1
|
Non-Antibody-Based Binders for the Enrichment of Proteins for Analysis by Mass Spectrometry. Biomolecules 2021; 11:biom11121791. [PMID: 34944435 PMCID: PMC8698613 DOI: 10.3390/biom11121791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 02/07/2023] Open
Abstract
There is often a need to isolate proteins from body fluids, such as plasma or serum, prior to further analysis with (targeted) mass spectrometry. Although immunoglobulin or antibody-based binders have been successful in this regard, they possess certain disadvantages, which stimulated the development and validation of alternative, non-antibody-based binders. These binders are based on different protein scaffolds and are often selected and optimized using phage or other display technologies. This review focuses on several non-antibody-based binders in the context of enriching proteins for subsequent liquid chromatography-mass spectrometry (LC-MS) analysis and compares them to antibodies. In addition, we give a brief introduction to approaches for the immobilization of binders. The combination of non-antibody-based binders and targeted mass spectrometry is promising in areas, like regulated bioanalysis of therapeutic proteins or the quantification of biomarkers. However, the rather limited commercial availability of these binders presents a bottleneck that needs to be addressed.
Collapse
|
2
|
Roy D, Ramasamy R, Schmidt AM. Journey to a Receptor for Advanced Glycation End Products Connection in Severe Acute Respiratory Syndrome Coronavirus 2 Infection: With Stops Along the Way in the Lung, Heart, Blood Vessels, and Adipose Tissue. Arterioscler Thromb Vasc Biol 2021; 41:614-627. [PMID: 33327744 PMCID: PMC7837689 DOI: 10.1161/atvbaha.120.315527] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/30/2020] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide and the pandemic has yet to wane. Despite its associated significant morbidity and mortality, there are no definitive cures and no fully preventative measures to combat SARS-CoV-2. Hence, the urgency to identify the pathobiological mechanisms underlying increased risk for and the severity of SARS-CoV-2 infection is mounting. One contributing factor, the accumulation of damage-associated molecular pattern molecules, is a leading trigger for the activation of nuclear factor-kB and the IRF (interferon regulatory factors), such as IRF7. Activation of these pathways, particularly in the lung and other organs, such as the heart, contributes to a burst of cytokine release, which predisposes to significant tissue damage, loss of function, and mortality. The receptor for advanced glycation end products (RAGE) binds damage-associated molecular patterns is expressed in the lung and heart, and in priming organs, such as the blood vessels (in diabetes) and adipose tissue (in obesity), and transduces the pathological signals emitted by damage-associated molecular patterns. It is proposed that damage-associated molecular pattern-RAGE enrichment in these priming tissues, and in the lungs and heart during active infection, contributes to the widespread tissue damage induced by SARS-CoV-2. Accordingly, the RAGE axis might play seminal roles in and be a target for therapeutic intervention in SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Divya Roy
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine (D.R., R.R., A.M.S.)
- New York Institute of Technology College of Osteopathic Medicine, Glen Head (D.R.)
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine (D.R., R.R., A.M.S.)
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine (D.R., R.R., A.M.S.)
| |
Collapse
|
3
|
NoPv1: a synthetic antimicrobial peptide aptamer targeting the causal agents of grapevine downy mildew and potato late blight. Sci Rep 2020; 10:17574. [PMID: 33067553 PMCID: PMC7567880 DOI: 10.1038/s41598-020-73027-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/26/2020] [Indexed: 01/14/2023] Open
Abstract
Grapevine (Vitis vinifera L.) is a crop of major economic importance. However, grapevine yield is guaranteed by the massive use of pesticides to counteract pathogen infections. Under temperate-humid climate conditions, downy mildew is a primary threat for viticulture. Downy mildew is caused by the biotrophic oomycete Plasmopara viticola Berl. & de Toni, which can attack grapevine green tissues. In lack of treatments and with favourable weather conditions, downy mildew can devastate up to 75% of grape cultivation in one season and weaken newly born shoots, causing serious economic losses. Nevertheless, the repeated and massive use of some fungicides can lead to environmental pollution, negative impact on non-targeted organisms, development of resistance, residual toxicity and can foster human health concerns. In this manuscript, we provide an innovative approach to obtain specific pathogen protection for plants. By using the yeast two-hybrid approach and the P. viticola cellulose synthase 2 (PvCesA2), as target enzyme, we screened a combinatorial 8 amino acid peptide library with the aim to identify interacting peptides, potentially able to inhibit PvCesa2. Here, we demonstrate that the NoPv1 peptide aptamer prevents P. viticola germ tube formation and grapevine leaf infection without affecting the growth of non-target organisms and without being toxic for human cells. Furthermore, NoPv1 is also able to counteract Phytophthora infestans growth, the causal agent of late blight in potato and tomato, possibly as a consequence of the high amino acid sequence similarity between P. viticola and P. infestans cellulose synthase enzymes.
Collapse
|
4
|
Abstract
Receptor for advanced glycation end products (RAGE) is an immunoglobulin-like receptor present on cell surface. RAGE binds to an array of structurally diverse ligands, acts as a pattern recognition receptor (PRR) and is expressed on cells of different origin performing different functions. RAGE ligation leads to the initiation of a cascade of signaling events and is implicated in diseases, such as inflammation, cancer, diabetes, vascular dysfunctions, retinopathy, and neurodegenerative diseases. Because of the significant involvement of RAGE in the progression of numerous diseases, RAGE signaling has been targeted through use of inhibitors and anti-RAGE antibodies as a treatment strategy and therapy. Here in this review, we have summarized the physical and physiological aspects of RAGE biology in mammalian system and the importance of targeting this molecule in the treatment of various RAGE mediated pathologies. Highlights Receptor for advanced glycation end products (RAGE) is a member of immunoglobulin superfamily of receptors and involved in many pathophysiological conditions. RAGE ligation with its ligands leads to initiation of distinct signaling cascades and activation of numerous transcription factors. Targeting RAGE signaling through inhibitors and anti-RAGE antibodies can be promising treatment strategy.
Collapse
Affiliation(s)
- Nitish Jangde
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, India.,Manipal Academy of Higher Education, Manipal, India
| | - Rashmi Ray
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, India
| | - Vivek Rai
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, India
| |
Collapse
|
5
|
Jeevanandam J, Tan KX, Danquah MK, Guo H, Turgeson A. Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications-The Role of Molecular Dynamics Simulation. Biotechnol J 2020; 15:e1900368. [PMID: 31840436 DOI: 10.1002/biot.201900368] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/06/2019] [Indexed: 12/24/2022]
Abstract
Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface. Bioaffinity offers a unique mechanism to bind specific target and receptor molecules from a range of non-targets. The binding efficacy depends on the specificity of the affinity ligand toward the target molecule even at low concentrations. Aptamers are fragments of genetic materials, peptides, or oligonucleotides which possess enhanced specificity in targeting desired cell surface receptor molecules. Aptamer-target binding results from several inter-molecular interactions including hydrogen bond formation, aromatic stacking of flat moieties, hydrophobic interaction, electrostatic, and van der Waals interactions. Advancements in Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has created the opportunity to artificially generate aptamers that specifically bind to desired cancer and tumor surface receptors with high affinities. This article discusses the potential application of molecular dynamics (MD) simulation to advance aptamer-mediated receptor targeting in targeted cancer therapy. MD simulation offers real-time analysis of the molecular drivers of the aptamer-receptor binding and generate optimal receptor binding conditions for theranostic applications. The article also provides an overview of different cancer types with focus on receptor biomarking and targeted treatment approaches, conventional molecular probes, and aptamers that have been explored for cancer cells targeting.
Collapse
Affiliation(s)
- Jaison Jeevanandam
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University, Miri, Sarawak, 98009, Malaysia
| | - Kei Xian Tan
- School of Materials Science & Engineering, Nanyang Technological University, Singapore, 639798
| | | | - Haobo Guo
- Department of Computer Science and Engineering, University of Tennessee, Chattanooga, TN, 37403, USA.,SimCenter, University of Tennessee, Chattanooga, TN, 37403, USA
| | - Andrew Turgeson
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, 37403, USA
| |
Collapse
|
6
|
Thaler M, Luppa PB. Highly sensitive immunodiagnostics at the point of care employing alternative recognition elements and smartphones: hype, trend, or revolution? Anal Bioanal Chem 2019; 411:7623-7635. [PMID: 31236649 DOI: 10.1007/s00216-019-01974-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
Abstract
Immunodiagnostic tests performed at the point of care (POC) today usually employ antibodies for biorecognition and are read out either visually or with specialized equipment. Availability of alternative biorecognition elements with promising features as well as smartphone-based approaches for signal readout, however, challenge the described established configuration in terms of analytical performance and practicability. Assessing these developments' clinical relevance and their impact on POC immunodiagnostics is demanding. The first part of this review will therefore give an overview on suitable diagnostic biosensors based on alternative recognition elements (such as nucleic acid-based aptamers or engineered binding proteins) and exemplify advantages and drawbacks of these biomolecules on the base of selected assays. The second part of the review then focuses on smartphone-connected diagnostics and discusses the indispensable considerations required for successful future clinical POCT implementation. Together, the joint depiction of two of the most innovative and exciting developments in the field will enable the reader to cast a glance into the distant future of POC immunodiagnostics.
Collapse
Affiliation(s)
- Markus Thaler
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar der TU München, Ismaninger Str. 22, 81675, Munich, Germany
| | - Peter B Luppa
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar der TU München, Ismaninger Str. 22, 81675, Munich, Germany.
| |
Collapse
|
7
|
Jangde N, Ray R, Sinha S, Rana K, Singh SK, Khandagale P, Acharya N, Rai V. Cysteine mediated disulfide bond formation in RAGE V domain facilitates its functionally relevant dimerization. Biochimie 2018; 154:55-61. [PMID: 30076903 DOI: 10.1016/j.biochi.2018.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023]
Abstract
Receptor for Advanced Glycation End product (RAGE) is a multiligand receptor implicated in diverse pathological conditions such as diabetes, atherosclerosis, cancer and neural diseases. Extracellular, RAGE consists of V, C1 and C2 domains. Here, we show RAGE exists as a monomer in equilibrium with a fraction of a covalently linked dimer of monomers via its V domain through cysteine. In order to understand the functional implication of this dimer, we examined the binding capacity and functional potential of RAGE dimer via advanced glycation end products (AGEs) which shows enhanced binding capacity towards V domain, ERK phosphorylation, cytokine release and actin polymerization ability of the dimeric form for AGEs compared with the reduced monomeric form. Our data, suggests that the dimeric state of RAGE controls its function and ligand mediated signaling which may play important role in RAGE mediated various diseases.
Collapse
Affiliation(s)
- Nitish Jangde
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Rashmi Ray
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sunita Sinha
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Khokan Rana
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Satyendra Kumar Singh
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Vivek Rai
- Laboratory of Vascular Immunology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| |
Collapse
|
8
|
DeMott CM, Girardin R, Cobbert J, Reverdatto S, Burz DS, McDonough K, Shekhtman A. Potent Inhibitors of Mycobacterium tuberculosis Growth Identified by Using in-Cell NMR-based Screening. ACS Chem Biol 2018; 13:733-741. [PMID: 29359908 DOI: 10.1021/acschembio.7b00879] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In-cell NMR spectroscopy was used to screen for drugs that disrupt the interaction between prokaryotic ubiquitin like protein, Pup, and mycobacterial proteasome ATPase, Mpa. This interaction is critical for Mycobacterium tuberculosis resistance against nitric oxide (NO) stress; interruption of this process was proposed as a mechanism to control latent infection. Three compounds isolated from the NCI Diversity set III library rescued the physiological proteasome substrate from degradation suggesting that the proteasome degradation pathway was selectively targeted. Two of the compounds bind to Mpa with sub-micromolar to nanomolar affinity, and all three exhibit potency toward mycobacteria comparable to antibiotics currently available on the market, inhibiting growth in the low micromolar range.
Collapse
Affiliation(s)
- Christopher M. DeMott
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Roxie Girardin
- Wadsworth Center, New York Department of Health, Albany, New York 12208, United States
| | - Jacqueline Cobbert
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S. Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Kathleen McDonough
- Wadsworth Center, New York Department of Health, Albany, New York 12208, United States
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| |
Collapse
|
9
|
Breindel L, DeMott C, Burz DS, Shekhtman A. Real-Time In-Cell Nuclear Magnetic Resonance: Ribosome-Targeted Antibiotics Modulate Quinary Protein Interactions. Biochemistry 2018; 57:540-546. [PMID: 29266932 DOI: 10.1021/acs.biochem.7b00938] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How ribosome antibiotics affect a wide range of biochemical pathways is not well understood; changes in RNA-mediated protein quinary interactions and consequent activity inside the crowded cytosol may provide one possible mechanism. We developed real-time (RT) in-cell nuclear magnetic resonance (NMR) spectroscopy to monitor temporal changes in protein quinary structure, for ≥24 h, in response to external and internal stimuli. RT in-cell NMR consists of a bioreactor containing gel-encapsulated cells inside a 5 mm NMR tube, a gravity siphon for continuous exchange of medium, and a horizontal drip irrigation system to supply nutrients to the cells during the experiment. We showed that adding antibiotics that bind to the small ribosomal subunit results in more extensive quinary interactions between thioredoxin and mRNA. The results substantiate the idea that RNA-mediated modulation of quinary protein interactions may provide the physical basis for ribosome inhibition and other regulatory pathways.
Collapse
Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher DeMott
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| |
Collapse
|
10
|
Shekhtman A, Ramasamy R, Schmidt AM. Glycation & the RAGE axis: targeting signal transduction through DIAPH1. Expert Rev Proteomics 2016; 14:147-156. [PMID: 27967251 DOI: 10.1080/14789450.2017.1271719] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The consequences of chronic disease are vast and unremitting; hence, understanding the pathogenic mechanisms mediating such disorders holds promise to identify therapeutics and diminish the consequences. The ligands of the receptor for advanced glycation end products (RAGE) accumulate in chronic diseases, particularly those characterized by inflammation and metabolic dysfunction. Although first discovered and reported as a receptor for advanced glycation end products (AGEs), the expansion of the repertoire of RAGE ligands implicates the receptor in diverse milieus, such as autoimmunity, chronic inflammation, obesity, diabetes, and neurodegeneration. Areas covered: This review summarizes current knowledge regarding the ligand families of RAGE and data from human subjects and animal models on the role of the RAGE axis in chronic diseases. The recent discovery that the cytoplasmic domain of RAGE binds to the formin homology 1 (FH1) domain, DIAPH1, and that this interaction is essential for RAGE ligand-stimulated signal transduction, is discussed. Finally, we review therapeutic opportunities targeting the RAGE axis as a means to mitigate chronic diseases. Expert commentary: With the aging of the population and the epidemic of cardiometabolic disease, therapeutic strategies to target molecular pathways that contribute to the sequelae of these chronic diseases are urgently needed. In this review, we propose that the ligand/RAGE axis and its signaling nexus is a key factor in the pathogenesis of chronic disease and that therapeutic interruption of this pathway may improve quality and duration of life.
Collapse
Affiliation(s)
- Alexander Shekhtman
- a Department of Chemistry , University at Albany, State University of New York , Albany , NY , 12222 , USA
| | - Ravichandran Ramasamy
- b Diabetes Research Program, Division of Endocrinology, Department of Medicine , NYU Langone Medical Center , New York , NY , 10016 , USA
| | - Ann Marie Schmidt
- b Diabetes Research Program, Division of Endocrinology, Department of Medicine , NYU Langone Medical Center , New York , NY , 10016 , USA
| |
Collapse
|
11
|
Xue J, Manigrasso M, Scalabrin M, Rai V, Reverdatto S, Burz DS, Fabris D, Schmidt AM, Shekhtman A. Change in the Molecular Dimension of a RAGE-Ligand Complex Triggers RAGE Signaling. Structure 2016; 24:1509-22. [PMID: 27524199 DOI: 10.1016/j.str.2016.06.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/20/2016] [Accepted: 06/16/2016] [Indexed: 01/13/2023]
Abstract
The weak oligomerization exhibited by many transmembrane receptors has a profound effect on signal transduction. The phenomenon is difficult to characterize structurally due to the large sizes of and transient interactions between monomers. The receptor for advanced glycation end products (RAGE), a signaling molecule central to the induction and perpetuation of inflammatory responses, is a weak constitutive oligomer. The RAGE domain interaction surfaces that mediate homo-dimerization were identified by combining segmental isotopic labeling of extracellular soluble RAGE (sRAGE) and nuclear magnetic resonance spectroscopy with chemical cross-linking and mass spectrometry. Molecular modeling suggests that two sRAGE monomers orient head to head forming an asymmetric dimer with the C termini directed toward the cell membrane. Ligand-induced association of RAGE homo-dimers on the cell surface increases the molecular dimension of the receptor, recruiting Diaphanous 1 (DIAPH1) and activating signaling pathways.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Animals
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Cross-Linking Reagents/chemistry
- Formins
- Gene Expression
- Genes, Reporter
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HEK293 Cells
- Humans
- Ligands
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Maleimides/chemistry
- Mitogen-Activated Protein Kinases/chemistry
- Mitogen-Activated Protein Kinases/genetics
- Mitogen-Activated Protein Kinases/metabolism
- Molecular Docking Simulation
- Nuclear Magnetic Resonance, Biomolecular
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Structure, Secondary
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Signal Transduction
- Thermodynamics
Collapse
Affiliation(s)
- Jing Xue
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | | | - Matteo Scalabrin
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Vivek Rai
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - David S Burz
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Daniele Fabris
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Ann Marie Schmidt
- New York University, Langone Medical Center, New York, NY 10016, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA.
| |
Collapse
|
12
|
López-Díez R, Shekhtman A, Ramasamy R, Schmidt AM. Cellular mechanisms and consequences of glycation in atherosclerosis and obesity. Biochim Biophys Acta Mol Basis Dis 2016; 1862:2244-2252. [PMID: 27166197 DOI: 10.1016/j.bbadis.2016.05.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/28/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023]
Abstract
Post-translational modification of proteins imparts diversity to protein functions. The process of glycation represents a complex set of pathways that mediates advanced glycation endproduct (AGE) formation, detoxification, intracellular disposition, extracellular release, and induction of signal transduction. These processes modulate the response to hyperglycemia, obesity, aging, inflammation, and renal failure, in which AGE formation and accumulation is facilitated. It has been shown that endogenous anti-AGE protective mechanisms are thwarted in chronic disease, thereby amplifying accumulation and detrimental cellular actions of these species. Atop these considerations, receptor for advanced glycation endproducts (RAGE)-mediated pathways downregulate expression and activity of the key anti-AGE detoxification enzyme, glyoxalase-1 (GLO1), thereby setting in motion an interminable feed-forward loop in which AGE-mediated cellular perturbation is not readily extinguished. In this review, we consider recent work in the field highlighting roles for glycation in obesity and atherosclerosis and discuss emerging strategies to block the adverse consequences of AGEs. This article is part of a Special Issue entitled: The role of post-translational protein modifications on heart and vascular metabolism edited by Jason R.B. Dyck & Jan F.C. Glatz.
Collapse
Affiliation(s)
- Raquel López-Díez
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, New York, NY 10016, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, New York, NY 10016, United States
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, NYU Langone Medical Center, New York, NY 10016, United States.
| |
Collapse
|
13
|
Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
Collapse
Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| |
Collapse
|
14
|
Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
Collapse
Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
15
|
Ramasamy R, Shekhtman A, Schmidt AM. The multiple faces of RAGE--opportunities for therapeutic intervention in aging and chronic disease. Expert Opin Ther Targets 2015; 20:431-46. [PMID: 26558318 DOI: 10.1517/14728222.2016.1111873] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION This review focuses on the multi-ligand receptor of the immunoglobulin superfamily--receptor for advanced glycation endproducts (RAGE). The accumulation of the multiple ligands of RAGE in cellular stress milieux links RAGE to the pathobiology of chronic disease and natural aging. AREAS COVERED In this review, we present a discussion on the ligands of RAGE and the implications of these ligand families in disease. We review the recent literature on the role of ligand-RAGE interaction in the consequences of natural aging; the macro- and microvascular complications of diabetes; obesity and insulin resistance; autoimmune disorders and chronic inflammation; and tumors and Alzheimer's disease. We discuss the mechanisms of RAGE signaling through its intracellular binding effector molecule--the formin DIAPH1. Physicochemical evidence of how the RAGE cytoplasmic domain binds to the FH1 (formin homology 1) domain of DIAPH1, and the consequences thereof, are also reviewed. EXPERT OPINION We discuss the modalities of RAGE antagonism currently in preclinical and clinical studies. Finally, we present the rationale behind potentially targeting the RAGE cytoplasmic domain-DIAPH1 interaction as a logical strategy for therapeutic intervention in the pathological settings of chronic diseases and aging wherein RAGE ligands accumulate and signal.
Collapse
Affiliation(s)
- Ravichandran Ramasamy
- a Diabetes Research Program, Division of Endocrinology, Department of Medicine , New York University Langone Medical Center , New York , NY 10016 , USA
| | - Alexander Shekhtman
- b Department of Chemistry , University at Albany, State University of New York , Albany , NY 12222 , USA
| | - Ann Marie Schmidt
- a Diabetes Research Program, Division of Endocrinology, Department of Medicine , New York University Langone Medical Center , New York , NY 10016 , USA
| |
Collapse
|
16
|
Colombo M, Mizzotti C, Masiero S, Kater MM, Pesaresi P. Peptide aptamers: The versatile role of specific protein function inhibitors in plant biotechnology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:892-901. [PMID: 25966787 DOI: 10.1111/jipb.12368] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/05/2015] [Indexed: 06/04/2023]
Abstract
In recent years, peptide aptamers have emerged as novel molecular tools that have attracted the attention of researchers in various fields of basic and applied science, ranging from medicine to analytical chemistry. These artificial short peptides are able to specifically bind, track, and inhibit a given target molecule with high affinity, even molecules with poor immunogenicity or high toxicity, and represent a remarkable alternative to antibodies in many different applications. Their use is on the rise, driven mainly by the medical and pharmaceutical sector. Here we discuss the enormous potential of peptide aptamers in both basic and applied aspects of plant biotechnology and food safety. The different peptide aptamer selection methods available both in vivo and in vitro are introduced, and the most important possible applications in plant biotechnology are illustrated. In particular, we discuss the generation of broad-based virus resistance in crops, "reverse genetics" and aptasensors in bioassays for detecting contaminations in food and feed. Furthermore, we suggest an alternative to the transfer of peptide aptamers into plant cells via genetic transformation, based on the use of cell-penetrating peptides that overcome the limits imposed by both crop transformation and Genetically Modified Organism commercialization.
Collapse
Affiliation(s)
- Monica Colombo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (Trento), Italy
| | - Chiara Mizzotti
- Department of Biosciences, University of Milan, Milano, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milano, Italy
| | - Martin M Kater
- Department of Biosciences, University of Milan, Milano, Italy
| | - Paolo Pesaresi
- Department of Biosciences, University of Milan, Milano, Italy
| |
Collapse
|
17
|
Litwinoff E, Hurtado Del Pozo C, Ramasamy R, Schmidt AM. Emerging Targets for Therapeutic Development in Diabetes and Its Complications: The RAGE Signaling Pathway. Clin Pharmacol Ther 2015; 98:135-44. [PMID: 25974754 DOI: 10.1002/cpt.148] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 12/16/2022]
Abstract
Types 1 and 2 diabetes are on the rise worldwide. Although the treatment of hyperglycemia has benefited from recent advances, aggressive efforts to maintain euglycemia may be fraught with risk, especially in older subjects or in subjects vulnerable to hypoglycemic unawareness. Hence, strategies to prevent and treat the complications of hyperglycemia are essential. In this review we summarize recent updates on the biology of the receptor for advanced glycation endproducts (RAGE) in the pathogenesis of both micro- and macrovascular complications of diabetes, insights from the study of mouse models of obesity and diabetic complications, and from associative studies in human subjects. The study of the mechanisms and consequences of the interaction of the RAGE cytoplasmic domain with the formin, mDia1, in RAGE signal transduction, will be discussed. Lastly, we review the "state-of-the-art" on RAGE-directed therapeutics. Tackling RAGE/mDia1 may identify a novel class of therapeutics preventing diabetes and its complications.
Collapse
Affiliation(s)
- Ems Litwinoff
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - C Hurtado Del Pozo
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - R Ramasamy
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - A M Schmidt
- Diabetes Research Program, Division of Endocrinology, Department of Medicine, New York University School of Medicine, New York, New York, USA
| |
Collapse
|
18
|
Majumder S, Xue J, DeMott CM, Reverdatto S, Burz DS, Shekhtman A. Probing protein quinary interactions by in-cell nuclear magnetic resonance spectroscopy. Biochemistry 2015; 54:2727-38. [PMID: 25894651 DOI: 10.1021/acs.biochem.5b00036] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Historically introduced by McConkey to explain the slow mutation rate of highly abundant proteins, weak protein (quinary) interactions are an emergent property of living cells. The protein complexes that result from quinary interactions are transient and thus difficult to study biochemically in vitro. Cross-correlated relaxation-induced polarization transfer-based in-cell nuclear magnetic resonance allows the characterization of protein quinary interactions with atomic resolution inside live prokaryotic and eukaryotic cells. We show that RNAs are an important component of protein quinary interactions. Protein quinary interactions are unique to the target protein and may affect physicochemical properties, protein activity, and interactions with drugs.
Collapse
Affiliation(s)
- Subhabrata Majumder
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jing Xue
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| |
Collapse
|
19
|
Cobbert JD, DeMott C, Majumder S, Smith EA, Reverdatto S, Burz DS, McDonough KA, Shekhtman A. Caught in action: selecting peptide aptamers against intrinsically disordered proteins in live cells. Sci Rep 2015; 5:9402. [PMID: 25801767 PMCID: PMC4371151 DOI: 10.1038/srep09402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) or unstructured segments within proteins play an important role in cellular physiology and pathology. Low cellular concentration, multiple binding partners, frequent post-translational modifications and the presence of multiple conformations make it difficult to characterize IDP interactions in intact cells. We used peptide aptamers selected by using the yeast-two-hybrid scheme and in-cell NMR to identify high affinity binders to transiently structured IDP and unstructured segments at atomic resolution. Since both the selection and characterization of peptide aptamers take place inside the cell, only physiologically relevant conformations of IDPs are targeted. The method is validated by using peptide aptamers selected against the prokaryotic ubiquitin-like protein, Pup, of the mycobacterium proteasome. The selected aptamers bind to distinct sites on Pup and have vastly different effects on rescuing mycobacterial proteasome substrate and on the survival of the Bacille-Calmette-Guèrin, BCG, strain of M. bovis. This technology can be applied to study the elusive action of IDPs under near physiological conditions.
Collapse
Affiliation(s)
| | | | | | - Eric A Smith
- Wadsworth Center, NY State Department of Health, Albany, NY
| | | | - David S Burz
- Department of Chemistry, University at Albany, Albany, NY
| | | | | |
Collapse
|
20
|
Modeling the interaction between quinolinate and the receptor for advanced glycation end products (RAGE): relevance for early neuropathological processes. PLoS One 2015; 10:e0120221. [PMID: 25757085 PMCID: PMC4354912 DOI: 10.1371/journal.pone.0120221] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/20/2015] [Indexed: 01/13/2023] Open
Abstract
The receptor for advanced glycation end products (RAGE) is a pattern-recognition receptor involved in neurodegenerative and inflammatory disorders. RAGE induces cellular signaling upon binding to a variety of ligands. Evidence suggests that RAGE up-regulation is involved in quinolinate (QUIN)-induced toxicity. We investigated the QUIN-induced toxic events associated with early noxious responses, which might be linked to signaling cascades leading to cell death. The extent of early cellular damage caused by this receptor in the rat striatum was characterized by image processing methods. To document the direct interaction between QUIN and RAGE, we determined the binding constant (Kb) of RAGE (VC1 domain) with QUIN through a fluorescence assay. We modeled possible binding sites of QUIN to the VC1 domain for both rat and human RAGE. QUIN was found to bind at multiple sites to the VC1 dimer, each leading to particular mechanistic scenarios for the signaling evoked by QUIN binding, some of which directly alter RAGE oligomerization. This work contributes to the understanding of the phenomenon of RAGE-QUIN recognition, leading to the modulation of RAGE function.
Collapse
|
21
|
Gong P, Quan H, He C. Targeting MAGO proteins with a peptide aptamer reinforces their essential roles in multiple rice developmental pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:905-14. [PMID: 25230811 DOI: 10.1111/tpj.12672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/08/2014] [Accepted: 09/14/2014] [Indexed: 05/16/2023]
Abstract
Peptide aptamers are artificial short peptides that potentially interfere with the biological roles of their target proteins; however, this technology has not yet been applied to plant functional genomics. MAGO and Y14, the two core subunits of the exon junction complex (EJC), form obligate heterodimers in eukaryotes. In Oryza sativa L. (rice), each of the two genes has two homologs, designated OsMAGO1 and OsMAGO2, and OsY14a and OsY14b, respectively. Here, we characterized a 16-amino acida peptide aptamer (PAP) for the rice MAGO proteins. PAP and rice Y14 bound competitively to rice MAGO proteins. Specifically targeting the MAGO proteins by expressing the aptamer in transgenic rice plants did not affect the endogenous synthesis and accumulation of MAGO proteins; however, the phenotypic variations observed in multiple organs phenocopied those of transgenic rice plants harboring RNA interference (RNAi) constructs in which the accumulation of MAGO and/or OsY14a transcripts and MAGO proteins was downregulated severely. Morphologically, the aptamer transgenic plants were short with abnormally developed flowers, and the stamens exhibited reduced degradation and absorption of both the endothecium and tapetum, thus confirming that EJC core heterodimers play essential roles in rice development, growth and reproduction. This study reveals that as a complementary approach of RNAi, peptide aptamers are powerful tools for interfering with the function of proteins in higher plants.
Collapse
Affiliation(s)
- Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
| | | | | |
Collapse
|