1
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Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023; 435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [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: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription (Tat) is a small, intrinsically disordered basic protein that plays diverse roles in the HIV-1 replication cycle, including promotion of efficient viral RNA transcription. Tat is released by infected cells and subsequently absorbed by healthy cells, thereby contributing to HIV-1 pathogenesis including HIV-associated neurocognitive disorder. It has been shown that, in HIV-1-infected primary CD4 T-cells, Tat accumulates at the plasma membrane (PM) for secretion, a mechanism mediated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, the structural basis for Tat interaction with the PM and thereby secretion is lacking. Herein, we employed NMR and biophysical methods to characterize Tat86 (86 amino acids) interactions with PI(4,5)P2 and lipid nanodiscs (NDs). Our data revealed that Arg49, Lys50 and Lys51 (RKK motif) constitute the PI(4,5)P2 binding site, that Tat86 interaction with lipid NDs is dependent on PI(4,5)P2 and phosphatidylserine (PS), and that the arginine-rich motif (RRQRRR) preferentially interacts with PS. Furthermore, we show that Trp11, previously implicated in Tat secretion, penetrates deeply in the membrane; substitution of Trp11 severely reduced Tat86 interaction with membranes. Deletion of the entire highly basic region and Trp11 completely abolished Tat86 binding to lipid NDs. Our data support a mechanism by which HIV-1 Tat secretion from the PM is mediated by a tripartite signal consisting of binding of the RKK motif to PI(4,5)P2, arginine-rich motif to PS, and penetration of Trp11 in the membrane. Altogether, these findings provide new insights into the molecular requirements for Tat binding to membranes during secretion.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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2
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Hoshino F, Sakane F. Docosahexaenoic acid-containing phosphatidic acid interacts with clathrin coat assembly protein AP180 and regulates its interaction with clathrin. Biochem Biophys Res Commun 2022; 587:69-77. [PMID: 34864549 PMCID: PMC8628603 DOI: 10.1016/j.bbrc.2021.11.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/12/2021] [Accepted: 11/27/2021] [Indexed: 11/18/2022]
Abstract
The clathrin coat assembly protein AP180 drives endocytosis, which is crucial for numerous physiological events, such as the internalization and recycling of receptors, uptake of neurotransmitters and entry of viruses, including SARS-CoV-2, by interacting with clathrin. Moreover, dysfunction of AP180 underlies the pathogenesis of Alzheimer's disease. Therefore, it is important to understand the mechanisms of assembly and, especially, disassembly of AP180/clathrin-containing cages. Here, we identified AP180 as a novel phosphatidic acid (PA)-binding protein from the mouse brain. Intriguingly, liposome binding assays using various phospholipids and PA species revealed that AP180 most strongly bound to 1-stearoyl-2-docosahexaenoyl-PA (18:0/22:6-PA) to a comparable extent as phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), which is known to associate with AP180. An AP180 N-terminal homology domain (1–289 aa) interacted with 18:0/22:6-PA, and a lysine-rich motif (K38–K39–K40) was essential for binding. The 18:0/22:6-PA in liposomes in 100 nm diameter showed strong AP180-binding activity at neutral pH. Notably, 18:0/22:6-PA significantly attenuated the interaction of AP180 with clathrin. However, PI(4,5)P2 did not show such an effect. Taken together, these results indicate the novel mechanism by which 18:0/22:6-PA selectively regulates the disassembly of AP180/clathrin-containing cages.
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Affiliation(s)
- Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
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3
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Synaptic AP2 CCV life cycle regulation by the Eps15, ITSN1, Sgip1/AP2, synaptojanin1 interactome. Sci Rep 2021; 11:8007. [PMID: 33850201 PMCID: PMC8044098 DOI: 10.1038/s41598-021-87591-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/30/2021] [Indexed: 11/18/2022] Open
Abstract
The AP1/σ1B knockout causes impaired synaptic vesicle recycling and enhanced protein sorting into endosomes, leading to severe intellectual disability. These disturbances in synaptic protein sorting induce as a secondary phenotype the upregulation of AP2 CCV mediated endocytosis. Synapses contain canonical AP2 CCV and AP2 CCV with a more stable coat and thus extended life time. In AP1/σ1B knockout synapses, pool sizes of both CCV classes are doubled. Additionally, stable CCV of the knockout are more stabilised than stable wt CCV. One mechanism responsible for enhanced CCV stabilisation is the reduction of synaptojanin1 CCV levels, the PI-4,5-P2 phosphatase essential for AP2 membrane dissociation. To identify mechanisms regulating synaptojanin1 recruitment, we compared synaptojanin1 CCV protein interactome levels and CCV protein interactions between both CCV classes from wt and knockout mice. We show that ITSN1 determines synaptojanin1 CCV levels. Sgip1/AP2 excess hinders synaptojanin1 binding to ITSN1, further lowering its levels. ITSN1 levels are determined by Eps15, not Eps15L1. In addition, the data reveal that reduced amounts of pacsin1 can be counter balanced by its enhanced activation. These data exemplify the complexity of CCV life cycle regulation and indicate how cargo proteins determine the life cycle of their CCV.
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Hendus-Altenburger R, Vogensen J, Pedersen ES, Luchini A, Araya-Secchi R, Bendsoe AH, Prasad NS, Prestel A, Cardenas M, Pedraz-Cuesta E, Arleth L, Pedersen SF, Kragelund BB. The intracellular lipid-binding domain of human Na +/H + exchanger 1 forms a lipid-protein co-structure essential for activity. Commun Biol 2020; 3:731. [PMID: 33273619 PMCID: PMC7713384 DOI: 10.1038/s42003-020-01455-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pHi) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical αα-hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pHi and the rate of pHi recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Jens Vogensen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Emilie Skotte Pedersen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Raul Araya-Secchi
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Anne H Bendsoe
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Nanditha Shyam Prasad
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Marité Cardenas
- Biofilms Research Center for Biointerfaces, Malmö University, Per Albin Hanssons Väg 35, 214 32, Malmö, Sweden
| | - Elena Pedraz-Cuesta
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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5
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Putta P, Creque E, Piontkivska H, Kooijman EE. Lipid-protein interactions for ECA1 an N-ANTH domain protein involved in stress signaling in plants. Chem Phys Lipids 2020; 231:104919. [PMID: 32416105 DOI: 10.1016/j.chemphyslip.2020.104919] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 01/27/2023]
Abstract
Epsin-like Clathrin Adaptor 1 (ECA1/ PICALM1A) is an A/ENTH domain protein that acts as an adaptor protein in clathrin-mediated endocytosis. ECA1 is recruited to the membrane during salt stress signaling in plants in a phosphatidic acid (PA)-dependent manner. PA is a lipid second messenger that rapidly and transiently increases in concentration under stress stimuli. Upon an increase in PA concentration another lipid, diacylglycerol pyrophosphate (DGPP), starts to accumulate. The accumulation of DGPP is suggested to be a cue for attenuating PA signaling during stress in plants. We showed in vitro that ECA1-PA binding is modulated as a function of membrane curvature stress and charge. In this work, we investigate ECA1 binding to DGPP in comparison with PA. We show that ECA1 has more affinity for the less charged PA, and this binding is pH dependent. Additionally, plant PA binding proteins SnRK2.10, TGD2C, and PDK1-PH2 were investigated for their interaction with DGPP, since no known DGPP binding proteins are available in the literature to date. Our results shed further light on DGPP and its interactions with membrane proteins which brings us closer toward understanding the complexity of protein interactions with anionic lipids, especially the enigmatic anionic lipid DGPP.
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Affiliation(s)
- Priya Putta
- Biological Sciences, Kent State University, PO Box 5109, 44242 Kent, OH, USA.
| | - Emily Creque
- Biological Sciences, Kent State University, PO Box 5109, 44242 Kent, OH, USA.
| | - Helen Piontkivska
- Biological Sciences, Kent State University, PO Box 5109, 44242 Kent, OH, USA.
| | - Edgar E Kooijman
- Biological Sciences, Kent State University, PO Box 5109, 44242 Kent, OH, USA.
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6
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Nadiminti SSP, Kamak M, Koushika SP. Tied up: Does altering phosphoinositide-mediated membrane trafficking influence neurodegenerative disease phenotypes? J Genet 2018; 97:753-771. [PMID: 30027907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphoinositides are a class of membrane lipids that are found on several intracellular compartments and play diverse roles inside cells, such as vesicle formation, protein trafficking, endocytosis etc. Intracellular distribution and levels of phosphoinositides are regulated by enzymes that generate and breakdown these lipids as well as other proteins that associate with phosphoinositides. These events lead to differing levels of specific phosphoinositides on different intracellular compartments. At these intracellular locations, phosphoinositides and their associated proteins, such as Rab GTPases, dynamin and BAR domain-containing proteins, regulate a variety of membrane trafficking pathways. Neurodegenerative phenotypes in disorders such as Parkinson's disease (PD) can arise as a consequence of altered or hampered intracellular trafficking. Altered trafficking can cause proteins such as α-synuclein to aggregate intracellularly. Several trafficking pathways are regulated bymaster regulators such as LRRK2,which is known to regulate the activity of phosphoinositide effector proteins. Perturbing either the levels of phosphoinositides or their interactions with different proteins disrupts intracellular trafficking pathways, contributing to phenotypes often observed in disorders such as Alzheimer's or PDs. Thus, studying phosphoinositide regulation and its role in trafficking can give us a deeper understanding of the contribution of disrupted trafficking to neurodegenerative phenotypes.
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Affiliation(s)
- Sravanthi S P Nadiminti
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India.
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8
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Takatori S, Tomita T. AP180 N-Terminal Homology (ANTH) and Epsin N-Terminal Homology (ENTH) Domains: Physiological Functions and Involvement in Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1111:55-76. [DOI: 10.1007/5584_2018_218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Unraveling the differential structural stability and dynamics features of T7 endolysin partially folded conformations. Biochim Biophys Acta Gen Subj 2018; 1862:924-935. [DOI: 10.1016/j.bbagen.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/21/2023]
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10
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Cytosolic proteins can exploit membrane localization to trigger functional assembly. PLoS Comput Biol 2018; 14:e1006031. [PMID: 29505559 PMCID: PMC5854442 DOI: 10.1371/journal.pcbi.1006031] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/15/2018] [Accepted: 02/09/2018] [Indexed: 12/03/2022] Open
Abstract
Cell division, endocytosis, and viral budding would not function without the localization and assembly of protein complexes on membranes. What is poorly appreciated, however, is that by localizing to membranes, proteins search in a reduced space that effectively drives up concentration. Here we derive an accurate and practical analytical theory to quantify the significance of this dimensionality reduction in regulating protein assembly on membranes. We define a simple metric, an effective equilibrium constant, that allows for quantitative comparison of protein-protein interactions with and without membrane present. To test the importance of membrane localization for driving protein assembly, we collected the protein-protein and protein-lipid affinities, protein and lipid concentrations, and volume-to-surface-area ratios for 46 interactions between 37 membrane-targeting proteins in human and yeast cells. We find that many of the protein-protein interactions between pairs of proteins involved in clathrin-mediated endocytosis in human and yeast cells can experience enormous increases in effective protein-protein affinity (10–1000 fold) due to membrane localization. Localization of binding partners thus triggers robust protein complexation, suggesting that it can play an important role in controlling the timing of endocytic protein coat formation. Our analysis shows that several other proteins involved in membrane remodeling at various organelles have similar potential to exploit localization. The theory highlights the master role of phosphoinositide lipid concentration, the volume-to-surface-area ratio, and the ratio of 3D to 2D equilibrium constants in triggering (or preventing) constitutive assembly on membranes. Our simple model provides a novel quantitative framework for interpreting or designing in vitro experiments of protein complexation influenced by membrane binding. In a multitude of cellular processes, including cell division and endocytosis, proteins must bind to one another to form large multi-protein complexes. To initiate the formation of these critical multi-protein assemblies at the right time and the right place, the constituent proteins must be present at sufficient concentrations. We show here that membrane localization offers a powerful way of controlling protein concentrations by reducing the dimensionality of the protein’s search space. We present a simple and practical analytical theory that determines the significance of membrane localization for triggering protein-protein interactions. We show that protein binding partners will often form substantially more complexes when both partners can localize to surfaces, and thus localization can regulate the timing of multi-protein assembly. We collect in vitro binding data and cellular concentrations of proteins and lipids involved in pathways including clathrin-mediated endocytosis to demonstrate how cellular proteins could exploit membrane localization to regulate assembly.
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11
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Tencer AH, Gatchalian J, Klein BJ, Khan A, Zhang Y, Strahl BD, van Wely KHM, Kutateladze TG. A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. Structure 2017; 25:1530-1539.e3. [PMID: 28919441 DOI: 10.1016/j.str.2017.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/26/2017] [Accepted: 08/15/2017] [Indexed: 01/07/2023]
Abstract
The protein partner of Sans-fille (PPS) and its human homolog DIDO mediate diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing in Drosophila. Here, we show that the PHD fingers of PPS and DIDO recognize the histone mark H3K4me3 in a pH-dependent manner: the binding is enhanced at high pH values but is decreased at low pH. Structural analysis reveals that the pH dependency is due to the presence of a histidine residue in the K4me3-binding aromatic cage of PPS. The pH-dependent mechanism is conserved in DIDO but is lost in yeast Bye1. Acidification of cells leads to the accelerated efflux of endogenous DIDO, indicating the pH-dependent sensing of H3K4me3 in vivo. This novel mode for the recognition of H3K4me3 establishes the PHD fingers of PPS and DIDO as unique epigenetic readers and high pH sensors and suggests a role for the histidine switch during mitosis.
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Affiliation(s)
- Adam H Tencer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jovylyn Gatchalian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Abid Khan
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Karel H M van Wely
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, 28049 Madrid, Spain
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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12
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Webb BA, White KA, Grillo-Hill BK, Schönichen A, Choi C, Barber DL. A Histidine Cluster in the Cytoplasmic Domain of the Na-H Exchanger NHE1 Confers pH-sensitive Phospholipid Binding and Regulates Transporter Activity. J Biol Chem 2016; 291:24096-24104. [PMID: 27650500 DOI: 10.1074/jbc.m116.736215] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/18/2016] [Indexed: 01/26/2023] Open
Abstract
The Na-H exchanger NHE1 contributes to intracellular pH (pHi) homeostasis in normal cells and the constitutively increased pHi in cancer. NHE1 activity is allosterically regulated by intracellular protons, with greater activity at lower pHi However, the molecular mechanism for pH-dependent NHE1 activity remains incompletely resolved. We report that an evolutionarily conserved cluster of histidine residues located in the C-terminal cytoplasmic domain between two phosphatidylinositol 4,5-bisphosphate binding sites (PI(4,5)P2) of NHE1 confers pH-dependent PI(4,5)P2 binding and regulates NHE1 activity. A GST fusion of the wild type C-terminal cytoplasmic domain of NHE1 showed increased maximum PI(4,5)P2 binding at pH 7.0 compared with pH 7.5. However, pH-sensitive binding is abolished by substitutions of the His-rich cluster to arginine (RXXR3) or alanine (AXXA3), mimicking protonated and neutral histidine residues, respectively, and the RXXR3 mutant had significantly greater PI(4,5)P2 binding than AXXA3. When expressed in cells, NHE1 activity and pHi were significantly increased with NHE1-RXXR3 and decreased with NHE1-AXXA3 compared with wild type NHE1. Additionally, fibroblasts expressing NHE1-RXXR3 had significantly more contractile actin filaments and focal adhesions compared with fibroblasts expressing wild type NHE1, consistent with increased pHi enabling cytoskeletal remodeling. These data identify a molecular mechanism for pH-sensitive PI(4,5)P2 binding regulating NHE1 activity and suggest that the evolutionarily conserved cluster of four histidines in the proximal cytoplasmic domain of NHE1 may constitute a proton modifier site. Moreover, a constitutively activated NHE1-RXXR3 mutant is a new tool that will be useful for studying how increased pHi contributes to cell behaviors, most notably the biology of cancer cells.
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Affiliation(s)
- Bradley A Webb
- From the Department of Cell and Tissue Biology, University of California, San Francisco, California 94143 and
| | - Katharine A White
- From the Department of Cell and Tissue Biology, University of California, San Francisco, California 94143 and
| | - Bree K Grillo-Hill
- From the Department of Cell and Tissue Biology, University of California, San Francisco, California 94143 and
| | - André Schönichen
- From the Department of Cell and Tissue Biology, University of California, San Francisco, California 94143 and
| | - Changhoon Choi
- the Department of Radiation Oncology, Samsung Medical Center, Seoul, South Korea 06351
| | - Diane L Barber
- From the Department of Cell and Tissue Biology, University of California, San Francisco, California 94143 and
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13
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Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes. Proc Natl Acad Sci U S A 2016; 113:E5117-24. [PMID: 27531962 DOI: 10.1073/pnas.1605259113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height-height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.
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14
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Holkar SS, Kamerkar SC, Pucadyil TJ. Spatial Control of Epsin-induced Clathrin Assembly by Membrane Curvature. J Biol Chem 2015; 290:14267-76. [PMID: 25837255 PMCID: PMC4505496 DOI: 10.1074/jbc.m115.653394] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/21/2022] Open
Abstract
Epsins belong to the family of highly conserved clathrin-associated sorting proteins that are indispensable for clathrin-mediated endocytosis, but their precise functions remain unclear. We have developed an assay system of budded supported membrane tubes displaying planar and highly curved membrane surfaces to analyze intrinsic membrane curvature preference shown by clathrin-associated sorting proteins. Using real-time fluorescence microscopy, we find that epsin preferentially partitions to and assembles clathrin on highly curved membrane surfaces. Sorting of epsin to regions of high curvature strictly depends on binding to phosphatidylinositol 4,5-bisphosphate. Fluorescently labeled clathrins rapidly assemble as foci, which in turn cluster epsin, while maintaining tube integrity. Clathrin foci grow in intensity with a typical time constant of ∼75 s, similar to the time scales for coated pit formation seen in cells. Epsin therefore effectively senses membrane curvature to spatially control clathrin assembly. Our results highlight the potential role of membrane curvature in orchestrating the myriad molecular interactions necessary for the success of clathrin-mediated membrane budding.
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Affiliation(s)
- Sachin S Holkar
- From the Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Sukrut C Kamerkar
- From the Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Thomas J Pucadyil
- From the Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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15
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Shishido T, Hachisuka M, Ryuzaki K, Miura Y, Tanabe A, Tamura Y, Kusayanagi T, Takeuchi T, Kamisuki S, Sugawara F, Sahara H. EpsinR, a target for pyrenocine B, role in endogenous MHC-II-restricted antigen presentation. Eur J Immunol 2014; 44:3220-31. [DOI: 10.1002/eji.201444475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 07/31/2014] [Accepted: 09/03/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Tatsuya Shishido
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Masami Hachisuka
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Kai Ryuzaki
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Yuko Miura
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Atsushi Tanabe
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
| | - Yasuaki Tamura
- Department of Pathology; Sapporo Medical University School of Medicine; Sapporo Japan
| | - Tomoe Kusayanagi
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Toshifumi Takeuchi
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Shinji Kamisuki
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Fumio Sugawara
- Genome and Drug Research Center; Tokyo University of Science; Chiba Japan
| | - Hiroeki Sahara
- Laboratory of Biology; Azabu University School of Veterinary Medicine; Sagamihara Japan
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16
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Rai S, Tanaka H, Suzuki M, Ogoh H, Taniguchi Y, Morita Y, Shimada T, Tanimura A, Matsui K, Yokota T, Oritani K, Tanabe K, Watanabe T, Kanakura Y, Matsumura I. Clathrin assembly protein CALM plays a critical role in KIT signaling by regulating its cellular transport from early to late endosomes in hematopoietic cells. PLoS One 2014; 9:e109441. [PMID: 25279552 PMCID: PMC4184852 DOI: 10.1371/journal.pone.0109441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 09/07/2014] [Indexed: 11/29/2022] Open
Abstract
CALM is implicated in the formation of clathrin-coated vesicles, which mediate endocytosis and intracellular trafficking of growth factor receptors and nutrients. We previously found that CALM-deficient mice suffer from severe anemia due to the impaired clathrin-mediated endocytosis of transferrin receptor in immature erythroblast. However, CALM has been supposed to regulate the growth and survival of hematopoietic stem/progenitor cells. So, in this study, we focused on the function of CALM in these cells. We here show that the number of Linage−Sca-1+KIT+ (LSK) cells decreased in the fetal liver of CALM−/− mice. Also, colony forming activity was impaired in CALM−/− LSK cells. In addition, SCF, FLT3, and TPO-dependent growth was severely impaired in CALM−/− LSK cells, while they can normally proliferate in response to IL-3 and IL-6. We also examined the intracellular trafficking of KIT using CALM−/− murine embryonic fibroblasts (MEFs) engineered to express KIT. At first, we confirmed that endocytosis of SCF-bound KIT was not impaired in CALM−/− MEFs by the internalization assay. However, SCF-induced KIT trafficking from early to late endosome was severely impaired in CALM−/− MEFs. As a result, although intracellular KIT disappeared 30 min after SCF stimulation in wild-type (WT) MEFs, it was retained in CALM−/− MEFs. Furthermore, SCF-induced phosphorylation of cytosolic KIT was enhanced and prolonged in CALM−/− MEFs compared with that in WT MEFs, leading to the excessive activation of Akt. Similar hyperactivation of Akt was observed in CALM−/− KIT+ cells. These results indicate that CALM is essential for the intracellular trafficking of KIT and its normal functions. Also, our data demonstrate that KIT located in the early endosome can activate downstream molecules as a signaling endosome. Because KIT activation is involved in the pathogenesis of some malignancies, the manipulation of CALM function would be an attractive therapeutic strategy.
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Affiliation(s)
- Shinya Rai
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Hirokazu Tanaka
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
- * E-mail:
| | - Mai Suzuki
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women’s University, Nara, Japan
| | - Honami Ogoh
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women’s University, Nara, Japan
| | - Yasuhiro Taniguchi
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Yasuyoshi Morita
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Takahiro Shimada
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Akira Tanimura
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiko Matsui
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takafumi Yokota
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenji Oritani
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenji Tanabe
- Medical Research Institute, Tokyo Women’s Medical University, Tokyo, Japan
| | - Toshio Watanabe
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women’s University, Nara, Japan
| | - Yuzuru Kanakura
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Itaru Matsumura
- Department of Hematology and Rheumatology, Kinki University Faculty of Medicine, Osaka, Japan
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17
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Shi Z, Baumgart T. Dynamics and instabilities of lipid bilayer membrane shapes. Adv Colloid Interface Sci 2014; 208:76-88. [PMID: 24529968 DOI: 10.1016/j.cis.2014.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/12/2014] [Accepted: 01/12/2014] [Indexed: 01/14/2023]
Abstract
Biological membranes undergo constant shape remodeling involving the formation of highly curved structures. The lipid bilayer represents the fundamental architecture of the cellular membrane with its shapes determined by the Helfrich curvature bending energy. However, the dynamics of bilayer shape transitions, especially their modulation by membrane proteins, and the resulting shape instabilities, are still not well understood. Here, we review in a unifying manner several theories that describe the fluctuations (i.e. undulations) of bilayer shapes as well as their local coupling with lipid or protein density variation. The coupling between local membrane curvature and lipid density gives rise to a 'slipping mode' in addition to the conventional 'bending mode' for damping the membrane fluctuation. This leads to a number of interesting experimental phenomena regarding bilayer shape dynamics. More importantly, curvature-inducing proteins can couple with membrane shape and eventually render the membrane unstable. A criterion for membrane shape instability is derived from a linear stability analysis. The instability criterion reemphasizes the importance of membrane tension in regulating the stability and dynamics of membrane geometry. Recent progresses in understanding the role of membrane tension in regulating dynamical cellular processes are also reviewed. Protein density is emphasized as a key factor in regulating membrane shape transitions: a threshold density of curvature coupling proteins is required for inducing membrane morphology transitions.
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Affiliation(s)
- Zheng Shi
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, PA 19104, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, PA 19104, USA.
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18
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Stahelin RV, Scott JL, Frick CT. Cellular and molecular interactions of phosphoinositides and peripheral proteins. Chem Phys Lipids 2014; 182:3-18. [PMID: 24556335 DOI: 10.1016/j.chemphyslip.2014.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 12/23/2022]
Abstract
Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection-specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.
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Affiliation(s)
- Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Cary T Frick
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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19
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Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annu Rev Biophys 2013; 42:289-314. [PMID: 23451893 DOI: 10.1146/annurev-biophys-050511-102349] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established posttranslational modifications such as phosphorylation or ubiquitination, posttranslational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, posttranslational modification by protons can drive dynamic changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and, in contrast to most other posttranslational modifications, does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton posttranslational modification of pH-sensing proteins regulating different cellular processes.
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Affiliation(s)
- André Schönichen
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
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20
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Ward KE, Ropa JP, Adu-Gyamfi E, Stahelin RV. C2 domain membrane penetration by group IVA cytosolic phospholipase A₂ induces membrane curvature changes. J Lipid Res 2012; 53:2656-66. [PMID: 22991194 DOI: 10.1194/jlr.m030718] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Group IVA cytosolic phospholipase A(2) (cPLA(2)α) is an 85 kDa enzyme that regulates the release of arachidonic acid (AA) from the sn-2 position of membrane phospholipids. It is well established that cPLA(2)α binds zwitterionic lipids such as phosphatidylcholine in a Ca(2+)-dependent manner through its N-terminal C2 domain, which regulates its translocation to cellular membranes. In addition to its role in AA synthesis, it has been shown that cPLA(2)α promotes tubulation and vesiculation of the Golgi and regulates trafficking of endosomes. Additionally, the isolated C2 domain of cPLA(2)α is able to reconstitute Fc receptor-mediated phagocytosis, suggesting that C2 domain membrane binding is sufficient for phagosome formation. These reported activities of cPLA(2)α and its C2 domain require changes in membrane structure, but the ability of the C2 domain to promote changes in membrane shape has not been reported. Here we demonstrate that the C2 domain of cPLA(2)α is able to induce membrane curvature changes to lipid vesicles, giant unilamellar vesicles, and membrane sheets. Biophysical assays combined with mutagenesis of C2 domain residues involved in membrane penetration demonstrate that membrane insertion by the C2 domain is required for membrane deformation, suggesting that C2 domain-induced membrane structural changes may be an important step in signaling pathways mediated by cPLA(2)α.
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Affiliation(s)
- Katherine E Ward
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46556, USA
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21
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Rozovsky S, Forstner MB, Sondermann H, Groves JT. Single molecule kinetics of ENTH binding to lipid membranes. J Phys Chem B 2012; 116:5122-31. [PMID: 22471245 DOI: 10.1021/jp210045r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transient recruitment of proteins to membranes is a fundamental mechanism by which the cell exerts spatial and temporal control over proteins' localization and interactions. Thus, the specificity and the kinetics of peripheral proteins' membrane residence are an attribute of their function. Here, we describe the membrane interactions of the interfacial epsin N-terminal homology (ENTH) domain with its target lipid phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P(2)). The direct visualization and quantification of interactions of single ENTH molecules with supported lipid bilayers is achieved using total internal reflection fluorescence microscopy (TIRFM) with a time resolution of 13 ms. This enables the recording of the kinetic behavior of ENTH interacting with membranes with physiologically relevant concentrations of PtdIns(4,5)P(2) despite the low effective binding affinity. Subsequent single fluorophore tracking permits us to build up distributions of residence times and to measure ENTH dissociation rates as a function of membrane composition. Furthermore, due to the high time resolution, we are able to resolve details of the motion of ENTH associated with a simple, homogeneous membrane. In this case ENTH's diffusive transport appears to be the result of at least three different diffusion processes.
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Affiliation(s)
- Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.
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22
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He J, Gajewiak J, Scott JL, Gong D, Ali M, Best MD, Prestwich GD, Stahelin RV, Kutateladze TG. Metabolically stabilized derivatives of phosphatidylinositol 4-phosphate: synthesis and applications. ACTA ACUST UNITED AC 2012; 18:1312-9. [PMID: 22035800 DOI: 10.1016/j.chembiol.2011.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 01/19/2023]
Abstract
Phosphatidylinositol 4-phosphate (PtdIns(4)P) lipid is an essential component of eukaryotic membranes and a marker of the Golgi complex. Here, we developed metabolically stabilized (ms) analogs of PtdIns(4)P and the inositol 1,4-bisphosphate (IP(2)) head group derivative and demonstrated that these compounds can substitute the natural lipid fully retaining its physiological activities. The methylenephosphonate (MP) and phosphorothioate (PT) analogs of PtdIns(4)P and the aminohexyl (AH)-IP(2) probe are recognized by the PtdIns(4)P-specific PH domain of four phosphate adaptor protein 1 (FAPP1). Binding of FAPP1 to the PtdIns(4)P derivatives stimulates insertion of the PH domain into the lipid layers and induces tubulation of membranes. Both ms analogs and IP(2) probes could be invaluable for identifying protein effectors and characterizing PtdIns(4)P-dependent signaling cascades within the trans-Golgi network (TGN).
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Affiliation(s)
- Ju He
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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23
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Suzuki M, Tanaka H, Tanimura A, Tanabe K, Oe N, Rai S, Kon S, Fukumoto M, Takei K, Abe T, Matsumura I, Kanakura Y, Watanabe T. The clathrin assembly protein PICALM is required for erythroid maturation and transferrin internalization in mice. PLoS One 2012; 7:e31854. [PMID: 22363754 PMCID: PMC3283694 DOI: 10.1371/journal.pone.0031854] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/17/2012] [Indexed: 11/21/2022] Open
Abstract
Phosphatidylinositol binding clathrin assembly protein (PICALM), also known as clathrin assembly lymphoid myeloid leukemia protein (CALM), was originally isolated as part of the fusion gene CALM/AF10, which results from the chromosomal translocation t(10;11)(p13;q14). CALM is sufficient to drive clathrin assembly in vitro on lipid monolayers and regulates clathrin-coated budding and the size and shape of the vesicles at the plasma membrane. However, the physiological role of CALM has yet to be elucidated. Here, the role of CALM in vivo was investigated using CALM-deficient mice. CALM-deficient mice exhibited retarded growth in utero and were dwarfed throughout their shortened life-spans. Moreover, CALM-deficient mice suffered from severe anemia, and the maturation and iron content in erythroid precursors were severely impaired. CALM-deficient erythroid cells and embryonic fibroblasts exhibited impaired clathrin-mediated endocytosis of transferrin. These results indicate that CALM is required for erythroid maturation and transferrin internalization in mice.
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Affiliation(s)
- Mai Suzuki
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Hirokazu Tanaka
- Division of Hematology, Department of Internal Medicine, Kinki University, Osaka, Japan
| | - Akira Tanimura
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenji Tanabe
- Department of Neuroscience, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Natsuko Oe
- Department of Neuroscience, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Shinya Rai
- Division of Hematology, Department of Internal Medicine, Kinki University, Osaka, Japan
| | - Syunsuke Kon
- Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Manabu Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kohji Takei
- Department of Neuroscience, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Itaru Matsumura
- Division of Hematology, Department of Internal Medicine, Kinki University, Osaka, Japan
| | - Yuzuru Kanakura
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Toshio Watanabe
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
- * E-mail:
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24
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Bhunia A, Mohanram H, Bhattacharjya S. Structural determinants of the specificity of a membrane binding domain of the scaffold protein Ste5 of budding yeast: implications in signaling by the scaffold protein in MAPK pathway. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1250-60. [PMID: 22285780 DOI: 10.1016/j.bbamem.2012.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 01/09/2012] [Accepted: 01/10/2012] [Indexed: 12/15/2022]
Abstract
In the mitogen activated protein kinase (MAPK) cascades of budding yeast, the scaffold protein Ste5 is recruited to the plasma membrane to transmit pheromone induced signal. A region or domain of Ste5 i.e. residues P44-R67, referred here as Ste5PM24, has been known to be involved in direct interactions with the membrane. In order to gain structural insights into membrane interactions of Ste5, here, we have investigated structures and interactions of two synthetic peptide fragments of Ste5, Ste5PM24, and a hyperactive mutant, Ste5PM24LM, by NMR, ITC, and fluorescence spectroscopy, with lipid membranes. We observed that Ste5PM24 predominantly interacted only with the anionic lipid vesicles. By contrast, Ste5PM24LM exhibited binding with negatively charged as well as zwitterionic or mixed lipid vesicles. Binding of Ste5 peptides with the negatively charged lipid vesicles were primarily driven by hydrophobic interactions. NMR studies revealed that Ste5PM24 assumes dynamic or transient conformations in zwitterionic dodecylphosphocholine (DPC) micelles. By contrast, NMR structure, obtained in anionic sodium dodecyl sulphate (SDS), demonstrated amphipathic helical conformations for the central segment of Ste5PM24. The hydrophobic surface of the helix was found to be buried inside the micelles. Taken together, these results provide important insights toward the structure and specificity determinants of the scaffold protein interactions with the plasma membrane.
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Affiliation(s)
- Anirban Bhunia
- School of Biological Sciences, Division of Structural and Computational, Nanyang Technological University, Singapore 637551, Singapore
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25
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Shin JJH, Loewen CJR. Putting the pH into phosphatidic acid signaling. BMC Biol 2011; 9:85. [PMID: 22136116 PMCID: PMC3229452 DOI: 10.1186/1741-7007-9-85] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 12/02/2011] [Indexed: 01/03/2023] Open
Abstract
The lipid phosphatidic acid (PA) has important roles in cell signaling and metabolic regulation in all organisms. New evidence indicates that PA also has an unprecedented role as a pH biosensor, coupling changes in pH to intracellular signaling pathways. pH sensing is a property of the phosphomonoester headgroup of PA. A number of other potent signaling lipids also contain headgroups with phosphomonoesters, implying that pH sensing by lipids may be widespread in biology.
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Affiliation(s)
- John J H Shin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada, V6T 1Z3
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26
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Rous sarcoma virus gag has no specific requirement for phosphatidylinositol-(4,5)-bisphosphate for plasma membrane association in vivo or for liposome interaction in vitro. J Virol 2011; 85:10851-60. [PMID: 21813603 DOI: 10.1128/jvi.00760-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MA domain of the retroviral Gag protein mediates interactions with the plasma membrane, which is the site of productive virus release. HIV-1 MA has a phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P₂] binding pocket; depletion of this phospholipid from the plasma membrane compromises Gag membrane association and virus budding. We used multiple methods to examine the possible role of PI(4,5)P₂ in Gag-membrane interaction of the alpharetrovirus Rous sarcoma virus (RSV). In contrast to HIV-1, which was tested in parallel, neither membrane localization of RSV Gag-GFP nor release of virus-like particles was affected by phosphatase-mediated depletion of PI(4,5)P₂ in transfected avian cells. In liposome flotation experiments, RSV Gag required acidic lipids for binding but showed no specificity for PI(4,5)P₂. Mono-, di-, and triphosphorylated phosphatidylinositol phosphate (PIP) species as well as high concentrations of phosphatidylserine (PS) supported similar levels of flotation. A mutation that increases the overall charge of RSV MA also enhanced Gag membrane binding. Contrary to previous reports, we found that high concentrations of PS, in the absence of PIPs, also strongly promoted HIV-1 Gag flotation. Taken together, we interpret these results to mean that RSV Gag membrane association is driven by electrostatic interactions and not by any specific association with PI(4,5)P₂.
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27
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He J, Scott JL, Heroux A, Roy S, Lenoir M, Overduin M, Stahelin RV, Kutateladze TG. Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain. J Biol Chem 2011; 286:18650-7. [PMID: 21454700 PMCID: PMC3099681 DOI: 10.1074/jbc.m111.233015] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 03/19/2011] [Indexed: 11/06/2022] Open
Abstract
Four-phosphate-adaptor protein 1 (FAPP1) regulates secretory transport from the trans-Golgi network (TGN) to the plasma membrane. FAPP1 is recruited to the Golgi through binding of its pleckstrin homology (PH) domain to phosphatidylinositol 4-phosphate (PtdIns(4)P) and a small GTPase ADP-ribosylation factor 1 (ARF1). Despite the critical role of FAPP1 in membrane trafficking, the molecular basis of its dual function remains unclear. Here, we report a 1.9 Å resolution crystal structure of the FAPP1 PH domain and detail the molecular mechanisms of the PtdIns(4)P and ARF1 recognition. The FAPP1 PH domain folds into a seven-stranded β-barrel capped by an α-helix at one edge, whereas the opposite edge is flanked by three loops and the β4 and β7 strands that form a lipid-binding pocket within the β-barrel. The ARF1-binding site is located on the outer side of the β-barrel as determined by NMR resonance perturbation analysis, mutagenesis, and measurements of binding affinities. The two binding sites have little overlap, allowing FAPP1 PH to associate with both ligands simultaneously and independently. Binding to PtdIns(4)P is enhanced in an acidic environment and is required for membrane penetration and tubulation activity of FAPP1, whereas the GTP-bound conformation of the GTPase is necessary for the interaction with ARF1. Together, these findings provide structural and biochemical insight into the multivalent membrane anchoring by the PH domain that may augment affinity and selectivity of FAPP1 toward the TGN membranes enriched in both PtdIns(4)P and GTP-bound ARF1.
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Affiliation(s)
- Ju He
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Jordan L. Scott
- the Department of Chemistry and Biochemistry and the Walther Center for Cancer Research, University of Notre Dame, Notre Dame, Indiana 46556
| | - Annie Heroux
- the Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Siddhartha Roy
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Marc Lenoir
- the School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Michael Overduin
- the School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Robert V. Stahelin
- the Department of Chemistry and Biochemistry and the Walther Center for Cancer Research, University of Notre Dame, Notre Dame, Indiana 46556
- the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, Indiana 46617
| | - Tatiana G. Kutateladze
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
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28
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Ktistakis NT. Lipid signaling and homeostasis: PA- is better than PA-H, but what about those PIPs? Sci Signal 2010; 3:pe46. [PMID: 21139136 DOI: 10.1126/scisignal.3151pe46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Although cellular membranes are composed of hundreds of distinct lipid species, the lipid composition is maintained within a narrow range. The regulatory circuit responsible for this homeostasis in yeast depends on a membrane-bound transcriptional repressor that translocates to the nucleus in response to the abundance of its lipid ligand on the membrane. Feedback control in this system is provided because the lipid ligand is also an end product of the activity of the transcription factor. This basic design is also evident in higher eukaryotes such as Drosophila and mammals, but with important differences in the lipid being sensed, the composition of the sensors, and the fine-tuning of the response. New work indicates that regulation of intracellular pH levels in yeast by glucose availability may fine-tune the binding of the repressor to its lipid ligand, providing a mechanism that connects phospholipid metabolism to nutrient sensing. The importance of pH effects in this pathway raises the possibility that additional lipid-signaling pathways may be regulated by the protonation state of the lipid or its effector.
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29
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Abstract
Biological macromolecules evolved to perform their function in specific cellular environment (subcellular compartments or tissues); therefore, they should be adapted to the biophysical characteristics of the corresponding environment, one of them being the characteristic pH. Many macromolecular properties are pH dependent, such as activity and stability. However, only activity is biologically important, while stability may not be crucial for the corresponding reaction. Here, we show that the pH-optimum of activity (the pH of maximal activity) is correlated with the pH-optimum of stability (the pH of maximal stability) on a set of 310 proteins with available experimental data. We speculate that such a correlation is needed to allow the corresponding macromolecules to tolerate small pH fluctuations that are inevitable with cellular function. Our findings rationalize the efforts of correlating the pH of maximal stability and the characteristic pH of subcellular compartments, as only pH of activity is subject of evolutionary pressure. In addition, our analysis confirmed the previous observation that pH-optimum of activity and stability are not correlated with the isoelectric point, pI, or with the optimal temperature.
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Affiliation(s)
- Kemper Talley
- Computational Biophysics and Bioinformatics, Physics Department, Clemson University, Clemson, South Carolina 29634, USA
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Capraro BR, Yoon Y, Cho W, Baumgart T. Curvature sensing by the epsin N-terminal homology domain measured on cylindrical lipid membrane tethers. J Am Chem Soc 2010; 132:1200-1. [PMID: 20050657 DOI: 10.1021/ja907936c] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protein epsin is believed to play important roles in clathrin-mediated endocytosis, including generation of the high membrane curvature necessary for vesicle formation. Here we assess the basis for this hypothesis by systematically quantifying the curvature dependence of the area density of epsin N-terminal homology (ENTH) domain on cylindrical membranes of controlled curvature. In cylindrical tethers pulled from micropipet-aspirated giant unilamellar vesicles, repartitioning of membrane-bound ENTH from vesicles onto highly curved membranes was observed by fluorescence microscopy. First-order thermodynamic theory used to analyze our data yielded the first measurement of Leibler's thermodynamic curvature-composition coupling coefficient to be reported for an endocytic accessory protein. Our results highlight the possibility that epsin contributes to cellular membrane curvature sensing and generation, and we believe that our method will provide useful contributions toward the goal of relating molecular descriptions of interactions to macroscopic membrane remodeling in cells and identifying and characterizing roles for proteins in these processes.
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Affiliation(s)
- Benjamin R Capraro
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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He J, Vora M, Haney RM, Filonov GS, Musselman CA, Burd CG, Kutateladze AG, Verkhusha VV, Stahelin RV, Kutateladze TG. Membrane insertion of the FYVE domain is modulated by pH. Proteins 2009; 76:852-60. [PMID: 19296456 DOI: 10.1002/prot.22392] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The FYVE domain associates with phosphatidylinositol 3-phosphate [PtdIns(3)P] in membranes of early endosomes and penetrates bilayers. Here, we detail principles of membrane anchoring and show that the FYVE domain insertion into PtdIns(3)P-enriched membranes and membrane-mimetics is substantially increased in acidic conditions. The EEA1 FYVE domain binds to POPC/POPE/PtdIns(3)P vesicles with a Kd of 49 nM at pH 6.0, however associates approximately 24 fold weaker at pH 8.0. The decrease in the affinity is primarily due to much faster dissociation of the protein from the bilayers in basic media. Lowering the pH enhances the interaction of the Hrs, RUFY1, Vps27p and WDFY1 FYVE domains with PtdIns(3)P-containing membranes in vitro and in vivo, indicating that pH-dependency is a general function of the FYVE finger family. The PtdIns(3)P binding and membrane insertion of the FYVE domain is modulated by the two adjacent His residues of the R(R/K)HHCRXCG signature motif. Mutation of either His residue abolishes the pH-sensitivity. Both protonation of the His residues and nonspecific electrostatic contacts stabilize the FYVE domain in the lipid-bound form, promoting its penetration and increasing the membrane residence time.
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Affiliation(s)
- Ju He
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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Watanabe H, Matsumaru H, Ooishi A, Feng Y, Odahara T, Suto K, Honda S. Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions. J Biol Chem 2009; 284:12373-83. [PMID: 19269963 PMCID: PMC2673305 DOI: 10.1074/jbc.m809236200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/23/2009] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by "enthalpy-entropy compensation." Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.
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Affiliation(s)
- Hideki Watanabe
- National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba 305-8566, Japan
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Abstract
The spatial and temporal regulation of lipid molecules in cell membranes is a hallmark of cellular signaling and membrane trafficking events. Lipid-mediated targeting provides for strict control and versatility, because cell membranes harbor a large number of lipid molecules with variation in head group and acyl chain structures. Signaling and trafficking proteins contain a large number of modular domains that exhibit specific lipid binding properties and play a critical role in their localization and function. Nearly 20 years of research including structural, computational, biochemical and biophysical studies have demonstrated how these lipid-binding domains recognize their target lipid and achieve subcellular localization. The integration of this individual lipid-binding domain data in the context of the full-length proteins, macromolecular signaling complexes, and the lipidome is only beginning to be unraveled and represents a target of therapeutic development. This review brings together recent findings and classical concepts to concisely summarize the lipid-binding domain field while illustrating where the field is headed and how the gaps may be filled in with new technologies.
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Affiliation(s)
- Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, Raclin-Carmichael Hall, 1234 Notre Dame Avenue, South Bend, IN 46617, USA.
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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