(173) can mediate structural and dynamic properties of the dimer. This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions.
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Affiliation(s)
- Yana A Vereshaga
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow V-437, 117997 GSP, Russia
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