101
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The Many Faces of Rap1 GTPase. Int J Mol Sci 2018; 19:ijms19102848. [PMID: 30241315 PMCID: PMC6212855 DOI: 10.3390/ijms19102848] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
This review addresses the issue of the numerous roles played by Rap1 GTPase (guanosine triphosphatase) in different cell types, in terms of both physiology and pathology. It is one among a myriad of small G proteins with endogenous GTP-hydrolyzing activity that is considerably stimulated by posttranslational modifications (geranylgeranylation) or guanine nucleotide exchange factors (GEFs), and inhibited by GTPase-activating proteins (GAPs). Rap1 is a ubiquitous protein that plays an essential role in the control of metabolic processes, such as signal transduction from plasma membrane receptors, cytoskeleton rearrangements necessary for cell division, intracellular and substratum adhesion, as well as cell motility, which is needed for extravasation or fusion. We present several examples of how Rap1 affects cells and organs, pointing to possible molecular manipulations that could have application in the therapy of several diseases.
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102
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018; 17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023] Open
Abstract
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.
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Affiliation(s)
- Nikolina Šoštarić
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Technical University of Berlin, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium; Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.
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103
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Vigneshwari L, Balasubramaniam B, Sethupathy S, Pandian SK, Balamurugan K. O-GlcNAcylation confers protection against Staphylococcus aureus infection in Caenorhabditis elegans through ubiquitination. RSC Adv 2018; 8:23089-23100. [PMID: 35540126 PMCID: PMC9081618 DOI: 10.1039/c8ra00279g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Glycosylation is one of the most prevalent post-translational modifications in biological systems. In Caenorhabditis elegans, O-GlcNAcylation has been shown to be actively involved in the regulation of dauer formation and detoxification of toxins secreted by invading pathogens. On this backdrop, the present study is focused on understanding the role of O-GlcNAcylation in C. elegans during Staphylococcus aureus infection using a gel based proteomic approach. Results of time course killing assays with wild-type and mutants of glycosylation and comparison of results revealed an increase in the survival of the C. elegans oga-1 mutant when compared to wild-type N2 and the ogt-1 mutant. Increased survival of C. elegans N2 upon S. aureus infection in the presence of O-(2-acetamido-2-deoxy-d-glucopyranosylidenamino) N-phenylcarbamate (PUGNAc-an OGA inhibitor) further confirmed the involvement of O-GlcNAcylation in protecting C. elegans from infection. The two-dimensional gel-based proteomic analysis of the control and S. aureus infected C. elegans oga-1 mutant followed by mass spectrometric identification of differentially expressed proteins has been carried out. The results revealed that key proteins involved in ubiquitination such as Cullin-1 (CUL-1), Cullin-3 (CUL-3), BTB and MATH domain-containing protein 15 (BATH-15), ubiquitin-conjugating enzyme E2 variant 3 (UEV-3) and probable ubiquitin-conjugating enzyme E2 7 (UBC-7) are upregulated. Real-time PCR analysis further confirms the upregulation of genes encoding the above-mentioned proteins which are involved in the ubiquitin-mediated pathways in C. elegans. In addition, treatment of C. elegans wild-type N2 and the oga-1 mutant with PUGNAc + suramin and suramin (an ubiquitination inhibitor), respectively has resulted in increased sensitivity to S. aureus infection. Hence, it is presumed that upregulation of proteins involved in the ubiquitination pathway could be the key regulatory mechanism responsible for the enhanced survival of the oga-1 mutant during S. aureus infection.
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Affiliation(s)
- Loganathan Vigneshwari
- Department of Biotechnology, Science Campus, Alagappa University Karaikudi 630 003 Tamil Nadu India +91 4565 229334 +91 4565 225215
| | - Boopathi Balasubramaniam
- Department of Biotechnology, Science Campus, Alagappa University Karaikudi 630 003 Tamil Nadu India +91 4565 229334 +91 4565 225215
| | - Sivasamy Sethupathy
- Department of Biotechnology, Science Campus, Alagappa University Karaikudi 630 003 Tamil Nadu India +91 4565 229334 +91 4565 225215
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University Karaikudi 630 003 Tamil Nadu India +91 4565 229334 +91 4565 225215
| | - Krishnaswamy Balamurugan
- Department of Biotechnology, Science Campus, Alagappa University Karaikudi 630 003 Tamil Nadu India +91 4565 229334 +91 4565 225215
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104
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Ahmed MS, Shahjaman M, Kabir E, Kamruzzaman M. Structure modeling to function prediction of Uncharacterized Human Protein C15orf41. Bioinformation 2018; 14:206-212. [PMID: 30108417 PMCID: PMC6077826 DOI: 10.6026/97320630014206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 01/18/2023] Open
Abstract
The dyserythropoietic anemia disease is a genetic disorder of erythropoiesis characterized by morphological abnormalities of erythroblasts. This is caused by human gene C15orf41 mutation. The uncharacterized C15orf41 protein is involved in the formation of a functional complex structure. The uncharacterized C15orf41 protein is thermostable, unstable and acidic. This is associated with TPD (Treponema Pallidum) domain (135 to 265 residue position) and three PTM sites such as K50 (Acetylation), T114 (Phosphorylation) and K176 (Ubiquitination). C15orf41 is paralogous to isoform-1 (gi|194018542|) and open reading frame isoform-CRA_c (gi|119612744|) of Homo sapiens located at chromosome 15. It interacts with the human ATP (Adenosine Triphosphate) binding domain 4 (ATPBD4) having similarity score 0.725 as per protein-protein interaction (PPI) network analysis. This data provides valuable insights towards the functional characterization of human gene C15orf41.
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Affiliation(s)
- Md. Shakil Ahmed
- Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Enamul Kabir
- School of Agricultural, Computational and Environmental Sciences, University of Southern Queensland, Australia
| | - Md. Kamruzzaman
- Data Science for Knowledge Creation Research Center, Seoul National University, Korea
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105
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Liu Y, Wang M, Xi J, Luo F, Li A. PTM-ssMP: A Web Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile. Int J Biol Sci 2018; 14:946-956. [PMID: 29989096 PMCID: PMC6036757 DOI: 10.7150/ijbs.24121] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/24/2018] [Indexed: 12/26/2022] Open
Abstract
Protein post-translational modifications (PTMs) are chemical modifications of a protein after its translation. Owing to its play an important role in deep understanding of various biological processes and the development of effective drugs, PTM site prediction have become a hot topic in bioinformatics. Recently, many online tools are developed to prediction various types of PTM sites, most of which are based on local sequence and some biological information. However, few of existing tools consider the relations between different PTMs for their prediction task. Here, we develop a web server called PTM-ssMP to predict PTM site, which adopts site-specific modification profile (ssMP) to efficiently extract and encode the information of both proximal PTMs and local sequence simultaneously. In PTM-ssMP we provide efficient prediction of multiple types of PTM site including phosphorylation, lysine acetylation, ubiquitination, sumoylation, methylation, O-GalNAc, O-GlcNAc, sulfation and proteolytic cleavage. To assess the performance of PTM-ssMP, a large number of experimentally verified PTM sites are collected from several sources and used to train and test the prediction models. Our results suggest that ssMP consistently contributes to remarkable improvement of prediction performance. In addition, results of independent tests demonstrate that PTM-ssMP compares favorably with other existing tools for different PTM types. PTM-ssMP is implemented as an online web server with user-friendly interface, which is freely available at http://bioinformatics.ustc.edu.cn/PTM-ssMP/index/.
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Affiliation(s)
- Yu Liu
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China
| | - Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China.,Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, China
| | - Jianing Xi
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China
| | - Fenglin Luo
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China.,Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, China
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106
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Islam MM, Saha S, Rahman MM, Shatabda S, Farid DM, Dehzangi A. iProtGly-SS: Identifying protein glycation sites using sequence and structure based features. Proteins 2018; 86:777-789. [PMID: 29675975 DOI: 10.1002/prot.25511] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/27/2018] [Accepted: 04/14/2018] [Indexed: 12/20/2022]
Abstract
Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly-SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly-SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/.
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Affiliation(s)
- Md Mofijul Islam
- Department of CSE, University of Dhaka, Dhaka, Bangladesh.,Department of CSE, United International University, Dhaka, Bangladesh
| | - Sanjay Saha
- Department of CSE, United International University, Dhaka, Bangladesh
| | | | - Swakkhar Shatabda
- Department of CSE, United International University, Dhaka, Bangladesh
| | - Dewan Md Farid
- Department of CSE, United International University, Dhaka, Bangladesh
| | - Abdollah Dehzangi
- Department of Computer Science, Morgan State University, Baltimore, MD, 21251, USA
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107
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Kumar S, Lombard DB. Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology. Crit Rev Biochem Mol Biol 2018; 53:311-334. [PMID: 29637793 DOI: 10.1080/10409238.2018.1458071] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sirtuins are NAD+-dependent protein deacylases/ADP-ribosyltransferases that have emerged as candidate targets for new therapeutics to treat metabolic disorders and other diseases, including cancer. The sirtuin SIRT5 resides primarily in the mitochondrial matrix and catalyzes the removal of negatively charged lysine acyl modifications; succinyl, malonyl, and glutaryl groups. Evidence has now accumulated to document the roles of SIRT5 as a significant regulator of cellular homeostasis, in a context- and cell-type specific manner, as has been observed previously for other sirtuin family members. SIRT5 regulates protein substrates involved in glycolysis, the TCA cycle, fatty acid oxidation, electron transport chain, ketone body formation, nitrogenous waste management, and ROS detoxification, among other processes. SIRT5 plays pivotal roles in cardiac physiology and stress responses and is involved in the regulation of numerous aspects of myocardial energy metabolism. SIRT5 is implicated in neoplasia, as both a tumor promoter and suppressor in a context-specific manner, and may serve a protective function in the setting of neurodegenerative disorders. Here, we review the current understanding of functional impacts of SIRT5 on its metabolic targets, and its molecular functions in both normal and pathological conditions. Finally, we will discuss the potential utility of SIRT5 as a drug target and also summarize the current status, progress, and challenges in developing small molecule compounds to modulate SIRT5 activity with high potency and specificity.
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Affiliation(s)
- Surinder Kumar
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA
| | - David B Lombard
- a Department of Pathology , University of Michigan , Ann Arbor , MI , USA.,b Institute of Gerontology , University of Michigan , Ann Arbor , MI , USA
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108
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Alleyn M, Breitzig M, Lockey R, Kolliputi N. The dawn of succinylation: a posttranslational modification. Am J Physiol Cell Physiol 2017; 314:C228-C232. [PMID: 29167150 DOI: 10.1152/ajpcell.00148.2017] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Posttranslational modifications affect almost all proteins and are critical to a well-functioning and diverse proteome; however, many modifications remain relatively unknown and unstudied. This paper will give a perspective on the rapidly developing, novel posttranslational modification called succinylation. This modification may be implicated in numerous diseases, such as hepatic, cardiac, and pulmonary diseases. Although the influences of this modification still remain poorly understood, we are confident that further research into succinylation will provide an enhanced understanding of the complex machinery within the mitochondria, as well as the imposing consequences associated with its dysfunction.
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Affiliation(s)
- Matthew Alleyn
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Mason Breitzig
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Richard Lockey
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
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109
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Audagnotto M, Kengo Lorkowski A, Dal Peraro M. Recruitment of the amyloid precursor protein by γ-secretase at the synaptic plasma membrane. Biochem Biophys Res Commun 2017; 498:334-341. [PMID: 29097209 DOI: 10.1016/j.bbrc.2017.10.164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/04/2017] [Accepted: 10/29/2017] [Indexed: 10/18/2022]
Abstract
Γ-secretase is a membrane-embedded protease that cleaves single transmembrane helical domains of various integral membrane proteins. The amyloid precursor protein (APP) is an important substrate due to its pathological relevance to Alzheimer's disease. The mechanism of the cleavage of APP by γ-secretase that leads to accumulation of Alzheimer's disease causing amyloid-β (Aβ) is still unknown. Coarse-grained molecular dynamics simulations in this study reveal initial lipids raft formation near the catalytic site of γ-secretase as well as changes in dynamic behavior of γ-secretase once interacting with APP. The results suggest a precursor of the APP binding mode and hint at conformational changes of γ-secretase in the nicastrin (NCT) domain upon APP binding.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland
| | - Alexander Kengo Lorkowski
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland.
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110
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Van Itallie CM, Anderson JM. Phosphorylation of tight junction transmembrane proteins: Many sites, much to do. Tissue Barriers 2017; 6:e1382671. [PMID: 29083946 DOI: 10.1080/21688370.2017.1382671] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation is a dynamic post-translational modification that can alter protein structure, localization, protein-protein interactions and stability. All of the identified tight junction transmembrane proteins can be multiply phosphorylated, but only in a few cases are the consequences of phosphorylation at specific sites well characterized. The goal of this review is to highlight some of the best understood examples of phosphorylation changes in the integral membrane tight junction proteins in the context of more general overview of the effects of phosphorylation throughout the proteome. We expect as that structural information for the tight junction proteins becomes more widely available and the molecular modeling algorithms improve, so will our understanding of the relevance of phosphorylation changes at single and multiple sites in tight junction proteins.
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Affiliation(s)
- Christina M Van Itallie
- a National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , MD , USA
| | - James M Anderson
- a National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , MD , USA
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