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Zhang P, Zhang B, Ji Y, Jiao J, Zhang Z, Tian C. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. MLIFE 2024; 3:277-290. [PMID: 38948139 PMCID: PMC11211677 DOI: 10.1002/mlf2.12132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.
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Affiliation(s)
- Pan Zhang
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Biliang Zhang
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yuan‐Yuan Ji
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Jian Jiao
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Ziding Zhang
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chang‐Fu Tian
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
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2
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Roterman I, Stapor K, Konieczny L. Transmembrane proteins-Different anchoring systems. Proteins 2024; 92:593-609. [PMID: 38062872 DOI: 10.1002/prot.26646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/17/2023] [Indexed: 04/13/2024]
Abstract
Transmembrane proteins are active in amphipathic environments. To stabilize the protein in such surrounding the exposure of hydrophobic residues on the protein surface is required. Transmembrane proteins are responsible for the transport of various molecules. Therefore, they often represent structures in the form of channels. This analysis focused on the stability and local flexibility of transmembrane proteins, particularly those related to their biological activity. Different forms of anchorage were identified using the fuzzy oil-drop model (FOD) and its modified form, FOD-M. The mainly helical as well as β-barrel structural forms are compared with respect to the mechanism of stabilization in the cell membrane. The different anchoring system was found to stabilize protein molecules with possible local fluctuation.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Krakow, Poland
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Krakow, Poland
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3
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Gorostiola González M, Rakers PRJ, Jespers W, IJzerman AP, Heitman LH, van Westen GJP. Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities. Int J Mol Sci 2024; 25:3698. [PMID: 38612509 PMCID: PMC11011372 DOI: 10.3390/ijms25073698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.
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Affiliation(s)
- Marina Gorostiola González
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| | - Pepijn R. J. Rakers
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Willem Jespers
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Adriaan P. IJzerman
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
| | - Laura H. Heitman
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (M.G.G.); (P.R.J.R.); (W.J.); (A.P.I.); (L.H.H.)
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4
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Conforti JM, Ziegler AM, Worth CS, Nambiar AM, Bailey JT, Taube JH, Gallagher ES. Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584881. [PMID: 38559195 PMCID: PMC10980087 DOI: 10.1101/2024.03.13.584881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. However, recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Thus, solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are detected and identified. We hypothesize that the mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. From these results, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.
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Affiliation(s)
- Jessica M. Conforti
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Amanda M. Ziegler
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Charli S. Worth
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Adhwaitha M. Nambiar
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Jacob T. Bailey
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Joseph H. Taube
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Elyssia S. Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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5
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Marin E, Kovalev K, Poelman T, Veenstra R, Borshchevskiy V, Guskov A. Custom Design of a Humidifier Chamber for InMeso Crystallization. CRYSTAL GROWTH & DESIGN 2024; 24:325-330. [PMID: 38188264 PMCID: PMC10767699 DOI: 10.1021/acs.cgd.3c01034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024]
Abstract
Membrane proteins are indispensable for every living organism, yet their structural organization remains underexplored. Despite the recent advancements in single-particle cryogenic electron microscopy and cryogenic electron tomography, which have significantly increased the structural coverage of membrane proteins across various kingdoms, certain scientific methods, such as time-resolved crystallography, still mostly rely on crystallization techniques, such as lipidic cubic phase (LCP) or in meso crystallization. In this study, we present an open-access blueprint for a humidity control chamber designed for LCP/in meso crystallization experiments using a Gryphon crystallization robot. Using this chamber, we have obtained crystals of a transmembrane aspartate transporter GltTk from Thermococcus kodakarensis in a lipidic environment using in meso crystallization. The data collected from these crystals allowed us to perform an analysis of lipids bound to the transporter. With this publication of our open-access design of a humidity chamber, we aim to improve the accessibility of in meso protein crystallization for the scientific community.
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Affiliation(s)
- Egor Marin
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Kirill Kovalev
- European
Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607 Hamburg, Germany
| | | | - Rick Veenstra
- University
of Groningen, 9747AG Groningen, The Netherlands
| | | | - Albert Guskov
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
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6
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Self-assembled Supramolecular Artificial Transmembrane Ion Channels: Recent Progress and Application. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2337-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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7
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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8
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Fuchs T, Melcher F, Rerop ZS, Lorenzen J, Shaigani P, Awad D, Haack M, Prem SA, Masri M, Mehlmer N, Brueck TB. Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology. Microb Cell Fact 2021; 20:205. [PMID: 34711240 PMCID: PMC8555327 DOI: 10.1186/s12934-021-01692-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Background The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available. Results In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide. Conclusions Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01692-2.
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Affiliation(s)
- Tobias Fuchs
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Felix Melcher
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Zora Selina Rerop
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Jan Lorenzen
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Pariya Shaigani
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Martina Haack
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sophia Alice Prem
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Mahmoud Masri
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - Thomas B Brueck
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
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9
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Schenkel M, Treff A, Deber CM, Krainer G, Schlierf M. Heat treatment of thioredoxin fusions increases the purity of α-helical transmembrane protein constructs. Protein Sci 2021; 30:1974-1982. [PMID: 34191368 PMCID: PMC8376418 DOI: 10.1002/pro.4150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 01/05/2023]
Abstract
Membrane proteins play key roles in cellular signaling and transport, represent the majority of drug targets, and are implicated in many diseases. Their relevance renders them important subjects for structural, biophysical, and functional investigations. However, obtaining membrane proteins in high purities is often challenging with conventional purification steps alone. To address this issue, we present here an approach to increase the purity of α-helical transmembrane proteins. Our approach exploits the Thioredoxin (Trx) tag system, which is able to confer some of its favorable properties, such as high solubility and thermostability, to its fusion partners. Using Trx fusions of transmembrane helical hairpin constructs derived from the human cystic fibrosis transmembrane conductance regulator (CFTR) and a bacterial ATP synthase, we establish conditions for the successful implementation of the selective heat treatment procedure to increase sample purity. We further examine systematically its efficacy with respect to different incubation times and temperatures using quantitative gel electrophoresis. We find that minute-timescale heat treatment of Trx-tagged fusion constructs with temperatures ranging from 50 to 90°C increases the purity of the membrane protein samples from ~60 to 98% even after affinity purification. We show that this single-step approach is even applicable in cases where regular selective heat purification from crude extracts, as reported for Trx fusions to soluble proteins, fails. Overall, our approach is easy to integrate into existing purification strategies and provides a facile route for increasing the purity of membrane protein constructs after purification by standard chromatography approaches.
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Affiliation(s)
- Mathias Schenkel
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
| | - Antoine Treff
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
| | - Charles M. Deber
- Division of Molecular Medicine, Research InstituteHospital for Sick ChildrenTorontoOntarioCanada
| | - Georg Krainer
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
- Centre for Misfolding Diseases, Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Michael Schlierf
- B CUBE – Center for Molecular BioengineeringTU DresdenDresdenGermany
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10
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Quezada C, Estay H, Cassano A, Troncoso E, Ruby-Figueroa R. Prediction of Permeate Flux in Ultrafiltration Processes: A Review of Modeling Approaches. MEMBRANES 2021; 11:368. [PMID: 34070146 PMCID: PMC8158366 DOI: 10.3390/membranes11050368] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/27/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023]
Abstract
In any membrane filtration, the prediction of permeate flux is critical to calculate the membrane surface required, which is an essential parameter for scaling-up, equipment sizing, and cost determination. For this reason, several models based on phenomenological or theoretical derivation (such as gel-polarization, osmotic pressure, resistance-in-series, and fouling models) and non-phenomenological models have been developed and widely used to describe the limiting phenomena as well as to predict the permeate flux. In general, the development of models or their modifications is done for a particular synthetic model solution and membrane system that shows a good capacity of prediction. However, in more complex matrices, such as fruit juices, those models might not have the same performance. In this context, the present work shows a review of different phenomenological and non-phenomenological models for permeate flux prediction in UF, and a comparison, between selected models, of the permeate flux predictive capacity. Selected models were tested with data from our previous work reported for three fruit juices (bergamot, kiwi, and pomegranate) processed in a cross-flow system for 10 h. The validation of each selected model's capacity of prediction was performed through a robust statistical examination, including a residual analysis. The results obtained, within the statistically validated models, showed that phenomenological models present a high variability of prediction (values of R-square in the range of 75.91-99.78%), Mean Absolute Percentage Error (MAPE) in the range of 3.14-51.69, and Root Mean Square Error (RMSE) in the range of 0.22-2.01 among the investigated juices. The non-phenomenological models showed a great capacity to predict permeate flux with R-squares higher than 97% and lower MAPE (0.25-2.03) and RMSE (3.74-28.91). Even though the estimated parameters have no physical meaning and do not shed light into the fundamental mechanistic principles that govern these processes, these results suggest that non-phenomenological models are a useful tool from a practical point of view to predict the permeate flux, under defined operating conditions, in membrane separation processes. However, the phenomenological models are still a proper tool for scaling-up and for an understanding the UF process.
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Affiliation(s)
- Carolina Quezada
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago 8940577, Chile;
- Programa de Doctorado en Ciencia de Materiales e Ingeniería de Procesos (Doctoral Program in Materials Science and Process Engineering), Universidad Tecnológica Metropolitana, Santiago 8940577, Chile
| | - Humberto Estay
- Advanced Mining Technology Center (AMTC), University of Chile, Av. Tupper 2007 (AMTC Building), Santiago 8370451, Chile;
| | - Alfredo Cassano
- Institute on Membrane Technology, ITM-CNR, via P. Bucci, 17/C, I-87030 Rende, Italy;
| | - Elizabeth Troncoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago 8940577, Chile;
| | - René Ruby-Figueroa
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago 8940577, Chile;
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11
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Almuhtaseb RM, Awadallah-F A, Al-Muhtaseb SA, Khraisheh M. Influence of Casting Solvents on CO 2/CH 4 Separation Using Polysulfone Membranes. MEMBRANES 2021; 11:286. [PMID: 33924710 PMCID: PMC8070651 DOI: 10.3390/membranes11040286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
Polysulfone membranes exhibit resistance to high temperature with low manufacturing cost and high efficiency in the separation process. The composition of gases is an important step that estimates the efficiency of separation in membranes. As membrane types are currently becoming in demand for CO2/CH4 segregation, polysulfone will be an advantageous alternative to have in further studies. Therefore, research is undertaken in this study to evaluate two solvents: chloroform (CF) and tetrahydrofuran (THF). These solvents are tested for casting polymeric membranes from polysulfone (PSF) to separate every single component from a binary gas mixture of CO2/CH4. In addition, the effect of gas pressure was conducted from 1 to 10 bar on the behavior of the permeability and selectivity. The results refer to the fact that the maximum permeability of CO2 and CH4 for THF is 62.32 and 2.06 barrer at 1 and 2 bars, respectively. Further, the maximum permeability of CF is 57.59 and 2.12 barrer at 1 and 2 bars, respectively. The outcome selectivity values are 48 and 36 for THF and CF at 1 bar, accordingly. Furthermore, the study declares that with the increase in pressure, the permeability and selectivity values drop for CF and THF. The performance for polysulfone (PSF) membrane that is manufactured with THF is superior to that of CF relative to the Robeson upper bound. Therefore, through the results, it can be deduced that the solvent during in-situ synthesis has a significant influence on the gas separation of a binary mixture of CO2/CH4.
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Affiliation(s)
| | | | | | - Majeda Khraisheh
- Department of Chemical Engineering, Qatar University, Doha P.O. Box 2713, Qatar; (R.M.A.); (A.A.-F.); (S.A.A.-M.)
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12
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Wojcik S, Kriechbaumer V. Go your own way: membrane-targeting sequences. PLANT PHYSIOLOGY 2021; 185:608-618. [PMID: 33822216 PMCID: PMC8133554 DOI: 10.1093/plphys/kiaa058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 05/05/2023]
Abstract
Membrane-targeting sequences, connected targeting mechanisms, and co-factors orchestrate primary targeting of proteins to membranes.
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Affiliation(s)
- Stefan Wojcik
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Verena Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Author for communication: (V.K.)
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13
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Sun J, Frishman D. Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning. Comput Struct Biotechnol J 2021; 19:1512-1530. [PMID: 33815689 PMCID: PMC7985279 DOI: 10.1016/j.csbj.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
Fast and accurate prediction of transmembrane protein interaction sites. First ever computational survey of interaction sites in membrane proteins. 10-30% of amino acid positions predicted to be involved in interactions.
Interactions between transmembrane (TM) proteins are fundamental for a wide spectrum of cellular functions, but precise molecular details of these interactions remain largely unknown due to the scarcity of experimentally determined three-dimensional complex structures. Computational techniques are therefore required for a large-scale annotation of interaction sites in TM proteins. Here, we present a novel deep-learning approach, DeepTMInter, for sequence-based prediction of interaction sites in α-helical TM proteins based on their topological, physiochemical, and evolutionary properties. Using a combination of ultra-deep residual neural networks with a stacked generalization ensemble technique DeepTMInter significantly outperforms existing methods, achieving the AUC/AUCPR values of 0.689/0.598. Across the main functional families of human transmembrane proteins, the percentage of amino acid sites predicted to be involved in interactions typically ranges between 10% and 25%, and up to 30% in ion channels. DeepTMInter is available as a standalone package at https://github.com/2003100127/deeptminter. The training and benchmarking datasets are available at https://data.mendeley.com/datasets/2t8kgwzp35.
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Affiliation(s)
- Jianfeng Sun
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
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14
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Yan T, Liu S, Luo Y, Zou Y, Liu J. Research Progress on the Macrocycle-Derived Artificial Transmembrane Ion Channels. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a21050222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Abstract
Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.
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16
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Mathangi S, Arvind Chandrasekharan HV, Ramya L. Exploring the molecular insights of intrinsically disordered mitochondrial intermembrane protein in its unbound and substrate-bound state. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1812600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- S. Mathangi
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - L. Ramya
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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17
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Gu X, Song LJ, Li LX, Liu T, Zhang MM, Li Z, Wang P, Li M, Zuo XL. Fusobacterium nucleatum Causes Microbial Dysbiosis and Exacerbates Visceral Hypersensitivity in a Colonization-Independent Manner. Front Microbiol 2020; 11:1281. [PMID: 32733392 PMCID: PMC7358639 DOI: 10.3389/fmicb.2020.01281] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Microbial dysbiosis is closely associated with visceral hypersensitivity and is involved in the pathogenesis of irritable bowel syndrome (IBS), but the specific strains that play a key role have yet to be identified. Previous bioinformatic studies have demonstrated that Fusobacterium is a shared microbial feature between IBS patients and maternal separation (MS)-stressed rats. In this study, we assessed the potential role of Fusobacterium nucleatum (F. nucleatum) in the pathogenesis of IBS. Methods: Fecal samples of patients with diarrhea predominant-IBS (IBS-D) and healthy controls were obtained. An MS rat model was established to receive gavage of either F. nucleatum or normal saline. Visceral sensitivity was evaluated through colorectal distension test, and fecal microbiota was analyzed by 16S rRNA gene sequencing. F. nucleatum-specific IgA levels in fecal supernatants were assessed by western blotting. The antigen reacted with the specific IgA of F. nucleatum was identified by mass spectrometry and the construction of a recombinant Escherichia coli BL21 (DE3). Results: IBS-D patients showed a lower Shannon index and a higher abundance of Fusobacterium. The F. nucleatum-gavage was shown to exacerbate visceral hypersensitivity in MS rats, with both the F. nucleatum-gavage and MS causing a decreased Shannon index and a clear segregation of fecal microbiota. In addition, specific IgA against F. nucleatum was detected in fecal supernatants of both the F. nucleatum-gavaged rats and the IBS-D patients. The FomA protein, which is a major outer membrane protein of F. nucleatum, was confirmed to react with the specific IgA of F. nucleatum in fecal supernatants. Conclusion:Fusobacterium increased significantly in IBS-D patients, and F. nucleatum was involved in the pathogenesis of IBS by causing microbial dysbiosis and exacerbating visceral hypersensitivity in a colonization-independent manner. Meanwhile, F. nucleatum was found to induce an increase in specific secretory IgA through FomA.
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Affiliation(s)
- Xiang Gu
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Li-Jin Song
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Li-Xiang Li
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Tong Liu
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Ming-Ming Zhang
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Zhen Li
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Peng Wang
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Ming Li
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
| | - Xiu-Li Zuo
- Department of Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan, China
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Ong ILH, Amstad E. Selectively Permeable Double Emulsions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903054. [PMID: 31517446 DOI: 10.1002/smll.201903054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Natural organisms are made of different types of microcompartments, many of which are enclosed by cell membranes. For these organisms to display a proper function, the microcompartments must be selectively permeable. For example, cell membranes are typically permeable toward small, uncharged molecules such as water, selected nutrients, and cell signaling molecules, but impermeable toward many larger biomolecules. Here, it is reported for the first time dynamic compartments, namely surfactant-stabilized double emulsions, that display selective and tunable permeability. Selective permeability is imparted to double emulsions by stabilizing them with catechol-functionalized surfactants that transport molecules across the oil shell of double emulsions only if they electrostatically or hydrophobically attract encapsulants. These double emulsions are employed as semipermeable picoliter-sized vessels to controllably perform complexation reactions inside picoliter-sized aqueous cores. This thus far unmet level of control over the transport of reagents across oil phases opens up new possibilities to use double emulsion drops as dynamic and selectively permeable microcompartments to initiate and maintain chemical and biochemical reactions in picoliter-sized cell-mimetic compartments.
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Affiliation(s)
- Irvine Lian Hao Ong
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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19
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Fry HC, Silveira GDQ, Cohn HM, Lee B. Diverse Bilayer Morphologies Achieved via α-Helix-to-β-Sheet Transitions in a Short Amphiphilic Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8961-8967. [PMID: 31192607 DOI: 10.1021/acs.langmuir.9b00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Transmembrane proteins are functional macromolecules that direct the flow of small molecules and ions across a lipid bilayer. Here, we propose the development of helical peptide amphiphiles that will serve as both the bilayer and the functional unit of a self-assembled peptide bilayer membrane. The peptide, K3L12, was designed not only to possess dimensions similar to that of a lipid bilayer but also to yield a structurally robust, α-helical bilayer. The formation of α-helices is pH-dependent, and upon annealing the sample, a transition from α-helices to β-sheets can be controlled, as indicated by optical and vibrational spectroscopies. Imaging the materials confirms morphologies similar to that of a lipid bilayer but rich in α-helices. Annealing the samples yields a shift in the morphology from bilayers to curled disks, fibers, and sheets. The structural robustness of the material can facilitate the incorporation of many functions into the bilayer assembly.
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20
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Sojo V. Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life. Bioessays 2019; 41:e1800251. [PMID: 30970170 DOI: 10.1002/bies.201800251] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/09/2019] [Indexed: 11/05/2022]
Abstract
Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. However, this would imply a rather elaborate evolutionary scenario, while negating simpler alternatives. In light of widespread horizontal gene transfer across the prokaryotic domains, hybrid membranes reveal that the lipid divide did not just occur once at the divergence of archaea and bacteria from LUCA. Instead, it continues to occur actively to this day.
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Affiliation(s)
- Victor Sojo
- College for Life Sciences, Wissenschaftskolleg zu Berlin (Institute for Advanced Study, Berlin), Germany
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21
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Xiong H, Yan J, Cai S, He Q, Peng D, Liu Z, Liu Y. Cancer protein biomarker discovery based on nucleic acid aptamers. Int J Biol Macromol 2019; 132:190-202. [PMID: 30926499 DOI: 10.1016/j.ijbiomac.2019.03.165] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/22/2019] [Accepted: 03/24/2019] [Indexed: 01/11/2023]
Abstract
Identification of biomarkers is essential for diagnosis, targeted therapy and prognosis evaluation of diseases, especially cancers. Currently, the number of ideal clinical biomarkers is still limited partially because of lacking efficient methods in biomarker discovery. Nucleic acid aptamers are artificial single-stranded DNA or RNA sequences that can selectively bind to various targets with high specificity and affinity. Moreover, aptamers possess desirable advantages, including easy synthesis, convenient modification, relative chemical stability and low immunogenicity. Recently, different aptamer-based strategies have been developed to facilitate the discovery of biomarkers. Based on cell-SELEX technology, the selected aptamers can be used to identify cell-surface protein biomarkers of different cancer cells. SOMAscan can analyze thousands of proteins of different biological samples, which becomes a multiplexed protein biomarker discovery platform. Additionally, secreted protein biomarkers can be discovered by aptamers screened through secretome SELEX. In order to facilitate the identification of target proteins, several covalent cross-linking strategies have been developed, such as aptamer-based affinity labeling (ABAL), DNA-templated aptamer and protein-aptamer template (PAT). In this review, we mainly highlight the emerging nucleic acid aptamer-based biomarker discovery strategies and demonstrate their unique technological advantages in discovering cancer biomarkers. The challenges and perspectives of aptamer-based methods are also discussed.
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Affiliation(s)
- Hongjie Xiong
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Jianhua Yan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Dongming Peng
- Department of Medicinal Chemistry, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China.
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22
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Wan LY, Yuan WF, Ai WB, Ai YW, Wang JJ, Chu LY, Zhang YQ, Wu JF. An exploration of aptamer internalization mechanisms and their applications in drug delivery. Expert Opin Drug Deliv 2019; 16:207-218. [PMID: 30691313 DOI: 10.1080/17425247.2019.1575808] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION As 'chemical antibodies', aptamers have some advantages, such as lack of immunogenicity, rapid tissue penetration, cell internalization and so on. Consequently, more and more aptamers have been screened out by the systematic evolution of ligands through exponential enrichment for the desired cells or membrane receptors. On the basis of the result, researchers use aptamers to guide drug targeting to the desired cells and internalization in vivo. AREAS COVERED In this review, we explore the mechanisms of cargo- or aptamer-mediated internalization, and then briefly summarize five strategies for exploring the mechanism of aptamer internalization. Finally, we focus on four types of applications involving aptamer internalization: aptamers as drugs, aptamers as chemical drug-delivery systems, aptamer-based chimeras and aptamer-conjugated nanoparticles or block copolymer micelles. EXPERT OPINION Two aptamer-internalization mechanisms are known, namely receptor-mediated endocytosis and macropinocytosis. The latter mechanism, which is has only been verified in the internalization of nucleolin aptamer shuttles between the nucleus and cytoplasm, may be important for nuclear internalization and cargo molecule escape from the endosomal compartment. Thus, it is feasible to use some strategies to further explore the macropinocytosis internalization mechanism and then to screen for aptamers similar to the nucleolin aptamer for use with the desired cell types as a targeted delivery tool.
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Affiliation(s)
- Lin-Yan Wan
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Wen-Fang Yuan
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Wen-Bing Ai
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
| | - Yao-Wei Ai
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Jiao-Jiao Wang
- c Medical College , China Three Gorges University , Yichang , China
| | - Liang-Yin Chu
- e School of Chemical Engineering , Sichuan University , Chengdu , China
| | - Yan-Qiong Zhang
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Jiang-Feng Wu
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
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23
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Yang X, Naughton SX, Han Z, He M, Zheng YG, Terry AV, Bartlett MG. Mass Spectrometric Quantitation of Tubulin Acetylation from Pepsin-Digested Rat Brain Tissue Using a Novel Stable-Isotope Standard and Capture by Anti-Peptide Antibody (SISCAPA) Method. Anal Chem 2018; 90:2155-2163. [PMID: 29320166 DOI: 10.1021/acs.analchem.7b04484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Acetylation of α-tubulin at Lys-40 is a potential biomarker for cognitive deficits in various neurological disorders. However, this key post-translational modification (PTM) has not been previously studied with mass spectrometry, due to the inadequate distribution of tryptic cleavage sites. Following peptic digestion, a surrogate sequence containing this key PTM site was identified and was found to be stable and quantitatively reproducible. A highly sensitive and specific SISCAPA-LC-MS method for quantitating rat brain tubulin acetylation was developed, validated, and applied, and only required a small amount of tissue (2.2 mg). This workflow includes peptic digestion, stable-isotope dilution, capture with antiacetylated peptide antibody bound on protein G beads, and quantitation using LC-MS. The method allowed a lower limit of quantitation at 2.50 pmol/mg and provided a linear range of 2.50-62.50 pmol/mg. Selectivity, intra and interday precision and accuracy were also validated. This method has been successfully applied in a preclinical study of organophosphate neurotoxicity, and we found that chronic exposure to chlorpyrifos led to a significant and persistent inhibition of brain tubulin acetylation.
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Affiliation(s)
- Xiangkun Yang
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy , 250 W. Green Street, Athens, Georgia 30602, United States
| | - Sean X Naughton
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University , Augusta, Georgia 30912, United States
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy , 250 W. Green Street, Athens, Georgia 30602, United States
| | - Maomao He
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy , 250 W. Green Street, Athens, Georgia 30602, United States
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy , 250 W. Green Street, Athens, Georgia 30602, United States
| | - Alvin V Terry
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University , Augusta, Georgia 30912, United States
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy , 250 W. Green Street, Athens, Georgia 30602, United States
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Duan M, Long Y, Yang C, Wu X, Sun Y, Li J, Hu X, Lin W, Han D, Zhao Y, Liu J, Ye M, Tan W. Selection and characterization of DNA aptamer for metastatic prostate cancer recognition and tissue imaging. Oncotarget 2017; 7:36436-36446. [PMID: 27183906 PMCID: PMC5095011 DOI: 10.18632/oncotarget.9262] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/02/2016] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PCa) is the second leading cause of death and most prevalent cancer in men. The absence of curative options for castration-resistant metastatic prostate cancer and biomarkers able to discriminate between indolent and aggressive tumors contribute to these statistics. In this study, a DNA aptamer termed DML-7 was successfully selected against human PCa cell line DU145 by using the cell-based systematic evolution of ligands by exponential enrichment (SELEX) method. The selected aptamer DML-7 was found to internalize into target cells in a temperature-dependent manner and exhibit high binding affinity for target cells with dissociation constants in the nanomolar range. Binding analysis further revealed that DML-7 only binds to DU145 and PC-3 cells with metastatic potential, but not to LNCaP or 22Rv1 cells with low or nonmetastatic potential, demonstrating that DML-7 has excellent selectivity for the recognition of the metastatic PCa cells. Clinical tissue imaging further confirmed these results. Therefore, both high binding affinity and specificity to metastatic PCa cells and tissues afford DML-7 with the potential for development into a novel tool for diagnosis and targeted drug delivery against metastatic prostate cancer.
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Affiliation(s)
- Minlan Duan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yuqian Long
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoqiu Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yang Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Wei Lin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Dongmei Han
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Jing Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China.,Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, University Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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25
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Wang S, Xiao C, Jiang L, Ling L, Chen X, Guo X. A high sensitive and contaminant tolerant matrix for facile detection of membrane proteins by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2017; 999:114-122. [PMID: 29254561 DOI: 10.1016/j.aca.2017.11.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 11/05/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023]
Abstract
Despite the significance of membrane proteins (MPs) in biological system is indisputable, their specific natures make them notoriously difficult to be analyzed. Particularly, the widely used Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) prefers analyses of hydrophilic cytosolic proteins and has a limited ionization efficiency towards hydrophobic MPs. Herein, a hydrophobic compound (E)-propyl α-Cyano-4-Hydroxyl Cinnamylate (CHCA-C3), a propyl-esterified derivative of α-cyano-4-hydroxycinnamic acid (CHCA), was applied as a contaminant tolerant matrix for high sensitivity MALDI-MS analyses of MPs. With CHCA-C3, the detection limits of hydrophobic peptides were 10- to 100-fold better than those using CHCA. Furthermore, high quality of spectra could be achieved in the presence of high concentration of chaotropes, salts and detergents, as well as human urinary and serum environment. Also, CHCA-C3 could generate uniform sample distribution even in the presence of contaminants. This high contaminant-resistance was revealed to be ascribed to the enhanced hydrophobicity of CHCA-C3 with a lower affinity towards hydrophilic contaminants. The application of CHCA-C3 is further demonstrated by the analysis of trypsin/CNBr digests of bacteriorhodopsin containing seven transmembrane domains (TMDs), which dramatically increased numbers of identified hydrophobic peptides in TMDs and sequence coverage (∼100%). Besides, a combined method by using CHCA-C3 with fluoride solvent and a patterned paraffin plate was established for analysis of integral MPs. We achieved a low detection limit of 10 fmol for integral bacteriorhodopsin, which could not be detected using traditional matrices such as 3,5-dimethoxy-4-hydroxycinamic acid, 2,5-dihydroxyacetophenone even at sample concentration of 10 pmol.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China
| | - Ling Ling
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China.
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26
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Hayashi T, Yasuda S, Škrbić T, Giacometti A, Kinoshita M. Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail. J Chem Phys 2017; 147:125102. [DOI: 10.1063/1.4999376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Huang B, Geng Z, Yan S, Li Z, Cai J, Wang Z. Water-Soluble Conjugated Polymer as a Fluorescent Probe for Monitoring Adenosine Triphosphate Level Fluctuation in Cell Membranes during Cell Apoptosis and in Vivo. Anal Chem 2017; 89:8816-8821. [PMID: 28752761 DOI: 10.1021/acs.analchem.7b01212] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Adenosine triphosphate (ATP) is used as the energy source in cells and plays crucial roles in various cellular events. The cellular membrane is the protective barrier for the cytoplasm of living cells and involved in many essential biological processes. Many fluorescent probes for ATP have been successfully developed, but few of these probes were appropriate for visualizing ATP level fluctuation in cell membranes during the apoptotic cell death process. Herein, we report the synthesis of a new water-soluble cationic polythiophene derivative that can be utilized as a fluorescent sensor for detecting ATP in cell membranes. Poly((3-((4-methylthiophen-3-yl)oxy)propyl)triphenylphosphonium chloride) (PMTPP) exhibits high sensitivity and good selectivity to ATP, and the detection limit is 27 nM. The polymer shows low toxicity to live cells and excellent photostability in cell membranes. PMTPP was practically utilized for real-time monitoring of ATP levels in the cell membrane through fluorescence microscopy. We have demonstrated that the ATP levels in cell membranes increased during the apoptotic cell death process. The probe was also capable of imaging ATP levels in living mice.
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Affiliation(s)
- Binghuan Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhirong Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Shihai Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zan Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Jun Cai
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
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Tamayo Tenorio A, Boom RM, van der Goot AJ. Understanding leaf membrane protein extraction to develop a food-grade process. Food Chem 2016; 217:234-243. [PMID: 27664631 DOI: 10.1016/j.foodchem.2016.08.093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/25/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
Abstract
Leaf membrane proteins are an underutilised protein fraction for food applications. Proteins from leaves can contribute to a more complete use of resources and help to meet the increasing protein demand. Leaf protein extraction and purification is applied by other disciplines, such as proteomics. Therefore, this study analysed proteomic extraction methods for membrane proteins as an inspiration for a food-grade alternative process. Sugar beet leaves were extracted with two proteomic protocols: solvent extraction and Triton X-114 phase partitioning method. Extraction steps contributed to protein purity and/or to selective fractionation, enabling the purification of specific proteins. It was observed that membrane proteins distributed among different solvents, buffers and solutions used due to their physicochemical heterogeneity. This heterogeneity does not allow a total membrane protein extraction by a unique method or even combinations of processing steps, but it enables the creation of different fractions with different physicochemical properties useful for food applications.
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Affiliation(s)
- Angelica Tamayo Tenorio
- Laboratory of Food Process Engineering, Wageningen University, PO Box 17, 6700 AA Wageningen, The Netherlands
| | - Remko M Boom
- Laboratory of Food Process Engineering, Wageningen University, PO Box 17, 6700 AA Wageningen, The Netherlands
| | - Atze Jan van der Goot
- Laboratory of Food Process Engineering, Wageningen University, PO Box 17, 6700 AA Wageningen, The Netherlands.
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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Sojo V, Dessimoz C, Pomiankowski A, Lane N. Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life. Mol Biol Evol 2016; 33:2874-2884. [PMID: 27501943 PMCID: PMC5062322 DOI: 10.1093/molbev/msw164] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine.
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Affiliation(s)
- Victor Sojo
- CoMPLEX, University College London, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Systems Biophysics, Faculty of Physics, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Christophe Dessimoz
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Andrew Pomiankowski
- CoMPLEX, University College London, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Nick Lane
- CoMPLEX, University College London, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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31
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Fehr N, García-Rubio I, Jeschke G, Paulsen H. Early folding events during light harvesting complex II assembly in vitro monitored by pulsed electron paramagnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:695-704. [PMID: 27063475 DOI: 10.1016/j.bbabio.2016.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Efficient energy transfer in the major light harvesting complex II (LHCII) of green plants is facilitated by the precise alignment of pigments due to the protein matrix they are bound to. Much is known about the import of the LHCII apoprotein into the chloroplast via the TOC/TIC system and its targeting to the thylakoid membrane but information is sparse about when and where the pigments are bound and how this is coordinated with protein folding. In vitro, the LHCII apoprotein spontaneously folds and binds its pigments if the detergent-solubilized protein is combined with a mixture of chlorophylls a and b and carotenoids. In the present work, we employed this approach to study apoprotein folding and pigment binding in a time-resolved manner by using pulsed electron paramagnetic resonance (EPR). Intra-molecular distances were measured before folding, after 255 ms and 40 s folding time in the absence of cryoprotectant, and in the fully folded and assembled LHCII. In accordance with earlier results, the most of the folding of the three membrane-spanning alpha helices precedes their apposition into the final tertiary structure. However, their formation follows different kinetics, partially extending into the final phase of LHCII formation during which much of the condensation of the pigment-protein structure occurs, presumably governed by the binding of chlorophyll b. A rough timetable is proposed to sort partial events into the LHCII formation process.
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Affiliation(s)
- Niklas Fehr
- Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany
| | - Inés García-Rubio
- Department of Physical Chemistry, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Gunnar Jeschke
- Department of Physical Chemistry, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Harald Paulsen
- Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany.
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32
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Attwood MM, Krishnan A, Pivotti V, Yazdi S, Almén MS, Schiöth HB. Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. BMC Genomics 2016; 17:268. [PMID: 27030248 PMCID: PMC4815072 DOI: 10.1186/s12864-016-2592-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/16/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Membrane proteins are key components in a large spectrum of diverse functions and thus account for the major proportion of the drug-targeted portion of the genome. From a structural perspective, the α-helical transmembrane proteins can be categorized into major groups based on the number of transmembrane helices and these groups are often associated with specific functions. When compared to the well-characterized seven-transmembrane containing proteins (7TM), other TM groups are less explored and in particular the 4TM group. In this study, we identify the complete 4TM complement from the latest release of the human genome and assess the 4TM structure group as a whole. We functionally characterize this dataset and evaluate the resulting groups and ubiquitous functions, and furthermore describe disease and drug target involvement. RESULTS We classified 373 proteins, which represents ~7 % of the human membrane proteome, and includes 69 more proteins than our previous estimate. We have characterized the 4TM dataset based on functional, structural, and/or evolutionary similarities. Proteins that are involved in transport activity constitute 37 % of the dataset, 23 % are receptor-related, and 13 % have enzymatic functions. Intriguingly, proteins involved in transport are more than double the 15 % of transporters in the entire human membrane proteome, which might suggest that the 4TM topological architecture is more favored for transporting molecules over other functions. Moreover, we found an interesting exception to the ubiquitous intracellular N- and C-termini localization that is found throughout the entire membrane proteome and 4TM dataset in the neurotransmitter gated ion channel families. Overall, we estimate that 58 % of the dataset has a known association to disease conditions with 19 % of the genes possibly involved in different types of cancer. CONCLUSIONS We provide here the most robust and updated classification of the 4TM complement of the human genome as a platform to further understand the characteristics of 4TM functions and to explore pharmacological opportunities.
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Affiliation(s)
- Misty M. Attwood
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Arunkumar Krishnan
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Valentina Pivotti
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Samira Yazdi
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Markus Sällman Almén
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B. Schiöth
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
- />Institutionen för neurovetenskap, BMC, Box 593, 751 24 Uppsala, Sweden
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Fang X, Qiao L, Yan G, Yang P, Liu B. Multifunctional nanoreactor for comprehensive characterization of membrane proteins based on surface functionalized mesoporous foams. Anal Chem 2015; 87:9360-7. [PMID: 26305297 DOI: 10.1021/acs.analchem.5b02135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient in situ digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research.
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Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
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34
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The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions. Structure 2015; 23:527-541. [PMID: 25703378 DOI: 10.1016/j.str.2015.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/17/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Abstract
α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure.
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35
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Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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36
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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37
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Van Simaeys D, Turek D, Champanhac C, Vaizer J, Sefah K, Zhen J, Sutphen R, Tan W. Identification of cell membrane protein stress-induced phosphoprotein 1 as a potential ovarian cancer biomarker using aptamers selected by cell systematic evolution of ligands by exponential enrichment. Anal Chem 2014; 86:4521-7. [PMID: 24654750 PMCID: PMC4018121 DOI: 10.1021/ac500466x] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/21/2014] [Indexed: 02/01/2023]
Abstract
In this paper, we describe the elucidation of the target of an aptamer against ovarian cancer previously obtained by cell-SELEX (SELEX = systematic evolution of ligands by exponential enrichment). The target's identity, stress-induced phosphoprotein 1 (STIP1), was determined by mass spectrometry and validated by flow cytometry, using siRNA silencing and protein blotting. Initial oncologic studies show that the aptamer inhibits cell invasion, indicating that STIP1, which is currently under investigation as a potential biomarker for ovarian cancer, plays a critical role in this process. These results serve as an excellent example of how protein target identification of aptamers obtained by cell-SELEX can serve as a means to identify promising biomarker candidates and can promote the development of aptamers as a new drug class to block important oncological processes.
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Affiliation(s)
- Dimitri Van Simaeys
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Diane Turek
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Carole Champanhac
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Julia Vaizer
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Kwame Sefah
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Jing Zhen
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, Colleges of Chemistry and Chemical Engineering and
of Biology, Collaborative Innovation Center for Molecular Engineering
and Theranostics, Hunan University, Changsha 410082, China
| | - Rebecca Sutphen
- Morsani
School of Medicine, University of South
Florida, Tampa, Florida 33612, United
States
| | - Weihong Tan
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, Colleges of Chemistry and Chemical Engineering and
of Biology, Collaborative Innovation Center for Molecular Engineering
and Theranostics, Hunan University, Changsha 410082, China
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Qin H, Lim L, Wei Y, Gupta G, Song J. Resolving the paradox for protein aggregation diseases: NMR structure and dynamics of the membrane-embedded P56S-MSP causing ALS imply a common mechanism for aggregation-prone proteins to attack membranes. F1000Res 2013; 2:221. [PMID: 25254094 PMCID: PMC4168755 DOI: 10.12688/f1000research.2-221.v2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2014] [Indexed: 12/12/2022] Open
Abstract
Paradoxically, aggregation of specific proteins is characteristic of many human diseases and aging, yet aggregates have increasingly been found to be unnecessary for initiating pathogenesis. Here we determined the NMR topology and dynamics of a helical mutant in a membrane environment transformed from the 125-residue cytosolic all-β MSP domain of vesicle-associated membrane protein-associated protein B (VAPB) by the ALS-causing P56S mutation. Despite its low hydrophobicity, the P56S major sperm protein (MSP) domain becomes largely embedded in the membrane environment with high backbone rigidity. Furthermore it is composed of five helices with amphiphilicity comparable to those of the partly-soluble membrane toxin mellitin and α-synuclein causing Parkinson's disease. Consequently, the mechanism underlying this chameleon transformation becomes clear: by disrupting the specific tertiary interaction network stabilizing the native all-β MSP fold to release previously-locked amphiphilic segments, the P56S mutation acts to convert the classic MSP fold into a membrane-active protein that is fundamentally indistinguishable from mellitin and α-synuclein which are disordered in aqueous solution but spontaneously partition into membrane interfaces driven by hydrogen-bond energetics gained from forming α-helix in the membrane environments. As segments with high amphiphilicity exist in all proteins, our study successfully resolves the paradox by deciphering that the proteins with a higher tendency to aggregate have a stronger potential to partition into membranes through the same mechanism as α-synuclein to initially attack membranes to trigger pathogenesis without needing aggregates. This might represent the common first step for various kinds of aggregated proteins to trigger familiar, sporadic and aging diseases. Therefore the homeostasis of aggregated proteins in vivo is the central factor responsible for a variety of human diseases including aging. The number and degree of the membrane attacks by aggregated proteins may act as an endogenous clock to count down the aging process. Consequently, a key approach to fight against them is to develop strategies and agents to maintain or even enhance the functions of the degradation machineries.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Yuanyuan Wei
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
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Qin H, Lim L, Wei Y, Gupta G, Song J. Resolving the paradox for protein aggregation diseases: NMR structure and dynamics of the membrane-embedded P56S-MSP causing ALS imply a common mechanism for aggregation-prone proteins to attack membranes. F1000Res 2013. [PMID: 25254094 DOI: 10.12688/f1000research.2-221.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Paradoxically, aggregation of specific proteins is characteristic of many human diseases and aging, yet aggregates have increasingly been found to be unnecessary for initiating pathogenesis. Here we determined the NMR topology and dynamics of a helical mutant in a membrane environment transformed from the 125-residue cytosolic all-β MSP domain of vesicle-associated membrane protein-associated protein B (VAPB) by the ALS-causing P56S mutation. Despite its low hydrophobicity, the P56S major sperm protein (MSP) domain becomes largely embedded in the membrane environment with high backbone rigidity. Furthermore it is composed of five helices with amphiphilicity comparable to those of the partly-soluble membrane toxin mellitin and α-synuclein causing Parkinson's disease. Consequently, the mechanism underlying this chameleon transformation becomes clear: by disrupting the specific tertiary interaction network stabilizing the native all-β MSP fold to release previously-locked amphiphilic segments, the P56S mutation acts to convert the classic MSP fold into a membrane-active protein that is fundamentally indistinguishable from mellitin and α-synuclein which are disordered in aqueous solution but spontaneously partition into membrane interfaces driven by hydrogen-bond energetics gained from forming α-helix in the membrane environments. As segments with high amphiphilicity exist in all proteins, our study successfully resolves the paradox by deciphering that the proteins with a higher tendency to aggregate have a stronger potential to partition into membranes through the same mechanism as α-synuclein to initially attack membranes to trigger pathogenesis without needing aggregates. This might represent the common first step for various kinds of aggregated proteins to trigger familiar, sporadic and aging diseases. Therefore the homeostasis of aggregated proteins in vivo is the central factor responsible for a variety of human diseases including aging. The number and degree of the membrane attacks by aggregated proteins may act as an endogenous clock to count down the aging process. Consequently, a key approach to fight against them is to develop strategies and agents to maintain or even enhance the functions of the degradation machineries.
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Affiliation(s)
- Haina Qin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Yuanyuan Wei
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119260, Singapore
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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Gromiha MM, Ou YY. Bioinformatics approaches for functional annotation of membrane proteins. Brief Bioinform 2013; 15:155-68. [DOI: 10.1093/bib/bbt015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Song J. Why do proteins aggregate? "Intrinsically insoluble proteins" and "dark mediators" revealed by studies on "insoluble proteins" solubilized in pure water. F1000Res 2013; 2:94. [PMID: 24555050 PMCID: PMC3869494 DOI: 10.12688/f1000research.2-94.v1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/22/2022] Open
Abstract
In 2008, I reviewed and proposed a model for our discovery in 2005 that unrefoldable and insoluble proteins could in fact be solubilized in unsalted water. Since then, this discovery has offered us and other groups a powerful tool to characterize insoluble proteins, and we have further addressed several fundamental and disease-relevant issues associated with this discovery. Here I review these results, which are conceptualized into several novel scenarios. 1) Unlike 'misfolded proteins', which still retain the capacity to fold into well-defined structures but are misled to 'off-pathway' aggregation, unrefoldable and insoluble proteins completely lack this ability and will unavoidably aggregate in vivo with ~150 mM ions, thus designated as 'intrinsically insoluble proteins (IIPs)' here. IIPs may largely account for the 'wastefully synthesized' DRiPs identified in human cells. 2) The fact that IIPs including membrane proteins are all soluble in unsalted water, but get aggregated upon being exposed to ions, logically suggests that ions existing in the background play a central role in mediating protein aggregation, thus acting as 'dark mediators'. Our study with 14 salts confirms that IIPs lack the capacity to fold into any well-defined structures. We uncover that salts modulate protein dynamics and anions bind proteins with high selectivity and affinity, which is surprisingly masked by pre-existing ions. Accordingly, I modified my previous model. 3) Insoluble proteins interact with lipids to different degrees. Remarkably, an ALS-causing P56S mutation transforms the β-sandwich MSP domain into a helical integral membrane protein. Consequently, the number of membrane-interacting proteins might be much larger than currently recognized. To attack biological membranes may represent a common mechanism by which aggregated proteins initiate human diseases. 4) Our discovery also implies a solution to the 'chicken-and-egg paradox' for the origin of primitive membranes embedded with integral membrane proteins, if proteins originally emerged in unsalted prebiotic media.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119260, Singapore
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Yasuda S, Oshima H, Kinoshita M. Structural stability of proteins in aqueous and nonpolar environments. J Chem Phys 2013; 137:135103. [PMID: 23039615 DOI: 10.1063/1.4755755] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A protein folds into its native structure with the α-helix and∕or β-sheet in aqueous solution under the physiological condition. The relative content of these secondary structures largely varies from protein to protein. However, such structural variability is not exhibited in nonaqueous environment. For example, there is a strong trend that alcohol induces a protein to form α-helices, and many of the membrane proteins within the lipid bilayer consists of α-helices. Here we investigate the structural stability of proteins in aqueous and nonpolar environments using our recently developed free-energy function F = (Λ - TS)∕(k(B)T(0)) = Λ∕(k(B)T(0)) - S∕k(B) (T(0) = 298 K and the absolute temperature T is set at T(0)) which is based on statistical thermodynamics. Λ∕(k(B)T(0)) and S∕k(B) are the energetic and entropic components, respectively, and k(B) is Boltzmann's constant. A smaller value of the positive quantity, -S, represents higher efficiency of the backbone and side-chain packing promoted by the entropic effect arising from the translational displacement of solvent molecules or the CH(2), CH(3), and CH groups which constitute nonpolar chains of lipid molecules. As for Λ, in aqueous solution, a transition to a more compact structure of a protein accompanies the break of protein-solvent hydrogen bonds: As the number of donors and acceptors buried without protein intramolecular hydrogen bonding increases, Λ becomes higher. In nonpolar solvent, lower Λ simply implies more intramolecular hydrogen bonds formed. We find the following. The α-helix and β-sheet are advantageous with respect to -S as well as Λ and to be formed as much as possible. In aqueous solution, the solvent-entropy effect on the structural stability is so strong that the close packing of side chains is dominantly important, and the α-helix and β-sheet contents are judiciously adjusted to accomplish it. In nonpolar solvent, the solvent-entropy effect is substantially weaker than in aqueous solution. Λ is crucial and the α-helix is more stable than the β-sheet in terms of Λ, which develops a tendency that α-helices are exclusively chosen. For a membrane protein, α-helices are stabilized as fundamental structural units for the same reason, but their arrangement is performed through the entropic effect mentioned above.
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Affiliation(s)
- Satoshi Yasuda
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
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Alvares RD, Tulumello DV, Macdonald PM, Deber CM, Prosser RS. Effects of a polar amino acid substitution on helix formation and aggregate size along the detergent-induced peptide folding pathway. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:373-81. [DOI: 10.1016/j.bbamem.2012.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 09/06/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022]
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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