References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu,...

18
123 References Abul-Husn, N., Bushlin, I., Moron, J., Jenkins, S., Dolios, G., Wang, R., Iyengar, R., Ma'ayan, A., and Devi, L. (2009). Systems approach to explore components and interactions in the presynapse. Proteomics 9, 3303-3315. Ahmad, M., Polepalli, J., Goswami, D., Yang, X., Kaeser-Woo, Y., Südhof, T., and Malenka, R. (2012). Postsynaptic complexin controls AMPA receptor exocytosis during LTP. Neuron 73, 260-267. Aicardi, G. (2012). Age-related impairment of visual recognition memory correlates with impaired synaptic distribution of GluA2 and protein kinase Mζ in the dentate gyrus. Rejuvenation research 15, 530533. Aikawa, Y., Xia, X., and Martin, T. (2006b). SNAP25, but not syntaxin 1A, recycles via an ARF6-regulated pathway in neuroendocrine cells. Molecular biology of the cell 17, 711722. Alberts, P., Rudge, R., Hinners, I., Muzerelle, A., Martinez-Arca, S., Irinopoulou, T., Marthiens, V., Tooze, S., Rathjen, F., Gaspar, P., et al. (2003). Cross talk between tetanus neurotoxin-insensitive vesicle-associated membrane protein-mediated transport and L1-mediated adhesion. Molecular biology of the cell 14, 42074220. Alt, A., Nisenbaum, E., Bleakman, D., and Witkin, J. (2006). A role for AMPA receptors in mood disorders. Biochemical pharmacology 71, 12731288. Anderson, G. (2012). Twin studies in autism: what might they say about genetic and environmental influences. Journal of autism and developmental disorders 42, 1526-1527. Anderson, G., Galfin, T., Xu, W., Aoto, J., Malenka, R., and Südhof, T. (2012). Candidate autism gene screen identifies critical role for cell-adhesion molecule CASPR2 in dendritic arborization and spine development. Proceedings of the National Academy of Sciences of the United States of America 109, 18120-18125. Anggono, V., and Huganir, R. (2012). Regulation of AMPA receptor trafficking and synaptic plasticity. Current opinion in neurobiology 22, 461-469. Antonin, W., Holroyd, C., Fasshauer, D., Pabst, S., Von Mollard, G., and Jahn, R. (2000a). A SNARE complex mediating fusion of late endosomes defines conserved properties of SNARE structure and function. The EMBO journal 19, 64536464. Antonin, W., Riedel, D., and von Mollard, G. (2000b). The SNARE Vti1a-beta is localized to small synaptic vesicles and participates in a novel SNARE complex. The Journal of neuroscience : the official journal of the Society for Neuroscience 20, 57245732.

Transcript of References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu,...

Page 1: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

123

References

Abul-Husn, N., Bushlin, I., Moron, J., Jenkins, S., Dolios, G., Wang, R., Iyengar, R., Ma'ayan, A., and

Devi, L. (2009). Systems approach to explore components and interactions in the

presynapse. Proteomics 9, 3303-3315.

Ahmad, M., Polepalli, J., Goswami, D., Yang, X., Kaeser-Woo, Y., Südhof, T., and Malenka, R. (2012).

Postsynaptic complexin controls AMPA receptor exocytosis during LTP. Neuron 73,

260-267.

Aicardi, G. (2012). Age-related impairment of visual recognition memory correlates with impaired

synaptic distribution of GluA2 and protein kinase Mζ in the dentate gyrus. Rejuvenation

research 15, 530–533.

Aikawa, Y., Xia, X., and Martin, T. (2006b). SNAP25, but not syntaxin 1A, recycles via an

ARF6-regulated pathway in neuroendocrine cells. Molecular biology of the cell 17,

711–722.

Alberts, P., Rudge, R., Hinners, I., Muzerelle, A., Martinez-Arca, S., Irinopoulou, T., Marthiens, V.,

Tooze, S., Rathjen, F., Gaspar, P., et al. (2003). Cross talk between tetanus

neurotoxin-insensitive vesicle-associated membrane protein-mediated transport and

L1-mediated adhesion. Molecular biology of the cell 14, 4207–4220.

Alt, A., Nisenbaum, E., Bleakman, D., and Witkin, J. (2006). A role for AMPA receptors in mood

disorders. Biochemical pharmacology 71, 1273–1288.

Anderson, G. (2012). Twin studies in autism: what might they say about genetic and environmental

influences. Journal of autism and developmental disorders 42, 1526-1527.

Anderson, G., Galfin, T., Xu, W., Aoto, J., Malenka, R., and Südhof, T. (2012). Candidate autism gene

screen identifies critical role for cell-adhesion molecule CASPR2 in dendritic arborization

and spine development. Proceedings of the National Academy of Sciences of the United

States of America 109, 18120-18125.

Anggono, V., and Huganir, R. (2012). Regulation of AMPA receptor trafficking and synaptic plasticity.

Current opinion in neurobiology 22, 461-469.

Antonin, W., Holroyd, C., Fasshauer, D., Pabst, S., Von Mollard, G., and Jahn, R. (2000a). A SNARE

complex mediating fusion of late endosomes defines conserved properties of SNARE

structure and function. The EMBO journal 19, 6453–6464.

Antonin, W., Riedel, D., and von Mollard, G. (2000b). The SNARE Vti1a-beta is localized to small

synaptic vesicles and participates in a novel SNARE complex. The Journal of neuroscience :

the official journal of the Society for Neuroscience 20, 5724–5732.

Page 2: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

124

Antonucci, F., Corradini, I., Morini, R., Fossati, G., Menna, E., Pozzi, D., Pacioni, S., Verderio, C., Bacci,

A., and Matteoli, M. (2013). Reduced SNAP-25 alters short-term plasticity at developing

glutamatergic synapses. EMBO reports 14.Bakkaloglu, B., O'Roak, B., Louvi, A., Gupta, A.,

Abelson, J., Morgan, T., Chawarska, K., Klin, A., Ercan-Sencicek, A., Stillman, A., et al.

(2008). Molecular cytogenetic analysis and resequencing of contactin associated

protein-like 2 in autism spectrum disorders. American journal of human genetics 82,

165-173.

Bal, M., Leitz, J., Reese, A., Ramirez, D., Durakoglugil, M., Herz, J., Monteggia, L., and Kavalali, E.

(2013). Reelin Mobilizes a VAMP7-Dependent Synaptic Vesicle Pool and Selectively

Augments Spontaneous Neurotransmission. Neuron 80, 934-946.

Barysch, S., Aggarwal, S., Jahn, R., and Rizzoli, S. (2009). Sorting in early endosomes reveals

connections to docking- and fusion-associated factors. Proceedings of the National

Academy of Sciences of the United States of America 106, 9697-9702.

Bastian M., Heymann S., Jacomy M. (2009). Gephi: an open source software for exploring and

manipulating networks. International AAAI Conference on Weblogs and Social Media.

Baumgartner, M., Weiss, A., Fritzius, T., Heinrich, J., and Moelling, K. (2009). The PDZ protein MPP2

interacts with c-Src in epithelial cells. Experimental cell research 315, 2888–2898.

Bayés, A., and Grant, S. (2009). Neuroproteomics: understanding the molecular organization and

complexity of the brain. Nature reviews Neuroscience 10, 635-646.

Becherer, U., and Rettig, J. (2006). Vesicle pools, docking, priming, and release. Cell and tissue

research 326, 393–407.

Beneyto, M., and Meador-Woodruff, J. (2004). Expression of transcripts encoding AMPAR subunits

and associated postsynaptic proteins in the macaque brain. The Journal of comparative

neurology 468, 530-554.

Benoist, M., Gaillard, S., and Castets, F. (2006). The striatin family: a new signaling platform in

dendritic spines. Journal of physiology, Paris 99, 146–153.

Benowitz, L., and Routtenberg, A. (1997). GAP-43: an intrinsic determinant of neuronal

development and plasticity. Trends in neurosciences 20, 84-91.

Betancur, C., Sakurai, T., and Buxbaum, J. (2009). The emerging role of synaptic cell-adhesion

pathways in the pathogenesis of autism spectrum disorders. Trends in neurosciences 32,

402-412.

Bildl, W., Haupt, A., Mueller, C. S., Biniossek, M. L. et al., Extending the dynamic range of label-free

mass spectrometric quantification of affinity purifications. Mol. Cell. Proteomics 2012, 11,

M111 007955.

Blatt, Gene J. (2010) Neuroscience of Autism. Encyclopedia of Life Sciences (eLS). John Wiley & Sons,

Ltd, Chichester.

Page 3: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

125

Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of

adaptor protein-3 is required for synaptic vesicle formation from endosomes. J. Neurosci.

21:8034–8042.

Boudreau, A., Reimers, J., Milovanovic, M., and Wolf, M. (2007). Cell surface AMPA receptors in the

rat nucleus accumbens increase during cocaine withdrawal but internalize after cocaine

challenge in association with altered activation of mitogen-activated protein kinases. The

Journal of neuroscience : the official journal of the Society for Neuroscience 27,

10621–10635.

Brandhorst, D., Zwilling, D., Rizzoli, S., Lippert, U., Lang, T., and Jahn, R. (2006). Homotypic fusion of

early endosomes: SNAREs do not determine fusion specificity. Proceedings of the National

Academy of Sciences of the United States of America 103, 2701–2706.

Burgalossi, A., Jung, S., Meyer, G., Jockusch, W., Jahn, O., Taschenberger, H., O’Connor, V., Nishiki,

T., Takahashi, M., Brose, N., et al. (2010). SNARE protein recycling by αSNAP and βSNAP

supports synaptic vesicle priming. Neuron 68, 473–487.

Burns, M., and Augustine, G. (1995). Synaptic structure and function: dynamic organization yields

architectural precision. Cell 83, 187–94.Burré, J., Sharma, M., Tsetsenis, T., Buchman, V.,

Etherton, M., and Südhof, T. (2010). Alpha-synuclein promotes SNARE-complex assembly

in vivo and in vitro. Science (New York, N.Y.)329, 1663–1667.

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M., Maeda, N., Oyama, R., Ravasi, T.,

Lenhard, B., Wells, C., et al. (2005). The transcriptional landscape of the mammalian

genome. Science (New York, N.Y.) 309, 1559–1563.

Carroll, R., Beattie, E., Xia, H., Lüscher, C., Altschuler, Y., Nicoll, R., Malenka, R., and von Zastrow, M.

(1999). Dynamin-dependent endocytosis of ionotropic glutamate receptors. Proceedings

of the National Academy of Sciences of the United States of America 96, 14112-14117.

Carroll, R., Lissin, D., von Zastrow, M., Nicoll, R., and Malenka, R. (1999). Rapid redistribution of

glutamate receptors contributes to long-term depression in hippocampal cultures. Nature

neuroscience 2, 454-460.

Castillo, P. (2012). Presynaptic LTP and LTD of excitatory and inhibitory synapses. Cold Spring Harbor

perspectives in biology 4.

Catterall, W., and Few, A. (2008). Calcium channel regulation and presynaptic plasticity. Neuron 59,

882-901.

Chang, E., Savage, M., Flood, D., Thomas, J., Levy, R., Mahadomrongkul, V., Shirao, T., Aoki, C., and

Huerta, P. (2006). AMPA receptor downscaling at the onset of Alzheimer’s disease

pathology in double knockin mice. Proceedings of the National Academy of Sciences of the

United States of America 103, 3410–3415.

Chapman, E. (2008). How does synaptotagmin trigger neurotransmitter release? Annual review of

biochemistry 77, 615-641.

Page 4: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

126

Chen, L., Chetkovich, D., Petralia, R., Sweeney, N., Kawasaki, Y., Wenthold, R., Bredt, D., and Nicoll,

R. (2000). Stargazin regulates synaptic targeting of AMPARs by two distinct mechanisms.

Nature 408, 936-943.

Chen, N., van der Schors, RC., Smit, AB. (2011). Chapter 12, A 1D-PAGE/LC-ESI Linear Ion Trap

Orbitrap MS Approach for the Analysis of Synapse Proteomes and Synaptic Protein

Complexes. Neuroproteomics. Humana Press. 159-168.

Chen, Y., and Scheller, R. (2001). SNARE-mediated membrane fusion. Nature reviews Molecular cell

biology 2, 98-106.

Cheng, D., Hoogenraad, C., Rush, J., Ramm, E., Schlager, M., Duong, D., Xu, P., Wijayawardana, S.,

Hanfelt, J., Nakagawa, T., et al. (2006). Relative and absolute quantification of postsynaptic

density proteome isolated from rat forebrain and cerebellum. Molecular & cellular

proteomics : MCP 5, 1158-1170.

Choi, H., Larsen, B., Lin, Z. Y., Breitkreutz, A. et al., SAINT: probabilistic scoring of affinity

purification-mass spectrometry data. Nat. Methods 2011, 8, 70–73.

Chowdhury, S., Shepherd, J., Okuno, H., Lyford, G., Petralia, R., Plath, N., Kuhl, D., Huganir, R., and

Worley, P. (2006). Arc/Arg3.1 interacts with the endocytic machinery to regulate AMPA

receptor trafficking. Neuron 52, 445-459.

Chua, J., Kindler, S., Boyken, J., and Jahn, R. (2010). The architecture of an excitatory synapse.

Journal of cell science 123, 819-823.

Citri, A., Bhattacharyya, S., Ma, C., Morishita, W., Fang, S., Rizo, J., and Malenka, R. (2010). Calcium

binding to PICK1 is essential for the intracellular retention of AMPA receptors underlying

long-term depression. The Journal of neuroscience : the official journal of the Society for

Neuroscience 30, 16437-16452.

Collingridge, G., Isaac, J., and Wang, Y. (2004). Receptor trafficking and synaptic plasticity. Nature

reviews Neuroscience 5, 952-962.

Coombs, I., and Cull-Candy, S. (2009). Transmembrane AMPAR regulatory proteins and AMPAR

function in the cerebellum. Neuroscience 162, 656-665.

Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine

integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794– 1805.

Dahlhaus, M., Li, K., van der Schors, R., Saiepour, M., van Nierop, P., Heimel, J., Hermans, J., Loos,

M., Smit, A., and Levelt, C. (2011). The synaptic proteome during development and

plasticity of the mouse visual cortex. Molecular & cellular proteomics : MCP 10.

Deng, L., Kaeser, P., Xu, W., and Südhof, T. (2011). RIM proteins activate vesicle priming by reversing

autoinhibitory homodimerization of Munc13. Neuron 69, 317-331.

Dittman, J., and Ryan, T. (2009). Molecular circuitry of endocytosis at nerve terminals. Annual

review of cell and developmental biology 25, 133-160.

Page 5: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

127

Duc, C., and Catsicas, S. (1995). Ultrastructural localization of SNAP-25 within the rat spinal cord and

peripheral nervous system. The Journal of comparative neurology 356, 152–63.Eastwood,

S., Kerwin, R., and Harrison, P. (1997). Immunoautoradiographic evidence for a loss of

alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate-preferring

non-N-methyl-D-aspartate glutamate receptors within the medial temporal lobe in

schizophrenia. Biological psychiatry 41, 636–643.

Elias, G., and Nicoll, R. (2007). Synaptic trafficking of glutamate receptors by MAGUK scaffolding

proteins. Trends in cell biology17, 343–352.

Emes, R., and Grant, S. (2012). Evolution of synapse complexity and diversity. Annual review of

neuroscience 35, 111-131.

Eubel, H., and Millar, A. (2009). Systematic monitoring of protein complex composition and

abundance by blue-native PAGE. Cold Spring Harbor protocols 2009.

Eubel, H., Braun, H., and Millar, A. (2005). Blue-native PAGE in plants: a tool in analysis of

protein-protein interactions. Plant methods 1, 11.

Faundez, V., J.T. Horng, and R.B. Kelly. 1998. A function for the AP3 coat complex in synaptic vesicle

formation from endosomes. Cell. 93:423–432.

Feng, W., and Zhang, M. (2009). Organization and dynamics of PDZ-domain-related supramodules in

the postsynaptic density. Nature reviews Neuroscience 10, 87-99.

Fernández, E., Collins, M., Uren, R., Kopanitsa, M., Komiyama, N., Croning, M., Zografos, L.,

Armstrong, J., Choudhary, J., and Grant, S. (2009). Targeted tandem affinity purification of

PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.

Molecular systems biology 5, 269.

Fernández-Chacón, R., Königstorfer, A., Gerber, S., García, J., Matos, M., Stevens, C., Brose, N., Rizo,

J., Rosenmund, C., and Südhof, T. (2001). Synaptotagmin I functions as a calcium regulator

of release probability. Nature 410, 41–49.

Filiou, M., Bisle, B., Reckow, S., Teplytska, L., Maccarrone, G., and Turck, C. (2010). Profiling of

mouse synaptosome proteome and phosphoproteome by IEF. Electrophoresis 31,

1294–301.Fioravante, D., and Regehr, W. (2011). Short-term forms of presynaptic

plasticity. Current opinion in neurobiology 21, 269–274.

Ganley, I., Espinosa, E., and Pfeffer, S. (2008). A syntaxin 10-SNARE complex distinguishes two

distinct transport routes from endosomes to the trans-Golgi in human cells. The Journal of

cell biology 180, 159–172.

Garber, K., Visootsak, J., and Warren, S. (2008). Fragile X syndrome. European journal of human

genetics : EJHG 16, 666–672.

García-Junco-Clemente, P., Linares-Clemente, P., and Fernández-Chacón, R. (2005). Active zones for

presynaptic plasticity in the brain. Molecular psychiatry 10, 185–200; image 131.

Page 6: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

128

Gengyo-Ando, K., Kuroyanagi, H., Kobayashi, T., Murate, M., Fujimoto, K., Okabe, S., and Mitani, S.

(2007). The SM protein VPS-45 is required for RAB-5-dependent endocytic transport in

Caenorhabditis elegans. EMBO reports 8, 152-157.

Gerhard, D., Wagner, L., Feingold, E., Shenmen, C., Grouse, L., Schuler, G., Klein, S., Old, S., Rasooly,

R., Good, P., et al. (2004). The status, quality, and expansion of the NIH full-length cDNA

project: the Mammalian Gene Collection (MGC). Genome research 14, 2121–2127.

Giraudo, C., Eng, W., Melia, T., and Rothman, J. (2006). A clamping mechanism involved in

SNARE-dependent exocytosis. Science (New York, NY) 313, 676-680.

Goudreault, M., D’Ambrosio, L., Kean, M., Mullin, M., Larsen, B., Sanchez, A., Chaudhry, S., Chen, G.,

Sicheri, F., Nesvizhskii, A., et al. (2009). A PP2A phosphatase high density interaction

network identifies a novel striatin-interacting phosphatase and kinase complex linked to

the cerebral cavernous malformation 3 (CCM3) protein. Molecular & cellular proteomics :

MCP 8, 157–171.

Greer, P., Hanayama, R., Bloodgood, B., Mardinly, A., Lipton, D., Flavell, S., Kim, T.-K., Griffith, E.,

Waldon, Z., Maehr, R., et al. (2010). The Angelman Syndrome protein Ube3A regulates

synapse development by ubiquitinating arc. Cell 140, 704–716.

Hanley, J., Khatri, L., Hanson, P., and Ziff, E. (2002). NSF ATPase and alpha-/beta-SNAPs disassemble

the AMPAR-PICK1 complex. Neuron 34, 53-67.

Harris, K., and Weinberg, R. (2012). Ultrastructure of synapses in the mammalian brain. Cold Spring

Harbor perspectives in biology 4.

Hatsuzawa, K., Lang, T., Fasshauer, D., Bruns, D., and Jahn, R. (2003). The R-SNARE motif of tomosyn

forms SNARE core complexes with syntaxin 1 and SNAP-25 and down-regulates exocytosis.

The Journal of biological chemistry 278, 31159–31166.

Hay, J., Fisette, P., Jenkins, G., Fukami, K., Takenawa, T., Anderson, R., and Martin, T. (1995).

ATP-dependent inositide phosphorylation required for Ca(2+)-activated secretion. Nature

374, 173–177.

Henne, W., Boucrot, E., Meinecke, M., Evergren, E., Vallis, Y., Mittal, R., and McMahon, H. (2010).

FCHo proteins are nucleators of clathrin-mediated endocytosis. Science (New York, N.Y.)

328, 1281–1284.

Herman, P., and Emr, S. (1990). Characterization of VPS34, a gene required for vacuolar protein

sorting and vacuole segregation in Saccharomyces cerevisiae. Molecular and cellular

biology 10, 6742-6754.

Holt, R., and Monaco, A. (2011). Links between genetics and pathophysiology in the autism

spectrum disorders. EMBO molecular medicine 3, 438-450.

Hong, W. (2005). SNAREs and traffic. Biochimica et biophysica acta 1744, 120–144.

Horresh, I., Poliak, S., Grant, S., Bredt, D., Rasband, M., and Peles, E. (2008). Multiple molecular

interactions determine the clustering of Caspr2 and Kv1 channels in myelinated axons. The

Page 7: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

129

Journal of neuroscience : the official journal of the Society for Neuroscience 28,

14213-14222.

Inda, M., DeFelipe, J., and Muñoz, A. (2006). Voltage-gated ion channels in the axon initial segment

of human cortical pyramidal cells and their relationship with chandelier cells. Proceedings

of the National Academy of Sciences of the United States of America 103, 2920-2925.

Insall, R. H., Machesky, L. M., Actin dynamics at the leading edge: from simplemachinery to complex

networks. Dev. Cell 2009, 17, 310–322.

Jackson, A., and Nicoll, R. (2011). The expanding social network of ionotropic glutamate receptors:

TARPs and other transmembrane auxiliary subunits. Neuron 70, 178-199.

Jahn, R., and Scheller, R. (2006). SNAREs--engines for membrane fusion. Nature reviews Molecular

cell biology 7, 631-643.

Kaake, R., Wang, X., and Huang, L. (2010). Profiling of protein interaction networks of protein

complexes using affinity purification and quantitative mass spectrometry. Molecular &

cellular proteomics : MCP 9, 1650-1665.

Kaeser, P., and Südhof, T. (2005). RIM function in short- and long-term synaptic plasticity.

Biochemical Society transactions 33, 1345–1349.

Kalashnikova, E., Lorca, R., Kaur, I., Barisone, G., Li, B., Ishimaru, T., Trimmer, J., Mohapatra, D., and

Díaz, E. (2010). SynDIG1: an activity-regulated, AMPA- receptor-interacting

transmembrane protein that regulates excitatory synapse development. Neuron 65,

80-93.

Karnak, D., Lee, S., and Margolis, B. (2002). Identification of multiple binding partners for the

amino-terminal domain of synapse-associated protein 97. The Journal of biological

chemistry 277, 46730–46735.

Kawabe, H., Sakisaka, T., Yasumi, M., Shingai, T. et al., A novel rabconnectin-3-binding protein that

directly binds a GDP/GTP exchange protein for Rab3A small G protein implicated in

Ca(2+)-dependent exocytosis of neurotransmitter. Genes Cells 2003, 8, 537–546.

Kawasaki, F., and Ordway, R. (2009). Molecular mechanisms determining conserved properties of

short-term synaptic depression revealed in NSF and SNAP-25 conditional mutants.

Proceedings of the National Academy of Sciences of the United States of America 106,

14658-14663.

Kessels, H., and Malinow, R. (2009). Synaptic AMPA receptor plasticity and behavior. Neuron 61,

340-350.

Kim, J., Liu, C., Zhang, F., Duan, X., Wen, Z., Song, J., Feighery, E., Lu, B., Rujescu, D., St Clair, D., et al.

(2012). Interplay between DISC1 and GABA signaling regulates neurogenesis in mice and

risk for schizophrenia. Cell 148, 1051–1064.

Klemmer, P., Smit, A., and Li, K. (2009). Proteomics analysis of immuno-precipitated synaptic

protein complexes. Journal of proteomics 72, 82–90.

Page 8: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

130

Körber, C., Horstmann, H., Sätzler, K., and Kuner, T. (2012). Endocytic structures and synaptic vesicle

recycling at a central synapse in awake rats. Traffic (Copenhagen, Denmark) 13,

1601-1611.

Krishnan, V., and Nestler, E. (2008). The molecular neurobiology of depression. Nature 455,

894–902.

Kunwar, A., Rickmann, M., Backofen, B., Browski, S., Rosenbusch, J., Schöning, S., Fleischmann, T.,

Krieglstein, K., and Fischer von Mollard, G. (2011). Lack of the endosomal SNAREs vti1a

and vti1b led to significant impairments in neuronal development. Proceedings of the

National Academy of Sciences of the United States of America 108, 2575-2580.

Lavallee-Adam, M., Cloutier, P., Coulombe, B., Blanchette, M., Modeling contaminants in AP-MS/MS

experiments. J. Proteome Res. 2011, 10, 886–895.

Lazzell, D., Belizaire, R., Thakur, P., Sherry, D., and Janz, R. (2004). SV2B regulates synaptotagmin 1

by direct interaction. J Biol Chem 279, 52124-52131.

Lebrand, C., Corti, M., Goodson, H., Cosson, P., Cavalli, V., Mayran, N., Fauré, J., and Gruenberg, J.

(2002). Late endosome motility depends on lipids via the small GTPase Rab7. The EMBO

journal 21, 1289–300.Li, F., Pincet, F., Perez, E., Eng, W., Melia, T., Rothman, J., and

Tareste, D. (2007). Energetics and dynamics of SNAREpin folding across lipid bilayers.

Nature structural & molecular biology 14, 890–896.

Li, F., Pincet, F., Perez, E., Giraudo, C., Tareste, D., and Rothman, J. (2011). Complexin activates and

clamps SNAREpins by a common mechanism involving an intermediate energetic state.

Nature structural & molecular biology 18, 941–946.

Li, K., and Jimenez, C. (2008). Synapse proteomics: current status and quantitative applications.

Expert review of proteomics 5, 353-360.

Li, K., and Smit, A. (2007). Proteomics of brain synapses and molecular dissection of synaptic

subdomains. Proteomics Clin Appl 1, 1476-1484.

Li, K., Chen, N., Klemmer, P., Koopmans, F., Karupothula, R., and Smit, A. (2012). Identifying true

protein complex constituents in interaction proteomics: the example of the DMXL2

protein complex. Proteomics 12, 2428-2432.

Li, K., Hornshaw, M., Van Der Schors, R., Watson, R., Tate, S., Casetta, B., Jimenez, C., Gouwenberg,

Y., Gundelfinger, E., Smalla, K.-H., et al. (2004). Proteomics analysis of rat brain

postsynaptic density. Implications of the diverse protein functional groups for the

integration of synaptic physiology. The Journal of biological chemistry 279, 987-1002.

Li, K., Klemmer, P., Smit, A. (2010). Interaction proteomics of synapse protein complexes. Anal.

Bioanal. Chemi. 397, 3195–3202.

Liu, X., Wen, F., Yang, J., Chen, L., and Wei, Y. (2010). A review of current applications of mass

spectrometry for neuroproteomics in epilepsy. Mass spectrometry reviews 29, 197-246.

Lonart, G., Janz, R., Johnson, K., and Südhof, T. (1998). Mechanism of action of rab3A in mossy fiber

LTP. Neuron 21, 1141-1150.

Page 9: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

131

Lonart, G., Schoch, S., Kaeser, P., Larkin, C., Südhof, T., and Linden, D. (2003). Phosphorylation of

RIM1alpha by PKA triggers presynaptic long-term potentiation at cerebellar parallel fiber

synapses. Cell 115, 49-60.

Lu, W., and Roche, K. (2012). Posttranslational regulation of AMPAR trafficking and function.

Current opinion in neurobiology 22, 470-479.

Lu, W., Shi, Y., Jackson, A., Bjorgan, K., During, M., Sprengel, R., Seeburg, P., and Nicoll, R. (2009).

Subunit composition of synaptic AMPARs revealed by a single-cell genetic approach.

Neuron 62, 254-268.

Lull, M., Freeman, W., VanGuilder, H., and Vrana, K. (2010). The use of neuroproteomics in drug

abuse research. Drug and alcohol dependence 107, 11-22.

Luscher, C., and Malenka, R. C. (2012). NMDA Receptor-Dependent Long-Term Potentiation and

Long-Term Depression (LTP/LTD). Cold Spring Harbor Perspectives in Biology 4.

Lüthi, A., Chittajallu, R., Duprat, F., Palmer, M., Benke, T., Kidd, F., Henley, J., Isaac, J., and

Collingridge, G. (1999). Hippocampal LTD expression involves a pool of AMPARs regulated

by the NSF-GluR2 interaction. Neuron 24, 389-399.

Mah, W., Ko, J., Nam, J., Han, K., Chung, W., and Kim, E. (2010). Selected SALM (synaptic

adhesion-like molecule) family proteins regulate synapse formation. The Journal of

neuroscience : the official journal of the Society for Neuroscience 30, 5559–5568.

Mallard, F., Tang, B., Galli, T., Tenza, D., Saint-Pol, A., Yue, X., Antony, C., Hong, W., Goud, B., and

Johannes, L. (2002). Early/recycling endosomes-to-TGN transport involves two SNARE

complexes and a Rab6 isoform. The Journal of cell biology 156, 653–664.

Malovannaya, A., Li, Y., Bulynko, Y., Jung, S. Y. et al., Streamlined analysis schema for

high-throughput identification of endogenous protein complexes. Proc. Natl. Acad. Sci.

U.S.A. 2010, 107, 2431–2436.

Malsam, J., Kreye, S., and Söllner, T. (2008). Membrane fusion: SNAREs and regulation. Cellular and

molecular life sciences : CMLS 65, 2814–2832.

Martens, S., Kozlov, M., and McMahon, H. (2007). How synaptotagmin promotes membrane fusion.

Science (New York, N.Y.) 316, 1205–1208.

Mao, L., Takamiya, K., Thomas, G., Lin, D.-T., and Huganir, R. (2010). GRIP1 and 2 regulate

activity-dependent AMPA receptor recycling via exocyst complex interactions. Proceedings

of the National Academy of Sciences of the United States of America 107, 19038-19043.

Martin, L., Blackstone, C., Levey, A., Huganir, R., and Price, D. (1993). AMPA glutamate receptor

subunits are differentially distributed in rat brain. Neuroscience 53, 327-358.

Masuda, E., Huang, B., Fisher, J., Luo, Y., and Scheller, R. (1998). Tomosyn binds t-SNARE proteins

via a VAMP-like coiled coil. Neuron 21, 479–480.

Maximov, A., Tang, J., Yang, X., Pang, Z., and Südhof, T. (2009). Complexin controls the force

transfer from SNARE complexes to membranes in fusion. Science (New York, N.Y.) 323,

Page 10: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

132

516–21.McMahon, H., and Boucrot, E. (2011). Molecular mechanism and physiological

functions of clathrin-mediated endocytosis. Nature reviews. Molecular cell biology 12,

517–533

McMahon, H., Missler, M., Li, C., and Südhof, T. (1995). Complexins: cytosolic proteins that regulate

SNAP receptor function. Cell 83, 111–119.

Missler, M., Südhof, T., and Biederer, T. (2012). Synaptic cell adhesion. Cold Spring Harbor

perspectives in biology 4, a005694.

Mochida, S. (2011). Activity-dependent regulation of synaptic vesicle exocytosis and presynaptic

short-term plasticity. Neuroscience research 70, 16-23.

Mohrmann, R., de Wit, H., Verhage, M., Neher, E., and Sørensen, J. (2010). Fast vesicle fusion in

living cells requires at least three SNARE complexes. Science (New York, N.Y.) 330,

502–505.

Montgomery, J., Zamorano, P., and Garner, C. (2004). MAGUKs in synapse assembly and function:

an emerging view. Cellular and molecular life sciences : CMLS 61, 911–929.

Moore, D., West, A., Dawson, V., and Dawson, T. (2005). Molecular pathophysiology of Parkinson’s

disease. Annual review of neuroscience 28, 57–87.

Morciano, M., Beckhaus, T., Karas, M., Zimmermann, H., and Volknandt, W. (2009). The proteome

of the presynaptic active zone: from docked synaptic vesicles to adhesion molecules and

maxi-channels. Journal of neurochemistry 108, 662–675.

Morgans, C., and Brandstätter, J. (2000). SNAP-25 is present on the Golgi apparatus of retinal

neurons. Neuroreport 11, 85–88.

Mukherjee, K., Yang, X., Gerber, S., Kwon, H.., Ho, A., Castillo, P., Liu, X., and Südhof, T. (2010).

Piccolo and bassoon maintain synaptic vesicle clustering without directly participating in

vesicle exocytosis. Proceedings of the National Academy of Sciences of the United States

of America 107, 6504-6509.

Muller, C. S., Haupt, A., Bildl, W., Schindler, J. et al., Quantitative proteomics of the Cav2 channel

nano-environments in the mammalian brain. Proc. Natl. Acad. Sci. U.S.A. 2010, 107,

14950–14957.

Nagano, F., Kawabe, H., Nakanishi, H., Shinohara, M. et al., Rabconnectin-3, a novel protein that

binds both GDP/GTP exchange protein and GTPase-activating protein for Rab3 small G

protein family. J. Biol. Chem. 2002, 277, 9629–9632.

Neves, G., Cooke, S., and Bliss, T. (2008). Synaptic plasticity, memory and the hippocampus: a neural

network approach to causality. Nature reviews Neuroscience 9, 65-75.

Newman, M. (2006). Modularity and community structure in networks. Proceedings of the National

Academy of Sciences of the United States of America 103, 8577–8582.

Nielsen, E., Christoforidis, S., Uttenweiler-Joseph, S., Miaczynska, M., Dewitte, F., Wilm, M., Hoflack,

B., and Zerial, M. (2000). Rabenosyn-5, a novel Rab5 effector, is complexed with hVPS45

Page 11: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

133

and recruited to endosomes through a FYVE finger domain. The Journal of cell biology 151,

601–612.

Offenhäuser, C., Lei, N., Roy, S., Collins, B., Stow, J., and Murray, R. (2011). Syntaxin 11 binds Vti1b

and regulates late endosome to lysosome fusion in macrophages. Traffic (Copenhagen,

Denmark) 12, 762–773.

Ogawa, Y., Oses-Prieto, J., Kim, M., Horresh, I., Peles, E., Burlingame, A., Trimmer, J., Meijer, D., and

Rasband, M. (2010). ADAM22, a Kv1 channel-interacting protein, recruits

membrane-associated guanylate kinases to juxtaparanodes of myelinated axons. The

Journal of neuroscience : the official journal of the Society for Neuroscience 30,

1038-1048.

Olsen, O., Moore, K., Nicoll, R., and Bredt, D. (2006). Synaptic transmission regulated by a

presynaptic MALS/Liprin-alpha protein complex. Current opinion in cell biology 18,

223-227.

O'Roak, B., and State, M. (2008). Autism genetics: strategies, challenges, and opportunities. Autism

research : official journal of the International Society for Autism Research 1, 4-17.

Pang, Z., and Südhof, T. (2010). Cell biology of Ca2+-triggered exocytosis. Current opinion in cell

biology 22, 496-505.

Peñagarikano, O., Abrahams, B., Herman, E., Winden, K., Gdalyahu, A., Dong, H., Sonnenblick, L.,

Gruver, R., Almajano, J., Bragin, A., et al. (2011). Absence of CNTNAP2 leads to epilepsy,

neuronal migration abnormalities, and core autism-related deficits. Cell 147, 235-246.

Peñagarikano, O., and Geschwind, D. (2012). What does CNTNAP2 reveal about autism spectrum

disorder? Trends in molecular medicine 18, 156-163.

Peng, J., Kim, M., Cheng, D., Duong, D., Gygi, S., and Sheng, M. (2004). Semiquantitative proteomic

analysis of rat forebrain postsynaptic density fractions by mass spectrometry. The Journal

of biological chemistry 279, 21003-21011.

Pernía-Andrade, A., and Jonas, P. (2011). The multiple faces of RIM. Neuron 69, 185-187.

Petralia, R., and Wenthold, R. (1992). Light and electron immunocytochemical localization of

AMPA-selective glutamate receptors in the rat brain. The Journal of comparative

neurology 318, 329-354.

Pflieger, D., Gonnet, F., de la Fuente van Bentem, S., Hirt, H. et al., Linking the proteins–elucidation

of proteome-scale networks using mass spectrometry. Mass Spectrom. Rev. 2011, 30,

268–297.

Pobbati, A., Razeto, A., Böddener, M., Becker, S., and Fasshauer, D. (2004). Structural basis for the

inhibitory role of tomosyn in exocytosis. The Journal of biological chemistry 279,

47192–47200.

Poliak, S., Salomon, D., Elhanany, H., Sabanay, H., Kiernan, B., Pevny, L., Stewart, C., Xu, X., Chiu,

S.-Y., Shrager, P., et al. (2003). Juxtaparanodal clustering of Shaker-like K+ channels in

Page 12: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

134

myelinated axons depends on Caspr2 and TAG-1. The Journal of cell biology 162,

1149-1160.

Pooley, R., Moynihan, K., Soukoulis, V., Reddy, S., Francis, R., Lo, C., Ma, L.-J., and Bader, D. (2008).

Murine CENPF interacts with syntaxin 4 in the regulation of vesicular transport. Journal of

cell science 121, 3413–3421.

Pryor, P., Mullock, B., Bright, N., Lindsay, M., Gray, S., Richardson, S., Stewart, A., James, D., Piper, R.,

and Luzio, J. (2004). Combinatorial SNARE complexes with VAMP7 or VAMP8 define

different late endocytic fusion events. EMBO reports 5, 590–595.

Raingo, J., Khvotchev, M., Liu, P., Darios, F., Li, Y., Ramirez, D., Adachi, M., Lemieux, P., Toth, K.,

Davletov, B., et al. (2012). VAMP4 directs synaptic vesicles to a pool that selectively

maintains asynchronous neurotransmission. Nature neuroscience 15, 738–745.

Regehr, W. Short-term presynaptic plasticity. (2012). Cold Spring Harbor perspectives in biology 4.

Reisinger, V., and Eichacker, L. (2007). How to analyze protein complexes by 2D blue native

SDS-PAGE. Proteomics 7 Suppl 1, 6-16.

Rekart, J., Meiri, K., and Routtenberg, A. (2005). Hippocampal-dependent memory is impaired in

heterozygous GAP-43 knockout mice. Hippocampus 15, 1-7.

Renner, M., Specht, C., and Triller, A. (2008). Molecular dynamics of postsynaptic receptors and

scaffold proteins. Current opinion in neurobiology 18, 532-540.

Rizo, J., and Rosenmund, C. (2008). Synaptic vesicle fusion. Nature structural & molecular biology 15,

665-674.

Rizo, J., and Südhof, T. (2012). The membrane fusion enigma: SNAREs, Sec1/Munc18 proteins, and

their accomplices--guilty as charged? Annual review of cell and developmental biology 28,

279–308.

Roche, Katherine W, and Isaac, John TR (2007). AMPA Receptors. Encyclopedia of Life Sciences (eLS).

John Wiley & Sons Ltd, Chichester.

Ronald, A., Simonoff, E., Kuntsi, J., Asherson, P., and Plomin, R. (2008). Evidence for overlapping

genetic influences on autistic and ADHD behaviours in a community twin sample. Journal

of child psychology and psychiatry, and allied disciplines 49, 535-542.

Rouach, N., Byrd, K., Petralia, R., Elias, G., Adesnik, H., Tomita, S., Karimzadegan, S., Kealey, C., Bredt,

D., and Nicoll, R. (2005). TARP gamma-8 controls hippocampal AMPAR number,

distribution and synaptic plasticity. Nature neuroscience 8, 1525-1533.

Saheki, Y., and De Camilli, P. (2012). Synaptic vesicle endocytosis. Cold Spring Harbor perspectives in

biology 4.

Scales, S., Hesser, B., Masuda, E., and Scheller, R. (2002). Amisyn, a novel syntaxin-binding protein

that may regulate SNARE complex assembly. The Journal of biological chemistry 277,

28271–28279.

Page 13: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

135

Schägger, H., and von Jagow, G. (1991). Blue native electrophoresis for isolation of membrane

protein complexes in enzymatically active form. Analytical biochemistry 199, 223-231.

Schägger, H., Cramer, W., and von Jagow, G. (1994). Analysis of molecular masses and oligomeric

states of protein complexes by blue native electrophoresis and isolation of membrane

protein complexes by two-dimensional native electrophoresis. Analytical biochemistry 217,

220-230.

Schaub, J., Lu, X., Doneske, B., Shin, Y.-K., and McNew, J. (2006). Hemifusion arrest by complexin is

relieved by Ca2+-synaptotagmin I. Nature structural & molecular biology 13, 748-750.

Schiavo, G., Stenbeck, G., Rothman, J., and Söllner, T. (1997). Binding of the synaptic vesicle

v-SNARE, synaptotagmin, to the plasma membrane t-SNARE, SNAP-25, can explain docked

vesicles at neurotoxin-treated synapses. Proceedings of the National Academy of Sciences

of the United States of America 94, 997–1001.

Schoch, S., and Gundelfinger, E. (2006). Molecular organization of the presynaptic active zone. Cell

and tissue research 326, 379-391.

Schweizer, Felix E (2001). Synapses. In: eLS. John Wiley & Sons Ltd, Chichester.

Schweizer, F.E. (2006) Neurotransmitter Release from Presynaptic Terminals. Encyclopedia of life

sciences (eLS). John Wiley & Sons Ltd, Chichester.

Schwenk, J., Harmel, N., Brechet, A., Zolles, G., Berkefeld, H., Müller, C., Bildl, W., Baehrens, D.,

Hüber, B., Kulik, A., et al. (2012). High-resolution proteomics unravel architecture and

molecular diversity of native AMPA receptor complexes. Neuron 74, 621-633.

Schwenk, J., Harmel, N., Zolles, G., Bildl, W., Kulik, A., Heimrich, B., Chisaka, O., Jonas, P., Schulte, U.,

Fakler, B., et al. (2009). Functional proteomics identify cornichon proteins as auxiliary

subunits of AMPA receptors. Science (New York, N.Y.) 323, 1313–1319.

Sethi, N., Yan, Y., Quek, D., Schupbach, T. et al., Rabconnectin-3 is a functional regulator of

mammalian Notch signaling. J. Biol. Chem. 2010, 285, 34757–34764.

Shanks, N., Savas, J., Maruo, T., Cais, O., Hirao, A., Oe, S., Ghosh, A., Noda, Y., Greger, I., Yates, J., et

al. (2012). Differences in AMPA and kainate receptor interactomes facilitate identification

of AMPA receptor auxiliary subunit GSG1L. Cell reports 1, 590–598.

Sharma, M., Burré, J., and Südhof, T. (2011). CSPα promotes SNARE-complex assembly by

chaperoning SNAP-25 during synaptic activity. Nature cell biology 13, 30–39.

Sheng, M., and Hoogenraad, C. (2007). The postsynaptic architecture of excitatory synapses: a more

quantitative view. Annual review of biochemistry 76, 823-847.

Sheth, P., Samak, G., Shull, J., Seth, A., and Rao, R. (2009). Protein phosphatase 2A plays a role in

hydrogen peroxide-induced disruption of tight junctions in Caco-2 cell monolayers. The

Biochemical journal 421, 59–70.

Siksou, L., Triller, A., and Marty, S. (2011). Ultrastructural organization of presynaptic terminals.

Current opinion in neurobiology 21, 261-268.

Page 14: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

136

Simonsen, A., Lippé, R., Christoforidis, S., Gaullier, J., Brech, A., Callaghan, J., Toh, B., Murphy, C.,

Zerial, M., and Stenmark, H. (1998). EEA1 links PI(3)K function to Rab5 regulation of

endosome fusion. Nature 394, 494–498.

Sinha, R., Ahmed, S., Jahn, R., and Klingauf, J. (2011). Two synaptobrevin molecules are sufficient for

vesicle fusion in central nervous system synapses. Proceedings of the National Academy of

Sciences of the United States of America 108, 14318–14323.

Sjöström, P., Rancz, E., Roth, A., and Häusser, M. (2008). Dendritic excitability and synaptic plasticity.

Physiological reviews 88, 769-840.

Smith, S., Renden, R., and von Gersdorff, H. (2008). Synaptic vesicle endocytosis: fast and slow

modes of membrane retrieval. Trends in neurosciences 31, 559-568.

Spijker, S. Chapter 2, Dissection of Rodent Brain Regions. Neuroproteomics. Humana Press. 2011,

159-168.

Spruston, N. (2008). Pyramidal neurons: dendritic structure and synaptic integration. Nature

reviews Neuroscience 9, 206-221.

State, M., and Levitt, P. (2011). The conundrums of understanding genetic risks for autism spectrum

disorders. Nature neuroscience 14, 1499-1506.

Stenmark, H. (2009). Rab GTPases as coordinators of vesicle traffic. Nature reviews Molecular cell

biology 10, 513-525.

Stevens, S., and Kobeissy, F. (2011). Neuroproteomics: deciphering brain dynamics. Electrophoresis

33, 3581.

Straub, C., and Tomita, S. (2012). The regulation of glutamate receptor trafficking and function by

TARPs and other transmembrane auxiliary subunits. Current opinion in neurobiology 22,

488-495.

Südhof, T. (2004). The synaptic vesicle cycle. Annual review of neuroscience 27, 509-547.

Südhof, T. (2006). Synaptic vesicles: an organelle comes of age. Cell 127, 671-673.

Südhof, T. (2012). The presynaptic active zone. Neuron 75, 11-25.

Südhof, T. (2013). A molecular machine for neurotransmitter release: synaptotagmin and beyond.

Nature medicine 19, 1227–1231.

Südhof, T., and Rizo, J. (2011). Synaptic vesicle exocytosis. Cold Spring Harbor perspectives in

biology 3.

Südhof, T., and Rothman, J. (2009). Membrane fusion: grappling with SNARE and SM proteins.

Science (New York, NY) 323, 474-477.

Suter, B., Kittanakom, S., and Stagljar, I. (2008). Two-hybrid technologies in proteomics research.

Current opinion in biotechnology 19, 316-323.

Sutton, M., and Schuman, E. (2006). Dendritic protein synthesis, synaptic plasticity, and memory.

Cell 127, 49-58.

Page 15: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

137

Swamy, M., Siegers, G., Minguet, S., Wollscheid, B., and Schamel, W. (2006). Blue native

polyacrylamide gel electrophoresis (BN-PAGE) for the identification and analysis of

multiprotein complexes. Science's STKE : signal transduction knowledge environment 2006,

pl4.

Takamori, S., Holt, M., Stenius, K., Lemke, E., Grønborg, M., Riedel, D., Urlaub, H., Schenck, S.,

Brügger, B., Ringler, P., Müller, S., Rammner, B., Gräter, F., Hub, J., De Groot, B., Mieskes,

G., Moriyama, Y., Klingauf, J., Grubmüller, H., Heuser, J., Wieland, F., and Jahn, R. (2006).

Molecular anatomy of a trafficking organelle. Cell 127, 831-846.

Tang, J., Maximov, A., Shin, O., Dai, H., Rizo, J., and Südhof, T. (2006). A complexin/synaptotagmin 1

switch controls fast synaptic vesicle exocytosis. Cell 126, 1175-1187.

Tao-Cheng, J., Du, J., and McBain, C. (2000). Snap-25 is polarized to axons and abundant along the

axolemma: an immunogold study of intact neurons. Journal of neurocytology 29, 67–77.

Tolar, L., and Pallanck, L. (1998). NSF function in neurotransmitter release involves rearrangement

of the SNARE complex downstream of synaptic vesicle docking. The Journal of

neuroscience : the official journal of the Society for Neuroscience 18, 10250–10256.

Tomita, S., Chen, L., Kawasaki, Y., Petralia, R., Wenthold, R., Nicoll, R., and Bredt, D. (2003).

Functional studies and distribution define a family of transmembrane AMPAR regulatory

proteins. The Journal of cell biology 161, 805-816.

Traka, M., Goutebroze, L., Denisenko, N., Bessa, M., Nifli, A., Havaki, S., Iwakura, Y., Fukamauchi, F.,

Watanabe, K., Soliven, B., et al. (2003). Association of TAG-1 with Caspr2 is essential for

the molecular organization of juxtaparanodal regions of myelinated fibers. The Journal of

cell biology 162, 1161-1172.

Traynelis, S., Wollmuth, L., McBain, C., Menniti, F., Vance, K., Ogden, K., Hansen, K., Yuan, H., Myers,

S., and Dingledine, R. (2010). Glutamate receptor ion channels: structure, regulation, and

function. Pharmacological reviews 62, 405-496.

Trinidad, J., Thalhammer, A., Specht, C., Lynn, A., Baker, P., Schoepfer, R., and Burlingame, A. (2008).

Quantitative analysis of synaptic phosphorylation and protein expression. Molecular &

cellular proteomics : MCP 7, 684–696.

Trinkle-Mulcahy, L. (2012). Resolving protein interactions and complexes by affinity purification

followed by label-based quantitative mass spectrometry. Proteomics 12, 1623-1638.

Van den Oever, M., Goriounova, N., Li, K., Van der Schors, R., Binnekade, R., Schoffelmeer, A.,

Mansvelder, H., Smit, A., Spijker, S., and De Vries, T. (2008). Prefrontal cortex AMPA

receptor plasticity is crucial for cue-induced relapse to heroin-seeking. Nature

neuroscience 11, 1053–1058.

Vandenberghe, W., Nicoll, R., and Bredt, D. (2005). Stargazin is an AMPA receptor auxiliary subunit.

Proceedings of the National Academy of Sciences of the United States of America 102,

485–490.

Page 16: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

138

Verhage, M., Maia, A., Plomp, J., Brussaard, A., Heeroma, J., Vermeer, H., Toonen, R., Hammer, R.,

van den Berg, T., Missler, M., et al. (2000). Synaptic assembly of the brain in the absence

of neurotransmitter secretion. Science (New York, N.Y.) 287, 864–9.

Verhage, M., and Sørensen, J. (2008). Vesicle docking in regulated exocytosis. Traffic (Copenhagen,

Denmark) 9, 1414-1424.

Volkel, P., Le Faou, P., Angrand, P. O., Interaction proteomics: characterization of protein complexes

using tandem affinity purification-mass spectrometry. Biochem. Soc. Trans. 2010, 38,

883–887.

von Engelhardt, J., Mack, V., Sprengel, R., Kavenstock, N., Li, K., Stern-Bach, Y., Smit, A., Seeburg, P.,

and Monyer, H. (2010). CKAMP44: a brain-specific protein attenuating short-term synaptic

plasticity in the dentate gyrus. Science (New York, NY) 327, 1518-1522.

Wang, C., Chang, K., Petralia, R., Wang, Y., Seabold, G., and Wenthold, R. (2006). A novel family of

adhesion-like molecules that interacts with the NMDA receptor. The Journal of

neuroscience : the official journal of the Society for Neuroscience 26, 2174–2183.

Wang, P., Seabold, G., and Wenthold, R. (2008). Synaptic adhesion-like molecules (SALMs) promote

neurite outgrowth. Molecular and cellular neurosciences 39, 83–94.

Wang, T., Ming, Z., Xiaochun, W., and Hong, W. (2011). Rab7: role of its protein interaction cascades

in endo-lysosomal traffic. Cellular signalling 23, 516–21.Wang, Y., and Tang, B. (2006).

SNAREs in neurons--beyond synaptic vesicle exocytosis (Review). Molecular membrane

biology 23, 377–384.

Washbourne, P., Thompson, P., Carta, M., Costa, E., Mathews, J., Lopez-Benditó, G., Molnár, Z.,

Becher, M., Valenzuela, C., Partridge, L., et al. (2002). Genetic ablation of the t-SNARE

SNAP-25 distinguishes mechanisms of neuroexocytosis. Nature neuroscience 5, 19–26.

Watanabe, Y., Katayama, N., Takeuchi, K., Togano, T., Itoh, R., Sato, M., Yamazaki, M., Abe, M., Sato,

T., Oda, K., et al. (2013). Point Mutation in Syntaxin-1A Causes Abnormal Vesicle Recycling,

Behaviors, and Short Term Plasticity. The Journal of biological chemistry 288,

34906–34919.

Wendler, F., Page, L., Urbé, S., and Tooze, S. (2001). Homotypic fusion of immature secretory

granules during maturation requires syntaxin 6. Molecular biology of the cell 12,

1699–1709.

Winter, U., Chen, X., and Fasshauer, D. (2009). A conserved membrane attachment site in

alpha-SNAP facilitates N-ethylmaleimide-sensitive factor (NSF)-driven SNARE complex

disassembly. The Journal of biological chemistry 284, 31817-31826.

Wittig, I., and Schägger, H. (2008). Features and applications of blue-native and clear-native

electrophoresis. Proteomics 8, 3974-3990.

Wittig, I., Braun, H., and Schägger, H. (2006). Blue native PAGE. Nature protocols 1, 418-428.

Wodak, S. J., Pu, S., Vlasblom, J., Seraphin, B., Challenges and rewards of interaction proteomics.

Mol. Cell. Proteomics 2009, 8, 3–18.

Page 17: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

References

139

Wolfe, M., and Selkoe, D. (2010). Giving Alzheimer’s the old one-two. Cell 142, 194–196.

Xu, J., Luo, F., Zhang, Z., Xue, L., Wu, X.-S., Chiang, H.-C., Shin, W., and Wu, L.-G. (2013). SNARE

proteins synaptobrevin, SNAP-25, and syntaxin are involved in rapid and slow endocytosis

at synapses. Cell reports 3, 1414–1421.

Yamagata, M., Sanes, J., and Weiner, J. (2003). Synaptic adhesion molecules. Current opinion in cell

biology 15, 621–632.

Yan, Y., Denef, N., Schupbach, T., The vacuolar proton pump, V-ATPase, is required for notch

signaling and endosomal trafficking in Drosophila. Dev. Cell 2009, 17, 387–402.

Young, S. (2005). Proteolysis of SNARE proteins alters facilitation and depression in a specific way.

Proceedings of the National Academy of Sciences of the United States of America 102,

2614-2619.

Zhang, T., and Hong, W. (2001). Ykt6 forms a SNARE complex with syntaxin 5, GS28, and Bet1 and

participates in a late stage in endoplasmic reticulum-Golgi transport. The Journal of

biological chemistry 276, 27480–27487.

Zhang, X., Jia, N., Zhao, X., Tang, G., Guan, L., Wang, D., Sun, H., Li, H., and Zhu, Z. (2013).

Involvement of pGluR1, EAAT2 and EAAT3 in offspring depression induced by prenatal

stress. Neuroscience 250, 333–341.

Zhang, Z., Wang, D., Sun, T., Xu, J., Chiang, H.-C., Shin, W., and Wu, L.-G. (2013). The SNARE proteins

SNAP25 and synaptobrevin are involved in endocytosis at hippocampal synapses. The

Journal of neuroscience : the official journal of the Society for Neuroscience 33,

9169–9175.

Page 18: References - research.vu.nl Reference.pdf · References 125 Blumstein, J., V. Faundez, F. Nakatsu, T. Saito, H. Ohno, and R.B. Kelly. 2001. The neuronal form of adaptor protein-3

140