1
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Van Dinh Q, Liu J, Dutta P. Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier. Biochem Biophys Rep 2020; 24:100845. [PMID: 33235924 PMCID: PMC7670242 DOI: 10.1016/j.bbrep.2020.100845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Calcium signaling and membrane fusion play key roles in exocytosis of drug-containing vesicles through the blood-brain barrier (BBB). Identifying the role of synaptotagmin-like protein4-a (Slp4-a) in the presence of Ca2+ ions, at the pre-fusion stage of a vesicle with the basolateral membrane of endothelial cell, can reveal brain drug transportation across BBB. Methods We utilized molecular dynamics (MD) simulations with a coarse-grained PACE force field to investigate the behaviors of Slp4-a with vesicular and endothelial membranes at the pre-fusion stage of exocytosis since all-atom MD simulation or experiments are more time-consuming and expensive to capture these behaviors. Results The Slp4-a pulls lipid membranes (vesicular and endothelial) into close proximity and disorganizes lipid arrangement at contact points, which are predictors for initiation of fusion. Our MD results also indicate that Slp4-a needs Ca2+ to bind with weakly-charged POPE lipids (phosphatidylethanolamine). Conclusions Slp4-a is an important trigger for membrane fusion in BBB exocytosis. It binds to lipid membranes at multiple binding sites and triggers membrane disruption for fusion in calcium-dependent case. General significance Understanding the prefusion process of the vesicle will help to design better drug delivery mechanisms to the brain through formidable BBB. Role of Ca2+ on Slp4-a is studied for vesicle pre-fusion in EC to initiate exocytosis. Coarse-grained MD is used to study large scale conformation change of Slp-4a. Interaction between C2A domain and lipids is much stronger than that of C2B. Slp4-a can bind to bilayer membrane in Ca2+-bound case to close membrane gap.
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Affiliation(s)
| | | | - Prashanta Dutta
- Corresponding author. School of Mechanical and Materials Engineering, Washington State University, Pullman, WA, 99164, USA.
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2
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Voleti R, Jaczynska K, Rizo J. Ca 2+-dependent release of synaptotagmin-1 from the SNARE complex on phosphatidylinositol 4,5-bisphosphate-containing membranes. eLife 2020; 9:57154. [PMID: 32808925 PMCID: PMC7498268 DOI: 10.7554/elife.57154] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Abstract
The Ca2+ sensor synaptotagmin-1 and the SNARE complex cooperate to trigger neurotransmitter release. Structural studies elucidated three distinct synaptotagmin-1-SNARE complex binding modes involving 'polybasic', 'primary' and 'tripartite' interfaces of synaptotagmin-1. We investigated these interactions using NMR and fluorescence spectroscopy. Synaptotagmin-1 binds to the SNARE complex through the polybasic and primary interfaces in solution. Ca2+-free synaptotagmin-1 binds to SNARE complexes anchored on PIP2-containing nanodiscs. R398Q/R399Q and E295A/Y338W mutations at the primary interface, which strongly impair neurotransmitter release, disrupt and enhance synaptotagmin-1-SNARE complex binding, respectively. Ca2+ induces tight binding of synaptotagmin-1 to PIP2-containing nanodiscs, disrupting synaptotagmin-1-SNARE interactions. Specific effects of mutations in the polybasic region on Ca2+-dependent synaptotagmin-1-PIP2-membrane interactions correlate with their effects on release. Our data suggest that synaptotagmin-1 binds to the SNARE complex through the primary interface and that Ca2+ releases this interaction, inducing PIP2/membrane binding and allowing cooperation between synaptotagmin-1 and the SNAREs in membrane fusion to trigger release.
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Affiliation(s)
- Rashmi Voleti
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
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3
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Nyenhuis SB, Thapa A, Cafiso DS. Phosphatidylinositol 4,5 Bisphosphate Controls the cis and trans Interactions of Synaptotagmin 1. Biophys J 2019; 117:247-257. [PMID: 31301806 DOI: 10.1016/j.bpj.2019.06.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 06/18/2019] [Indexed: 11/28/2022] Open
Abstract
Synaptotagmin 1 acts as the Ca2+ sensor for synchronous neurotransmitter release; however, the mechanism by which it functions is not understood and is presently a topic of considerable interest. Here, we describe measurements on full-length membrane-reconstituted synaptotagmin 1 using site-directed spin labeling in which we characterize the linker region as well as the cis (vesicle membrane) and trans (cytoplasmic membrane) binding of its two C2 domains. In the full-length protein, the C2A domain does not undergo membrane insertion in the absence of Ca2+; however, the C2B domain will bind to and penetrate in trans to a membrane containing phosphatidylinositol 4,5 bisphosphate, even if phosphatidylserine (PS) is present in the cis membrane. In the presence of Ca2+, the Ca2+ binding loops of C2A and C2B both insert into the membrane interface; moreover, C2A preferentially inserts into PS-containing bilayers and will bind in a cis configuration to membranes containing PS even if a phosphatidylinositol 4,5 bisphosphate membrane is presented in trans. The data are consistent with a bridging activity for synaptotagmin 1 in which the two domains bind to opposing vesicle and plasma membranes. The failure of C2A to bind membranes in the absence of Ca2+ and the long unstructured segment linking C2A to the vesicle membrane indicates that synaptotagmin 1 could act to significantly shorten the vesicle-plasma membrane distance with increasing levels of Ca2+.
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Affiliation(s)
- Sarah B Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Anusa Thapa
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
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4
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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5
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Bai H, Xue R, Bao H, Zhang L, Yethiraj A, Cui Q, Chapman ER. Different states of synaptotagmin regulate evoked versus spontaneous release. Nat Commun 2016; 7:10971. [PMID: 27001899 PMCID: PMC4804166 DOI: 10.1038/ncomms10971] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/05/2016] [Indexed: 12/22/2022] Open
Abstract
The tandem C2-domains of synaptotagmin 1 (syt) function as Ca2+-binding modules that trigger exocytosis; in the absence of Ca2+, syt inhibits spontaneous release. Here, we used proline linkers to constrain and alter the relative orientation of these C2-domains. Short poly-proline helices have a period of three, so large changes in the relative disposition of the C2-domains result from changing the length of the poly-proline linker by a single residue. The length of the linker was varied one residue at a time, revealing a periodicity of three for the ability of the linker mutants to interact with anionic phospholipids and drive evoked synaptic transmission; syt efficiently drove exocytosis when its tandem C2-domains pointed in the same direction. Analysis of spontaneous release revealed a reciprocal relationship between the activation and clamping activities of the linker mutants. Hence, different structural states of syt underlie the control of distinct forms of synaptic transmission. Synaptotagmin contains tandem Ca2+-binding C2-domains that interact with target membranes to trigger exocytosis. Here, Bai et al. manipulate the relative orientation of these two domains using a synthetic polyproline linker and show that a parallel orientation is most effective for membrane interaction and exocytosis.
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Affiliation(s)
- Hua Bai
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Renhao Xue
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Huan Bao
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
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6
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Calcium binding promotes conformational flexibility of the neuronal Ca(2+) sensor synaptotagmin. Biophys J 2016; 108:2507-2520. [PMID: 25992729 DOI: 10.1016/j.bpj.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 01/12/2023] Open
Abstract
Synaptotagmin 1 (Syt1) is a synaptic vesicle protein that serves as a calcium sensor of neuronal secretion. It is established that calcium binding to Syt1 triggers vesicle fusion and release of neuronal transmitters, however, the dynamics of this process is not fully understood. To investigate how Ca(2+) binding affects Syt1 conformational dynamics, we performed prolonged molecular dynamics (MD) simulations of Ca(2+)-unbound and Ca(2+)-bound forms of Syt1. MD simulations were performed at a microsecond scale and combined with Monte Carlo sampling. We found that in the absence of Ca(2+) Syt1 structure in the solution is represented by an ensemble of conformational states with tightly coupled domains. To investigate the effect of Ca(2+) binding, we used two different strategies to generate a molecular model of a Ca(2+)-bound form of Syt1. First, we employed subsequent replacements of monovalent cations transiently captured within Syt1 Ca(2+)-binding pockets by Ca(2+) ions. Second, we performed MD simulations of Syt1 at elevated Ca(2+) levels. All the simulations produced Syt1 structures bound to four Ca(2+) ions, two ions chelated at the binding pocket of each domain. MD simulations of the Ca(2+)-bound form of Syt1 revealed that Syt1 conformational flexibility drastically increased upon Ca(2+) binding. In the presence of Ca(2+), the separation between domains increased, and interdomain rotations became more frequent. These findings suggest that Ca(2+) binding to Syt1 may induce major changes in the Syt1 conformational state, which in turn may initiate the fusion process.
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7
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Stevens MA, McKay JE, Robinson JLS, El Mkami H, Smith GM, Norman DG. The use of the Rx spin label in orientation measurement on proteins, by EPR. Phys Chem Chem Phys 2016; 18:5799-806. [PMID: 26426572 PMCID: PMC4756314 DOI: 10.1039/c5cp04753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 12/15/2022]
Abstract
The bipedal spin label Rx is more restricted in its conformation and dynamics than its monopodal counterpart R1. To systematically investigate the utility of the Rx label, we have attempted to comprehensively survey the attachment of Rx to protein secondary structures. We have examined the formation, structure and dynamics of the spin label in relation to the underlying protein in order to determine feasibility and optimum conditions for distance and orientation measurement by pulsed EPR. The labeled proteins have been studied using molecular dynamics, CW EPR, pulsed EPR distance measurement at X-band and orientation measurement at W-band. The utility of different modes and positions of attachment have been compared and contrasted.
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Affiliation(s)
- M A Stevens
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - J E McKay
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - J L S Robinson
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - H El Mkami
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - G M Smith
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - D G Norman
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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8
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Liu H, Bai H, Xue R, Takahashi H, Edwardson JM, Chapman ER. Linker mutations reveal the complexity of synaptotagmin 1 action during synaptic transmission. Nat Neurosci 2014; 17:670-7. [PMID: 24657966 PMCID: PMC4139111 DOI: 10.1038/nn.3681] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/21/2014] [Indexed: 12/13/2022]
Abstract
The Ca(2+) sensor for rapid synaptic vesicle exocytosis, synaptotagmin 1 (syt), is largely composed of two Ca(2+)-sensing C2 domains, C2A and C2B. We investigated the apparent synergy between the tandem C2 domains by altering the length and rigidity of the linker that connects them. The behavior of the linker mutants revealed a correlation between the ability of the C2 domains to penetrate membranes in response to Ca(2+) and to drive evoked neurotransmitter release in cultured mouse neurons, uncovering a step in excitation-secretion coupling. Using atomic force microscopy, we found that the synergy between these C2 domains involved intra-molecular interactions between them. Thus, syt function is markedly affected by changes in the physical nature of the linker that connects its tandem C2 domains. Moreover, the linker mutations uncoupled syt-mediated regulation of evoked and spontaneous release, revealing that syt also acts as a fusion clamp before the Ca(2+) trigger.
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Affiliation(s)
- Huisheng Liu
- 1] Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA. [2] [3]
| | - Hua Bai
- 1] Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA. [2]
| | - Renhao Xue
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | | | | | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
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9
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Ziemba BP, Falke JJ. Lateral diffusion of peripheral membrane proteins on supported lipid bilayers is controlled by the additive frictional drags of (1) bound lipids and (2) protein domains penetrating into the bilayer hydrocarbon core. Chem Phys Lipids 2013; 172-173:67-77. [DOI: 10.1016/j.chemphyslip.2013.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 11/15/2022]
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10
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Negative coupling as a mechanism for signal propagation between C2 domains of synaptotagmin I. PLoS One 2012; 7:e46748. [PMID: 23071627 PMCID: PMC3465270 DOI: 10.1371/journal.pone.0046748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/05/2012] [Indexed: 11/28/2022] Open
Abstract
Synaptotagmin I (Syt I) is a vesicle-localized protein implicated in sensing the calcium influx that triggers fast synchronous release of neurotransmitter. How Syt I utilizes its two C2 domains to integrate signals and mediate neurotransmission has continued to be a controversial area of research, though prevalent hypotheses favor independent function. Using differential scanning calorimetry and fluorescence lifetime spectroscopy in a thermodynamic denaturation approach, we tested an alternative hypothesis in which both domains interact to cooperatively disseminate binding information. The free energy of stability was determined for C2A, C2B, and C2AB constructs by globally fitting both methods to a two-state model of unfolding. By comparing the additive free energies of C2A and C2B with C2AB, we identified a negative coupling interaction between the C2 domains of Syt I. This interaction not only provides a mechanistic means for propagating signals, but also a possible means for coordinating the molecular events of neurotransmission.
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11
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Scott JL, Musselman CA, Adu-Gyamfi E, Kutateladze TG, Stahelin RV. Emerging methodologies to investigate lipid-protein interactions. Integr Biol (Camb) 2012; 4:247-58. [PMID: 22327461 DOI: 10.1039/c2ib00143h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cellular membranes are composed of hundreds of different lipids, ion channels, receptors and scaffolding complexes that act as signalling and trafficking platforms for processes fundamental to life. Cellular signalling and membrane trafficking are often regulated by peripheral proteins, which reversibly interact with lipid molecules in highly regulated spatial and temporal fashions. In most cases, one or more modular lipid-binding domain(s) mediate recruitment of peripheral proteins to specific cellular membranes. These domains, of which more than 10 have been identified since 1989, harbour structurally selective lipid-binding sites. Traditional in vitro and in vivo studies have elucidated how these domains coordinate their cognate lipids and thus how the parent proteins associate with membranes. Cellular activities of peripheral proteins and subsequent physiological processes depend upon lipid binding affinities and selectivity. Thus, the development of novel sensitive and quantitative tools is essential in furthering our understanding of the function and regulation of these proteins. As this field expands into new areas such as computational biology, cellular lipid mapping, single molecule imaging, and lipidomics, there is an urgent need to integrate technologies to detail the molecular architecture and mechanisms of lipid signalling. This review surveys emerging cellular and in vitro approaches for studying protein-lipid interactions and provides perspective on how integration of methodologies directs the future development of the field.
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Affiliation(s)
- Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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12
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Duan L, Zhmurov A, Barsegov V, Dima RI. Exploring the mechanical stability of the C2 domains in human synaptotagmin 1. J Phys Chem B 2011; 115:10133-46. [PMID: 21776988 DOI: 10.1021/jp2025945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Human synaptotagmin 1 (Syt1) plays a crucial role in the bending of the membrane during neurotransmitter release at the synapse. Hence, resolving the structural details of Syt1 that underlie its biological function is fundamental for providing mechanistic insights into the nature of the synaptic response. We explored the unfolding micromechanics of Syt1 by analyzing the free energy landscape of the whole molecule and its C2A and C2B domains. We employed a self-organized polymer (SOP) model of a protein chain to carry out pulling simulations, accelerated on graphics processing units (GPUs), under experimental force loads. To resolve the atomic-level details, we complemented the SOP model simulations with atomistic simulations. On the basis of the results obtained, we hypothesize that (1) isolated single domains C2A and C2B present similar mechanical resistance against an applied pulling force but unfold following different kinetic pathways and that (2) C2B is more mechanically resistant in the C2AB complex due to stabilizing interactions with other domains. These findings correlate well with recent atomic force microscopy (AFM) studies on the Syt1 molecule, in which the increase in the unfolding force for C2B was detected when this domain was joined with C2A. Our results also suggest that the linkers (I27 domains) used in the experimental setup can modulate the mechanical behavior of this synaptic protein complex and alter not only the critical force for unfolding but also the unfolding pathways for the C2 domains. Interestingly, the presence of the C2A-C2B domain interface in the C2AB complex confers mechanical stability to either of the C2 domains. Our findings provide new insights into the relative conformational variability of the C2 domains, which we believe to be modulated, to a large extent, by intermolecular coupling with other proteins.
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Affiliation(s)
- Li Duan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
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13
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Lai AL, Tamm LK, Ellena JF, Cafiso DS. Synaptotagmin 1 modulates lipid acyl chain order in lipid bilayers by demixing phosphatidylserine. J Biol Chem 2011; 286:25291-300. [PMID: 21610074 DOI: 10.1074/jbc.m111.258848] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synaptotagmin 1 (syt1) functions as the Ca(2+) sensor in neuronal exocytosis, and it has been proposed to act by modulating lipid bilayer curvature. Here we examine the effect of the two C2 domains (C2A and C2B) of syt1 on membrane lipid order and lateral organization. In mixtures of phosphatidylcholine and phosphatidylserine (PS), attenuated total internal reflection Fourier transform infrared spectroscopy indicates that a fragment containing both domains (C2AB) or C2B alone disorders the lipid acyl chains, whereas the C2A domain has little effect upon chain order. Two observations suggest that these changes reflect a demixing of PS. First, the changes in acyl chain order are reversed at higher protein concentration; second, selective lipid deuteration demonstrates that the changes in lipid order are associated only with the PS component of the bilayer. Independent evidence for lipid demixing is obtained from fluorescence self-quenching of labeled lipid and from natural abundance (13)C NMR, where heteronuclear single quantum correlation spectra reveal Ca(2+)-dependent chemical shift changes for PS, but not for phosphatidylcholine, in the presence of the syt1 C2 domains. The ability of syt1 to demix PS is observed in a range of lipid mixtures that includes cholesterol, phosphatidylethanolamine, and varied PS content. These data suggest that syt1 might facilitate SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors)-mediated membrane fusion by phase separating PS, a process that is expected to locally buckle bilayers and disorder lipids due to the curvature tendencies of PS.
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Affiliation(s)
- Alex L Lai
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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14
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Janosi L, Gorfe AA. Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras. Biophys J 2011; 99:3666-74. [PMID: 21112291 DOI: 10.1016/j.bpj.2010.10.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/18/2010] [Accepted: 10/20/2010] [Indexed: 12/19/2022] Open
Abstract
The Kras protein, a member of the Ras family of bio-switches that are frequently mutated in cancer and developmental disorders, becomes functional when anchored to the inner surface of the plasma membrane. It is well known that membrane attachment involves the farnesylated and poylcationic C-terminus of the protein. However, little is known about the structure of the complex and the specific protein-lipid interactions that are responsible for the binding. On the basis of data from extensive (>0.55 μs) molecular dynamics simulations of multiple Kras anchors in bilayers of POPC/POPG lipids (4:1 ratio), we show that, as expected, Kras is tethered to the bilayer surface by specific lysine-POPG salt bridges and by nonspecific farnesyl-phospholipid van der Waals interactions. Unexpectedly, however, only the C-terminal five of the eight Kras Lys side chains were found to directly interact with the bilayer, with the N-terminal ones staying in water. Furthermore, the positively charged Kras anchors pull the negatively charged POPG lipids together, leading to the clustering of the POPG lipids around the proteins. This selective Kras-POPG interaction is directly related to the specific geometry of the backbone, which exists in two major conformational states: 1), a stable native-like ensemble of structures characterized by an extended geometry with a pseudohelical turn; and 2), less stable nonnative ensembles of conformers characterized by severely bent geometries. Finally, although the interface-bound anchor has little effect on the overall structure of the bilayer, it induces local thinning within a persistence length of ∼12 Å. Our results thus go beyond documenting how Kras attaches to a mixed bilayer of charged and neutral lipids; they highlight a fascinating process of protein-induced lipid sorting coupled with the (re)shaping of a surface-bound protein by the host lipids.
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Affiliation(s)
- Lorant Janosi
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
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15
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Ricci A, Marinello J, Bortolus M, Sánchez A, Grandas A, Pedroso E, Pommier Y, Capranico G, Maniero AL, Zagotto G. Electron paramagnetic resonance (EPR) study of spin-labeled camptothecin derivatives: a different look of the ternary complex. J Med Chem 2011; 54:1003-9. [PMID: 21254781 DOI: 10.1021/jm101232t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Camptothecin (CPT) derivatives are clinically effective poisons of DNA topoisomerase I (Top1) able to form a ternary complex with the Top1-DNA complex. The aim of this investigation was to examine the dynamic aspects of the ternary complex formation by means of site-directed spin labeling electron paramagnetic resonance (SDSL-EPR). Two semisynthetic CPT derivatives bearing the paramagnetic moiety were synthesized, and their biological activity was tested. A 22-mer DNA oligonucleotide sequence with high affinity cleavage site for Top1 was also synthesized. EPR experiments were carried out on modified CPT in the presence of DNA, of Top1, or of both. In the last case, a slow motion component in the EPR signal appeared, indicating the formation of the ternary complex. Deconvolution of the EPR spectrum allowed to obtain the relative drug amounts in the complex. It was also possible to demonstrate that the residence time of CPT "trapped" in the ternary complex is longer than hundreds of microseconds.
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Affiliation(s)
- Antonio Ricci
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 30039 Padova, Italy
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16
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Lai AL, Huang H, Herrick DZ, Epp N, Cafiso DS. Synaptotagmin 1 and SNAREs form a complex that is structurally heterogeneous. J Mol Biol 2010; 405:696-706. [PMID: 21087613 DOI: 10.1016/j.jmb.2010.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/14/2010] [Accepted: 11/05/2010] [Indexed: 01/08/2023]
Abstract
Synaptotagmin 1 (syt1) functions as a Ca(2+)-sensor for neuronal exocytosis. Here, site-directed spin labeling was used to examine the complex formed between a soluble fragment of syt1, which contains its two C2 domains, and the neuronal core soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex. Changes in electron paramagnetic resonance lineshape and accessibility for spin-labeled syt1 mutants indicate that in solution, the assembled core SNARE complex contacts syt1 in several regions. For the C2B domain, contact occurs in the polybasic face and sites opposite the Ca(2+)-binding loops. For the C2A domain, contact is seen with the SNARE complex in a region near loop 2. Double electron-electron resonance was used to estimate distances between the two C2 domains of syt1. These distances have broad distributions in solution, which do not significantly change when syt1 is fully associated with the core SNARE complex. The broad distance distributions indicate that syt1 is structurally heterogeneous when bound to the SNAREs and does not assume a well-defined structure. Simulated annealing using electron paramagnetic resonance-derived distance restraints produces a family of syt1 structures where the Ca(2+)-binding regions of each domain face in roughly opposite directions. The results suggest that when associated with the SNAREs, syt1 is configured to bind opposing bilayers, but that the syt1/SNARE complex samples multiple conformational states.
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Affiliation(s)
- Alex L Lai
- Department of Chemistry, Biophysics Program and Center for Membrane Biology at the University of Virginia, Charlottesville, VA 22904-4319, USA
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Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion. Nat Struct Mol Biol 2010; 17:325-31. [PMID: 20173762 PMCID: PMC2928146 DOI: 10.1038/nsmb.1764] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Accepted: 12/11/2009] [Indexed: 12/15/2022]
Abstract
In neurons, SNAREs, synaptotagmin, and other factors catalyze Ca2+-triggered fusion of vesicles with the plasma membrane. The molecular mechanism of this process remains an enigma, especially regarding the interaction between synaptotagmin and SNAREs. Here we characterized this interaction by single-molecule fluorescence microscopy and crystallography. The two rigid Ca2+-binding domains of synaptotagmin 3 undergo large relative motions in solution. Interaction with SNARE complex amplifies a particular state of the two domains that is further enhanced by Ca2+. This state is represented by the first SNARE-induced Ca2+-bound crystal structure of a synaptotagmin fragment containing both domains. The arrangement of the Ca2+-binding loops of this structure of synaptotagmin 3 matches that of SNARE-bound synaptotagmin 1, suggesting a conserved feature of synaptotagmins. The loops resemble the membrane-interacting loops of certain viral fusion proteins in the postfusion state, suggesting unexpected similarities between both fusion systems.
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Štrancar J, Kavalenka A, Urbančič I, Ljubetič A, Hemminga MA. SDSL-ESR-based protein structure characterization. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:499-511. [DOI: 10.1007/s00249-009-0510-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 06/23/2009] [Indexed: 10/20/2022]
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Herrick DZ, Kuo W, Huang H, Schwieters CD, Ellena JF, Cafiso DS. Solution and membrane-bound conformations of the tandem C2A and C2B domains of synaptotagmin 1: Evidence for bilayer bridging. J Mol Biol 2009; 390:913-23. [PMID: 19501597 DOI: 10.1016/j.jmb.2009.06.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 05/29/2009] [Accepted: 06/02/2009] [Indexed: 11/29/2022]
Abstract
Synaptotagmin 1 (syt1) is a synaptic vesicle membrane protein that functions as the Ca(2)(+) sensor in neuronal exocytosis. Here, site-directed spin labeling was used to generate models for the solution and membrane-bound structures of a soluble fragment of syt1 containing its two C2 domains, C2A and C2B. In solution, distance restraints between the two C2 domains of syt1 were measured using double electron-electron resonance and used in a simulated annealing routine to generate models for the structure of the tandem C2A-C2B fragment. The data indicate that the two C2 domains are flexibly linked and do not interact with each other in solution, with or without Ca(2+). However, the favored orientation is one where the Ca(2+)-binding loops are oriented in opposite directions. A similar approach was taken for membrane-associated C2A-C2B, combining both distances and bilayer depth restraints with simulated annealing. The restraints can only be satisfied if the Ca(2+) and membrane-binding surfaces of the domains are oriented in opposite directions so that C2A and C2B are docked to opposing bilayers. The result suggests that syt1 functions to bridge across the vesicle and plasma membrane surfaces in a Ca(2+)-dependent manner.
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Affiliation(s)
- Dawn Z Herrick
- Department of Chemistry and Biophysics, University of Virginia, Charlottesville, 22904-4319, USA
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Kuo W, Herrick DZ, Ellena JF, Cafiso DS. The calcium-dependent and calcium-independent membrane binding of synaptotagmin 1: two modes of C2B binding. J Mol Biol 2009; 387:284-94. [PMID: 19302798 DOI: 10.1016/j.jmb.2009.01.064] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 01/22/2009] [Accepted: 01/29/2009] [Indexed: 01/13/2023]
Abstract
The Ca2+-independent membrane interactions of the soluble C2 domains from synaptotagmin 1 (syt1) were characterized using a combination of site-directed spin labeling and vesicle sedimentation. The second C2 domain of syt1, C2B, binds to membranes containing phosphatidylserine and phosphatidylcholine in a Ca2+-independent manner with a lipid partition coefficient of approximately 3.0 x 10(2) M(-1). A soluble fragment containing the first and second C2 domains of syt1, C2A and C2B, has a similar affinity, but C2A alone has no detectable affinity to phosphatidylcholine/phosphatidylserine bilayers in the absence of Ca2+. Although the Ca2+-independent membrane affinity of C2B is modest, it indicates that this domain will never be free in solution within the cell. Site-directed spin labeling was used to obtain bilayer depth restraints, and a simulated annealing routine was used to generate a model for the membrane docking of C2B in the absence of Ca2+. In this model, the polybasic strand of C2B forms the membrane binding surface for the domain; however, this face of C2B does not penetrate the bilayer but is localized within the aqueous double layer when C2B is bound. This double-layer location indicates that C2B interacts in a purely electrostatic manner with the bilayer interface. In the presence of Ca2+, the membrane affinity of C2B is increased approximately 20-fold, and the domain rotates so that the Ca2+-binding loops of C2B insert into the bilayer. This Ca2+-triggered conformational change may act as a switch to modulate the accessibility of the polybasic face of C2B and control interactions of syt1 with other components of the fusion machinery.
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Affiliation(s)
- Weiwei Kuo
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904-4319, USA
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