1
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Gulen B, Casey A, Orth K. AMPylation of small GTPases by Fic enzymes. FEBS Lett 2023; 597:883-891. [PMID: 36239538 PMCID: PMC10050140 DOI: 10.1002/1873-3468.14516] [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: 07/06/2022] [Revised: 09/17/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022]
Abstract
Small GTPases orchestrate numerous cellular pathways, acting as molecular switches and regulatory hubs to transmit molecular signals and because of this, they are often the target of pathogens. During infection, pathogens manipulate host cellular networks using post-translational modifications (PTMs). AMPylation, the modification of proteins with AMP, has been identified as a common PTM utilized by pathogens to hijack GTPase signalling during infection. AMPylation is primarily carried out by enzymes with a filamentation induced by cyclic-AMP (Fic) domain. Modification of small GTPases by AMP renders GTPases impervious to upstream regulatory inputs, resulting in unregulated downstream effector outputs for host cellular processes. Here, we overview Fic-mediated AMPylation of small GTPases by pathogens and other related PTMs catalysed by Fic enzymes on GTPases.
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Affiliation(s)
- Burak Gulen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX and Howard Hughes Medical Institute, Dallas, TX, USA
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2
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Reif MM, Zacharias M. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications. J Chem Theory Comput 2022; 18:3873-3893. [PMID: 35653503 DOI: 10.1021/acs.jctc.1c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an approach combining alchemical modifications and physical-pathway methods to calculate absolute binding free energies. The employed physical-pathway method is either a stratified umbrella sampling to calculate a potential of mean force or nonequilibrium pulling. We devised two basic approaches: the simultaneous approach (S-approach), where, along the physical unbinding pathway, an alchemical transformation of ligand-protein interactions is installed and deinstalled, and the prior-plus-simultaneous approach (PPS-approach), where, prior to the physical-pathway simulation, an alchemical transformation of ligand-protein interactions is installed in the binding site and deinstalled during the physical-pathway simulation. Using a mutant of T4 lysozyme with a benzene ligand as an example, we show that installation and deinstallation of soft-core interactions concurrent with physical ligand unbinding (S-approach) allow successful potential of mean force calculations and nonequilibrium pulling simulations despite the problems posed by the occluded nature of the lysozyme binding pocket. Good agreement between the potential of the mean-force-based S-approach and double decoupling simulations as well as a remarkable efficiency and accuracy of the nonequilibrium-pulling-based S-approach is found. The latter turned out to be more compute-efficient than the potential of mean force calculation by approximately 70%. Furthermore, we illustrate the merits of reducing ligand-protein interactions prior to potential of mean force calculations using the murine double minute homologue protein MDM2 with a p53-derived peptide ligand (PPS-approach). Here, the problem of breaking strong interactions in the binding pocket is transferred to a prior alchemical transformation that reduces the free-energy barrier between the bound and unbound state in the potential of mean force. Besides, disentangling physical ligand displacement from the deinstallation of ligand-protein interactions was seen to allow a more uniform sampling of distance histograms in the umbrella sampling. In the future, physical ligand unbinding combined with simultaneous alchemical modifications may prove useful in the calculation of protein-protein binding free energies, where sampling problems posed by multiple, possibly sticky interactions and potential steric clashes can thus be reduced.
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Affiliation(s)
- Maria M Reif
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
| | - Martin Zacharias
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
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3
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Stévenin V, Neefjes J. Control of host PTMs by intracellular bacteria: An opportunity toward novel anti-infective agents. Cell Chem Biol 2022; 29:741-756. [PMID: 35512694 DOI: 10.1016/j.chembiol.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/15/2022] [Accepted: 04/15/2022] [Indexed: 02/08/2023]
Abstract
Intracellular bacteria have developed a multitude of mechanisms to influence the post-translational modifications (PTMs) of host proteins to pathogen advantages. The recent explosion of insights into the diversity and sophistication of host PTMs and their manipulation by infectious agents challenges us to formulate a comprehensive vision of this complex and dynamic facet of the host-pathogen interaction landscape. As new discoveries continue to shed light on the central roles of PTMs in infectious diseases, technological advances foster our capacity to detect old and new PTMs and investigate their control and impact during pathogenesis, opening new possibilities for chemical intervention and infection treatment. Here, we present a comprehensive overview of these pathogenic mechanisms and offer perspectives on how these insights may contribute to the development of a new class of therapeutics that are urgently needed to face rising antibiotic resistances.
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Affiliation(s)
- Virginie Stévenin
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center (LUMC), Leiden 2333 ZC, the Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center (LUMC), Leiden 2333 ZC, the Netherlands
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4
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Pourjafar-Dehkordi D, Zacharias M. Influence of a Ser111-phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations. Proteins 2021; 89:1324-1332. [PMID: 34056776 DOI: 10.1002/prot.26153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/18/2021] [Accepted: 03/10/2021] [Indexed: 11/06/2022]
Abstract
Rab GTPases constitute the largest branch of the Ras protein superfamily that regulate intra-cellular membrane trafficking. Their signaling activity is mediated by the transition between an active GTP-bound state and an inactive GDP-bound state. In the inactive state the switch I and II segments adopt largely disordered flexible conformations, whereas in the active state these regions are in well-defined conformations. The switch I and II states are central for recognition of Rab GTPases by interacting partners. Phosphorylation of the Rab1b-GTPase at residue Ser111 (pS111) results in modulation of the signaling activity due to alterations of the protein interaction interface and also due to modulation of the conformational flexibility. We have studied the flexibility of native and pS111-Rab1b in complex with GTP or GDP using extensive Molecular Dynamics (MD) simulations and an advanced sampling method called DIhedral Angle-biasing potential Replica-Exchange Molecular dynamics (DIA-REMD). The DIA-REMD method promotes backbone and side chain dihedral transitions along a series of replica simulations in selected protein segments and through exchanges also improves sampling in an unbiased reference simulation. Application to the Rab1b system results in significantly enhanced sampling of different switch I/II conformational states in the GDP-bound Rab1b state. The pS111 modification is found to reduce the conformational flexibility even in the presence of GDP, which may influence signaling activities. The stabilizing effect can be attributed to the formation of additional surface salt bridges between Arg-residues and pS111 not present in the native structure. The DIA-REMD method could be a valuable approach for studying also other signaling proteins that contain flexible segments.
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Affiliation(s)
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University of Munich, Garching, Germany
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5
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Du J, Wrisberg MKV, Gulen B, Stahl M, Pett C, Hedberg C, Lang K, Schneider S, Itzen A. Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Nat Commun 2021; 12:460. [PMID: 33469029 PMCID: PMC7815794 DOI: 10.1038/s41467-020-20702-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
Legionella pneumophila infects eukaryotic cells by forming a replicative organelle - the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulator Rab1. As a result, Rab1 is modified with an adenosine monophosphate (AMP), and this process is referred to as AMPylation. Here, we use a chemical approach to stabilise low-affinity Rab:DrrA complexes in a site-specific manner to gain insight into the molecular basis of the interaction between the Rab protein and the AMPylation domain of DrrA. The crystal structure of the Rab:DrrA complex reveals a previously unknown non-conventional Rab-binding site (NC-RBS). Biochemical characterisation demonstrates allosteric stimulation of the AMPylation activity of DrrA via Rab binding to the NC-RBS. We speculate that allosteric control of DrrA could in principle prevent random and potentially cytotoxic AMPylation in the host, thereby perhaps ensuring efficient infection by Legionella.
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Affiliation(s)
- Jiqing Du
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Matthias Stahl
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Christian Pett
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany.
| | - Sabine Schneider
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Ludwig-Maximilians-University Munich, München, 81377, Germany.
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany. .,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany. .,Center for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
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6
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Abstract
Posttranslational modifications (PTMs) are important physiological means to regulate the activities and structures of central regulatory proteins in health and disease. Small GTPases have been recognized as important molecules that are targeted by PTMs during infections of mammalian cells by bacterial pathogens. The enzymes DrrA/SidM and AnkX from Legionella pneumophila AMPylate and phosphocholinate Rab1b during infection, respectively. Cdc42 is AMPylated by IbpA from Histophilus somni at tyrosine 32 or by VopS from Vibrio parahaemolyticus at threonine 35. These modifications take place in the important regulatory switch I or switch II regions of the GTPases. Since Rab1b and Cdc42 are central regulators of intracellular vesicular trafficking and of the actin cytoskeleton, their modifications by bacterial pathogens have a profound impact on the course of infection. Here, we addressed the biochemical and structural consequences of GTPase AMPylation and phosphocholination. By combining biochemical experiments and NMR analysis, we demonstrate that AMPylation can overrule the activity state of Rab1b that is commonly dictated by binding to guanosine diphosphate or guanosine triphosphate. Thus, PTMs may exert conformational control over small GTPases and may add another previously unrecognized layer of activity control to this important regulatory protein family.
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7
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Luo PM, Boyce M. Directing Traffic: Regulation of COPI Transport by Post-translational Modifications. Front Cell Dev Biol 2019; 7:190. [PMID: 31572722 PMCID: PMC6749011 DOI: 10.3389/fcell.2019.00190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
The coat protein complex I (COPI) is an essential, highly conserved pathway that traffics proteins and lipids between the endoplasmic reticulum (ER) and the Golgi. Many aspects of the COPI machinery are well understood at the structural, biochemical and genetic levels. However, we know much less about how cells dynamically modulate COPI trafficking in response to changing signals, metabolic state, stress or other stimuli. Recently, post-translational modifications (PTMs) have emerged as one common theme in the regulation of the COPI pathway. Here, we review a range of modifications and mechanisms that govern COPI activity in interphase cells and suggest potential future directions to address as-yet unanswered questions.
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Affiliation(s)
- Peter M Luo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
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8
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Reif MM, Fischer M, Fredriksson K, Hagn F, Zacharias M. The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding. J Mol Biol 2019; 431:223-243. [DOI: 10.1016/j.jmb.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/11/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022]
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9
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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10
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Schöpel M, Shkura O, Seidel J, Kock K, Zhong X, Löffek S, Helfrich I, Bachmann HS, Scherkenbeck J, Herrmann C, Stoll R. Allosteric Activation of GDP-Bound Ras Isoforms by Bisphenol Derivative Plasticisers. Int J Mol Sci 2018; 19:ijms19041133. [PMID: 29642594 PMCID: PMC5979466 DOI: 10.3390/ijms19041133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 01/13/2023] Open
Abstract
The protein family of small GTPases controls cellular processes by acting as a binary switch between an active and an inactive state. The most prominent family members are H-Ras, N-Ras, and K-Ras isoforms, which are highly related and frequently mutated in cancer. Bisphenols are widespread in modern life because of their industrial application as plasticisers. Bisphenol A (BPA) is the best-known member and has gained significant scientific as well as public attention as an endocrine disrupting chemical, a fact that eventually led to its replacement. However, compounds used to replace BPA still contain the molecular scaffold of bisphenols. BPA, BPAF, BPB, BPE, BPF, and an amine-substituted BPAF-derivate all interact with all GDP-bound Ras-Isoforms through binding to a common site on these proteins. NMR-, SOScat-, and GDI- assay-based data revealed a new bisphenol-induced, allosterically activated GDP-bound Ras conformation that define these plasticisers as Ras allosteric agonists.
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Affiliation(s)
- Miriam Schöpel
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Oleksandr Shkura
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Jana Seidel
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Klaus Kock
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Xueyin Zhong
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Stefanie Löffek
- Skin Cancer Unit of the Dermatology Department, West German Cancer Center, University Hospital Essen, University Duisburg-Essen and the German Cancer Consortium (DKTK), D-45147 Essen, Germany.
| | - Iris Helfrich
- Skin Cancer Unit of the Dermatology Department, West German Cancer Center, University Hospital Essen, University Duisburg-Essen and the German Cancer Consortium (DKTK), D-45147 Essen, Germany.
| | - Hagen S Bachmann
- Institute of Pharmacology and Toxicology, Witten/Herdecke University, Stockumer Str. 10, D-58453 Witten, Germany.
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, D-42119 Wuppertal, Germany.
| | - Christian Herrmann
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
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11
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Abstract
Posttranslational modifications are covalent changes made to proteins that typically alter the function or location of the protein. AMPylation is an emerging posttranslational modification that involves the addition of adenosine monophosphate (AMP) to a protein. Like other, more well-studied posttranslational modifications, AMPylation is predicted to regulate the activity of the modified target proteins. However, the scope of this modification both in bacteria and in eukaryotes remains to be fully determined. In this review, we provide an up to date overview of the known AMPylating enzymes, the regulation of these enzymes, and the effect of this modification on target proteins.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
- Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
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12
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Martins de Oliveira V, Godoi Contessoto VD, Bruno da Silva F, Zago Caetano DL, Jurado de Carvalho S, Pereira Leite VB. Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. Biophys J 2018; 114:65-75. [PMID: 29320697 PMCID: PMC5984902 DOI: 10.1016/j.bpj.2017.11.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/20/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Cα. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.
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Affiliation(s)
- Vinícius Martins de Oliveira
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vinícius de Godoi Contessoto
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil; Brazilian Bioethanol Science and Technology Laboratory- (CTBE), Campinas, Brazil
| | - Fernando Bruno da Silva
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Daniel Lucas Zago Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Sidney Jurado de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vitor Barbanti Pereira Leite
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil.
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