The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study (406 views)
Bba-Gen Subjects (ISSN: 0005-2736, 0006-3002e, 0005-2736print), 2013 Nov; 1828(11): 2637-2645.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 3.498, 5-year impact factor: 3.542
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84881513551&partnerID=40&md5=8ad82d9f932bc9c8f9494ac07d53d8a4
Keywords: Cd3 ζζ, Lipid Raft, Membrane Protein, Molecular Dynamics Popc, Transmembrane Helix, Cd3 Antigen, Cd3 Antigen Zeta Zeta, T Lymphocyte Receptor, Unclassified Drug, Amino Acid Sequence, Amino Terminal Sequence, Article, Binding Affinity, Carboxy Terminal Sequence, Controlled Study, Cytoplasm, Disulfide Bond, Hydrophobicity, Lipid Bilayer, Nuclear Magnetic Resonance, Oxygenation, Priority Journal, Protein Analysis, Protein Binding, Protein Conformation, Protein Domain, Protein Protein Interaction, Protein Secondary Structure, Protein Stability, Protein Structure, Sequence Alignment, Signal Transduction, Cell Receptor, Chol, Cholesterol, Palmitoyl-Oleoyl-Phosphatidylcholine, Radial Distribution Function, Root Mean Square Deviation, Sphingomyelin, Tcrt, 2-Dipalmitoylphosphatidylcholine, Dimerization, Membrane Microdomains, Models, Molecular Dynamics Simulation, Molecular Sequence Data, Sequence Homology,
Affiliations:
*** IBB - CNR ***
Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET), Chacabuco 461, S. M. de Tucumán, Tucumán T4000ILI, Argentina
Department of Chemical Sciences, University of Naples federico II, via Cintia, 80126 Napoli, Italy
Institute of Protein Biochemistry, CNR, via P. Castellino 111, 80131 Napoli, Italy
Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, 80100 Napoli, Italy
References:
Simons, K., Ikonen, E., Functional rafts in cell membranes (1997) Nature, 387, pp. 569-57
Lingwood, D., Simons, K., Lipid rafts as a membrane-organizing principle (2010) Science, 327, pp. 46-50. , (New York, N.Y.)
Fleishman, S.J., Unger, V.M., Ben-Tal, N., Transmembrane protein structures without X-rays (2006) Trends Biochem. Sci., 31, pp. 106-113
Stansfeld, P.J., Sansom, M.S., Molecular simulation approaches to membrane proteins (2011) Structure, 19, pp. 1562-1572
Khalid, S., Bond, P.J., Multiscale molecular dynamics simulations of membrane proteins (2013) Methods Mol. Biol., 924, pp. 635-657
Dror, R.O., Dirks, R.M., Grossman, J.P., Xu, H., Shaw, D.E., Biomolecular simulation: A computational microscope for molecular biology (2012) Annu. Rev. Biophys., 41, pp. 429-452
Krepkiy, D., Mihailescu, M., Freites, J.A., Schow, E.V., Worcester, D.L., Gawrisch, K., Tobias, D.J., Swartz, K.J., Structure and hydration of membranes embedded with voltage-sensing domains (2009) Nature, 462, pp. 473-479
Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., Pastor, R.W., Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types (2010) J. Phys. Chem. B, 114, pp. 7830-7843
Hurst, D.P., Schmeisser, M., Reggio, P.H., Endogenous lipid activated G protein-coupled receptors: Emerging structural features from crystallography and molecular dynamics simulations (2013) Chem. Phys. Lipids, 169, pp. 46-56
Aittoniemi, J., Niemela, P.S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., Insight into the putative specific interactions between cholesterol, sphingomyelin, and palmitoyl-oleoyl phosphatidylcholine (2007) Biophys. J., 92, pp. 1125-1137
Taddese, B., Simpson, L.M., Wall, I.D., Blaney, F.E., Kidley, N.J., Clark, H.S., Smith, R.E., Reynolds, C.A., G-protein-coupled receptor dynamics: Dimerization and activation models compared with experiment (2012) Biochem. Soc. Trans., 40, pp. 394-399
Cordomi, A., Perez, J.J., Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers (2007) J. Phys. Chem. B, 111, pp. 7052-7063
Zhang, Z., Bhide, S.Y., Berkowitz, M.L., Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol (2007) J. Phys. Chem. B, 111, pp. 12888-12897
Róg, T., Murzyn, K., Karttunen, M., Pasenkiewicz-Gierula, M., Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies (2008) J. Pept. Sci., 14, pp. 374-382
Niemela, P.S., Ollila, S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., Assessing the nature of lipid raft membranes (2007) PLoS Comput. Biol., 3, p. 34
Bjelkmar, P., Niemela, P.S., Vattulainen, I., Lindahl, E., Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel (2009) PLoS Comput. Biol., 5, p. 1000289
Call, M.E., Schnell, J.R., Xu, C., Lutz, R.A., Chou, J.J., Wucherpfennig, K.W., The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor (2006) Cell, 127, pp. 355-368
Call, M.E., Pyrdol, J., Wiedmann, M., Wucherpfennig, K.W., The organizing principle in the formation of the T cell receptor-CD3 complex (2002) Cell, 111, pp. 967-979
Call, M.E., Wucherpfennig, K.W., Common themes in the assembly and architecture of activating immune receptors (2007) Nat. Rev. Immunol., 7, pp. 841-845
Palacios, E.H., Weiss, A., Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation (2004) Oncogene, 23, pp. 7990-8000
Zhang, H., Cordoba, S.P., Dushek, O., Van Der Merwe, P.A., Basic residues in the T-cell receptor zeta cytoplasmic domain mediate membrane association and modulate signaling (2011) Proc. Natl. Acad. Sci. U. S. A., 108, pp. 19323-19328
Horejsi, V., Lipid rafts and their roles in T-cell activation (2005) Microbes. Infect., 7, pp. 310-316
Harder, T., The T cell plasma membrane lipid bilayer stages TCR-proximal signaling events (2012) Front. Immunol., 3, p. 50
Zech, T., Ejsing, C.S., Gaus, K., De Wet, B., Shevchenko, A., Simons, K., Harder, T., Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling (2009) EMBO J., 28, pp. 466-476
Gaus, K., Chklovskaia, E., Fazekas De St Groth, B., Jessup, W., Harder, T., Condensation of the plasma membrane at the site of T lymphocyte activation (2005) J. Cell Biol., 171, pp. 121-131
Owen, A.D., Schapira, A.H., Jenner, P., Marsden, C.D., Oxidative stress and Parkinson's disease (1996) Ann. N. Y. Acad. Sci., 786, pp. 217-223
Rentero, C., Zech, T., Quinn, C.M., Engelhardt, K., Williamson, D., Grewal, T., Jessup, W., Gaus, K., Functional implications of plasma membrane condensation for T cell activation (2008) PLoS One, 3, p. 2262
Otahal, P., Pata, S., Angelisova, P., Horejsi, V., Brdicka, T., The effects of membrane compartmentalization of csk on TCR signaling (2011) Biochim. Biophys. Acta, 1813, pp. 367-376
Sharma, S., Juffer, A.H., An atomistic model for assembly of transmembrane domain of T cell receptor complex (2013) J. Am. Chem. Soc., 135, pp. 2188-2197
Merlino, A., Varriale, S., Coscia, M.R., Mazzarella, L., Oreste, U., Structure and dimerization of the teleost transmembrane immunoglobulin region (2008) J. Mol. Graph. Model., 27, pp. 401-407
Varriale, S., Merlino, A., Coscia, M.R., Mazzarella, L., Oreste, U., An evolutionary conserved motif is responsible for immunoglobulin heavy chain packing in the B cell membrane (2010) Mol. Phylogenet. Evol., 57, pp. 1238-1244
Vaccaro, L., Cross, K.J., Kleinjung, J., Straus, S.K., Thomas, D.J., Wharton, S.A., Skehel, J.J., Fraternali, F., Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers (2005) Biophys. J., 88, pp. 25-36
Mackerell, A.D.J., Bashford, D.M., Dunbrack, R.L., Evanseck, J., Field, M.J.J.D., Fischer, S., Gao, J., Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins (1998) J. Phys. Chem. B, 102, p. 3586
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Schulten, K., Scalable molecular dynamics with NAMD (2005) J. Comput. Chem., 26, pp. 1781-1802
Darden, T., York, D., Pedersen, L., Particle mesh Ewald: An N×log(N) method for Ewald sums in large systems (1993) J. Chem. Phys., 98, p. 10089
Harvey, M., Giupponi, G., De Fabritiis, G., ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale (2009) J. Chem. Theory Comput., 5, p. 1632
Harvey, M.J., De Fabritiis, G., An implementation of the smooth particle mesh Ewald method on GPU hardware (2009) J. Chem. Theory Comput., 5, pp. 2371-2377
Feenstra, K.A., Hess, B., Berendsen, H.J.C., Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems (1999) J. Comput. Chem., 20, p. 786
Merlino, A., Vitagliano, L., Ceruso, M.A., Mazzarella, L., Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin (2003) Proteins, 53, pp. 101-110
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Amadei, A., Linssen, A.B., Berendsen, H.J., Essential dynamics of proteins (1993) Proteins, 17, pp. 412-425
Merlino, A., Ceruso, M.A., Vitagliano, L., Mazzarella, L., Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A (2005) Biophys. J., 88, pp. 2003-2012
Renthal, R., Buried water molecules in helical transmembrane proteins (2008) Protein Sci., 17, pp. 293-298
Minguet, S., Swamy, M., Schamel, W.W., The short length of the extracellular domain of zeta is crucial for T cell antigen receptor function (2008) Immunol. Lett., 116, pp. 195-202
Aivazian, D., Stern, L.J., Phosphorylation of T cell receptor zeta is regulated by a lipid dependent folding transition (2000) Nat. Struct. Biol., 7, pp. 1023-1026
Fleishman, S. J., Unger, V. M., Ben-Tal, N., Transmembrane protein structures without X-rays (2006) Trends Biochem. Sci., 31, pp. 106-113
Stansfeld, P. J., Sansom, M. S., Molecular simulation approaches to membrane proteins (2011) Structure, 19, pp. 1562-1572
Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H., Shaw, D. E., Biomolecular simulation: A computational microscope for molecular biology (2012) Annu. Rev. Biophys., 41, pp. 429-452
Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., Pastor, R. W., Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types (2010) J. Phys. Chem. B, 114, pp. 7830-7843
Hurst, D. P., Schmeisser, M., Reggio, P. H., Endogenous lipid activated G protein-coupled receptors: Emerging structural features from crystallography and molecular dynamics simulations (2013) Chem. Phys. Lipids, 169, pp. 46-56
R g, T., Murzyn, K., Karttunen, M., Pasenkiewicz-Gierula, M., Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies (2008) J. Pept. Sci., 14, pp. 374-382
Niemela, P. S., Ollila, S., Hyvonen, M. T., Karttunen, M., Vattulainen, I., Assessing the nature of lipid raft membranes (2007) PLoS Comput. Biol., 3, p. 34
Call, M. E., Schnell, J. R., Xu, C., Lutz, R. A., Chou, J. J., Wucherpfennig, K. W., The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor (2006) Cell, 127, pp. 355-368
Call, M. E., Pyrdol, J., Wiedmann, M., Wucherpfennig, K. W., The organizing principle in the formation of the T cell receptor-CD3 complex (2002) Cell, 111, pp. 967-979
Call, M. E., Wucherpfennig, K. W., Common themes in the assembly and architecture of activating immune receptors (2007) Nat. Rev. Immunol., 7, pp. 841-845
Palacios, E. H., Weiss, A., Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation (2004) Oncogene, 23, pp. 7990-8000
Owen, A. D., Schapira, A. H., Jenner, P., Marsden, C. D., Oxidative stress and Parkinson's disease (1996) Ann. N. Y. Acad. Sci., 786, pp. 217-223
Mackerell, A. D. J., Bashford, D. M., Dunbrack, R. L., Evanseck, J., Field, M. J. J. D., Fischer, S., Gao, J., Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins (1998) J. Phys. Chem. B, 102, p. 3586
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Schulten, K., Scalable molecular dynamics with NAMD (2005) J. Comput. Chem., 26, pp. 1781-1802
Harvey, M. J., De Fabritiis, G., An implementation of the smooth particle mesh Ewald method on GPU hardware (2009) J. Chem. Theory Comput., 5, pp. 2371-2377
Feenstra, K. A., Hess, B., Berendsen, H. J. C., Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems (1999) J. Comput. Chem., 20, p. 786
Bba-Gen Subjects (ISSN: 0005-2736, 0006-3002e, 0005-2736print), 2013 Nov; 1828(11): 2637-2645.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 3.498, 5-year impact factor: 3.542
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84881513551&partnerID=40&md5=8ad82d9f932bc9c8f9494ac07d53d8a4
Keywords: Cd3 ζζ, Lipid Raft, Membrane Protein, Molecular Dynamics Popc, Transmembrane Helix, Cd3 Antigen, Cd3 Antigen Zeta Zeta, T Lymphocyte Receptor, Unclassified Drug, Amino Acid Sequence, Amino Terminal Sequence, Article, Binding Affinity, Carboxy Terminal Sequence, Controlled Study, Cytoplasm, Disulfide Bond, Hydrophobicity, Lipid Bilayer, Nuclear Magnetic Resonance, Oxygenation, Priority Journal, Protein Analysis, Protein Binding, Protein Conformation, Protein Domain, Protein Protein Interaction, Protein Secondary Structure, Protein Stability, Protein Structure, Sequence Alignment, Signal Transduction, Cell Receptor, Chol, Cholesterol, Palmitoyl-Oleoyl-Phosphatidylcholine, Radial Distribution Function, Root Mean Square Deviation, Sphingomyelin, Tcrt, 2-Dipalmitoylphosphatidylcholine, Dimerization, Membrane Microdomains, Models, Molecular Dynamics Simulation, Molecular Sequence Data, Sequence Homology,
Affiliations:
*** IBB - CNR ***
Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET), Chacabuco 461, S. M. de Tucumán, Tucumán T4000ILI, Argentina
Department of Chemical Sciences, University of Naples federico II, via Cintia, 80126 Napoli, Italy
Institute of Protein Biochemistry, CNR, via P. Castellino 111, 80131 Napoli, Italy
Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, 80100 Napoli, Italy
References:
Simons, K., Ikonen, E., Functional rafts in cell membranes (1997) Nature, 387, pp. 569-57
Lingwood, D., Simons, K., Lipid rafts as a membrane-organizing principle (2010) Science, 327, pp. 46-50. , (New York, N.Y.)
Fleishman, S.J., Unger, V.M., Ben-Tal, N., Transmembrane protein structures without X-rays (2006) Trends Biochem. Sci., 31, pp. 106-113
Stansfeld, P.J., Sansom, M.S., Molecular simulation approaches to membrane proteins (2011) Structure, 19, pp. 1562-1572
Khalid, S., Bond, P.J., Multiscale molecular dynamics simulations of membrane proteins (2013) Methods Mol. Biol., 924, pp. 635-657
Dror, R.O., Dirks, R.M., Grossman, J.P., Xu, H., Shaw, D.E., Biomolecular simulation: A computational microscope for molecular biology (2012) Annu. Rev. Biophys., 41, pp. 429-452
Krepkiy, D., Mihailescu, M., Freites, J.A., Schow, E.V., Worcester, D.L., Gawrisch, K., Tobias, D.J., Swartz, K.J., Structure and hydration of membranes embedded with voltage-sensing domains (2009) Nature, 462, pp. 473-479
Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., Pastor, R.W., Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types (2010) J. Phys. Chem. B, 114, pp. 7830-7843
Hurst, D.P., Schmeisser, M., Reggio, P.H., Endogenous lipid activated G protein-coupled receptors: Emerging structural features from crystallography and molecular dynamics simulations (2013) Chem. Phys. Lipids, 169, pp. 46-56
Aittoniemi, J., Niemela, P.S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., Insight into the putative specific interactions between cholesterol, sphingomyelin, and palmitoyl-oleoyl phosphatidylcholine (2007) Biophys. J., 92, pp. 1125-1137
Taddese, B., Simpson, L.M., Wall, I.D., Blaney, F.E., Kidley, N.J., Clark, H.S., Smith, R.E., Reynolds, C.A., G-protein-coupled receptor dynamics: Dimerization and activation models compared with experiment (2012) Biochem. Soc. Trans., 40, pp. 394-399
Cordomi, A., Perez, J.J., Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers (2007) J. Phys. Chem. B, 111, pp. 7052-7063
Zhang, Z., Bhide, S.Y., Berkowitz, M.L., Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol (2007) J. Phys. Chem. B, 111, pp. 12888-12897
Róg, T., Murzyn, K., Karttunen, M., Pasenkiewicz-Gierula, M., Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies (2008) J. Pept. Sci., 14, pp. 374-382
Niemela, P.S., Ollila, S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., Assessing the nature of lipid raft membranes (2007) PLoS Comput. Biol., 3, p. 34
Bjelkmar, P., Niemela, P.S., Vattulainen, I., Lindahl, E., Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel (2009) PLoS Comput. Biol., 5, p. 1000289
Call, M.E., Schnell, J.R., Xu, C., Lutz, R.A., Chou, J.J., Wucherpfennig, K.W., The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor (2006) Cell, 127, pp. 355-368
Call, M.E., Pyrdol, J., Wiedmann, M., Wucherpfennig, K.W., The organizing principle in the formation of the T cell receptor-CD3 complex (2002) Cell, 111, pp. 967-979
Call, M.E., Wucherpfennig, K.W., Common themes in the assembly and architecture of activating immune receptors (2007) Nat. Rev. Immunol., 7, pp. 841-845
Palacios, E.H., Weiss, A., Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation (2004) Oncogene, 23, pp. 7990-8000
Zhang, H., Cordoba, S.P., Dushek, O., Van Der Merwe, P.A., Basic residues in the T-cell receptor zeta cytoplasmic domain mediate membrane association and modulate signaling (2011) Proc. Natl. Acad. Sci. U. S. A., 108, pp. 19323-19328
Horejsi, V., Lipid rafts and their roles in T-cell activation (2005) Microbes. Infect., 7, pp. 310-316
Harder, T., The T cell plasma membrane lipid bilayer stages TCR-proximal signaling events (2012) Front. Immunol., 3, p. 50
Zech, T., Ejsing, C.S., Gaus, K., De Wet, B., Shevchenko, A., Simons, K., Harder, T., Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling (2009) EMBO J., 28, pp. 466-476
Gaus, K., Chklovskaia, E., Fazekas De St Groth, B., Jessup, W., Harder, T., Condensation of the plasma membrane at the site of T lymphocyte activation (2005) J. Cell Biol., 171, pp. 121-131
Owen, A.D., Schapira, A.H., Jenner, P., Marsden, C.D., Oxidative stress and Parkinson's disease (1996) Ann. N. Y. Acad. Sci., 786, pp. 217-223
Rentero, C., Zech, T., Quinn, C.M., Engelhardt, K., Williamson, D., Grewal, T., Jessup, W., Gaus, K., Functional implications of plasma membrane condensation for T cell activation (2008) PLoS One, 3, p. 2262
Otahal, P., Pata, S., Angelisova, P., Horejsi, V., Brdicka, T., The effects of membrane compartmentalization of csk on TCR signaling (2011) Biochim. Biophys. Acta, 1813, pp. 367-376
Sharma, S., Juffer, A.H., An atomistic model for assembly of transmembrane domain of T cell receptor complex (2013) J. Am. Chem. Soc., 135, pp. 2188-2197
Merlino, A., Varriale, S., Coscia, M.R., Mazzarella, L., Oreste, U., Structure and dimerization of the teleost transmembrane immunoglobulin region (2008) J. Mol. Graph. Model., 27, pp. 401-407
Varriale, S., Merlino, A., Coscia, M.R., Mazzarella, L., Oreste, U., An evolutionary conserved motif is responsible for immunoglobulin heavy chain packing in the B cell membrane (2010) Mol. Phylogenet. Evol., 57, pp. 1238-1244
Vaccaro, L., Cross, K.J., Kleinjung, J., Straus, S.K., Thomas, D.J., Wharton, S.A., Skehel, J.J., Fraternali, F., Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers (2005) Biophys. J., 88, pp. 25-36
Mackerell, A.D.J., Bashford, D.M., Dunbrack, R.L., Evanseck, J., Field, M.J.J.D., Fischer, S., Gao, J., Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins (1998) J. Phys. Chem. B, 102, p. 3586
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Schulten, K., Scalable molecular dynamics with NAMD (2005) J. Comput. Chem., 26, pp. 1781-1802
Darden, T., York, D., Pedersen, L., Particle mesh Ewald: An N×log(N) method for Ewald sums in large systems (1993) J. Chem. Phys., 98, p. 10089
Harvey, M., Giupponi, G., De Fabritiis, G., ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale (2009) J. Chem. Theory Comput., 5, p. 1632
Harvey, M.J., De Fabritiis, G., An implementation of the smooth particle mesh Ewald method on GPU hardware (2009) J. Chem. Theory Comput., 5, pp. 2371-2377
Feenstra, K.A., Hess, B., Berendsen, H.J.C., Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems (1999) J. Comput. Chem., 20, p. 786
Merlino, A., Vitagliano, L., Ceruso, M.A., Mazzarella, L., Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin (2003) Proteins, 53, pp. 101-110
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Amadei, A., Linssen, A.B., Berendsen, H.J., Essential dynamics of proteins (1993) Proteins, 17, pp. 412-425
Merlino, A., Ceruso, M.A., Vitagliano, L., Mazzarella, L., Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A (2005) Biophys. J., 88, pp. 2003-2012
Renthal, R., Buried water molecules in helical transmembrane proteins (2008) Protein Sci., 17, pp. 293-298
Minguet, S., Swamy, M., Schamel, W.W., The short length of the extracellular domain of zeta is crucial for T cell antigen receptor function (2008) Immunol. Lett., 116, pp. 195-202
Aivazian, D., Stern, L.J., Phosphorylation of T cell receptor zeta is regulated by a lipid dependent folding transition (2000) Nat. Struct. Biol., 7, pp. 1023-1026
Fleishman, S. J., Unger, V. M., Ben-Tal, N., Transmembrane protein structures without X-rays (2006) Trends Biochem. Sci., 31, pp. 106-113
Stansfeld, P. J., Sansom, M. S., Molecular simulation approaches to membrane proteins (2011) Structure, 19, pp. 1562-1572
Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H., Shaw, D. E., Biomolecular simulation: A computational microscope for molecular biology (2012) Annu. Rev. Biophys., 41, pp. 429-452
Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., Pastor, R. W., Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types (2010) J. Phys. Chem. B, 114, pp. 7830-7843
Hurst, D. P., Schmeisser, M., Reggio, P. H., Endogenous lipid activated G protein-coupled receptors: Emerging structural features from crystallography and molecular dynamics simulations (2013) Chem. Phys. Lipids, 169, pp. 46-56
R g, T., Murzyn, K., Karttunen, M., Pasenkiewicz-Gierula, M., Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies (2008) J. Pept. Sci., 14, pp. 374-382
Niemela, P. S., Ollila, S., Hyvonen, M. T., Karttunen, M., Vattulainen, I., Assessing the nature of lipid raft membranes (2007) PLoS Comput. Biol., 3, p. 34
Call, M. E., Schnell, J. R., Xu, C., Lutz, R. A., Chou, J. J., Wucherpfennig, K. W., The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor (2006) Cell, 127, pp. 355-368
Call, M. E., Pyrdol, J., Wiedmann, M., Wucherpfennig, K. W., The organizing principle in the formation of the T cell receptor-CD3 complex (2002) Cell, 111, pp. 967-979
Call, M. E., Wucherpfennig, K. W., Common themes in the assembly and architecture of activating immune receptors (2007) Nat. Rev. Immunol., 7, pp. 841-845
Palacios, E. H., Weiss, A., Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation (2004) Oncogene, 23, pp. 7990-8000
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The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study
Plasma membrane lipids significantly affect assembly and activity of many signaling networks. The present work is aimed at analyzing, by molecular dynamics simulations, the structure and dynamics of the CD3 zeta zeta dimer in palmitoyl-oleoyl-phosphatidylcholine bilayer (POPC) and in POPC/cholesterol/sphingomyelin bilayer, which resembles the raft membrane microdomain supposed to be the site of the signal transducing machinery. Both POPC and raft-like environment produce significant alterations in structure and flexibility of the CD3 zeta zeta with respect to nuclear magnetic resonance (NMR) model: the dimer is more compact, its secondary structure is slightly less ordered, the arrangement-of the Asp6 pair, which is important for binding to the Arg residue in the alpha chain of the T cell receptor (TCR), is stabilized by water molecules. Different interactions of charged residues with lipids at the lipid-cytoplasm boundary occur when the two environments are compared. Furthermore, in contrast to what is observed in POPC, in the raft-like environment correlated motions between transmembrane and cytoplasmic regions are observed. Altogether the data suggest that when the TCR complex resides in the raft domains, the CD3 zeta zeta dimer assumes a specific conformation probably necessary to the correct signal transduction. (C) 2013 Elsevier B. V. All rights reserved
Plasma membrane lipids significantly affect assembly and activity of many signaling networks. The present work is aimed at analyzing, by molecular dynamics simulations, the structure and dynamics of the CD3 zeta zeta dimer in palmitoyl-oleoyl-phosphatidylcholine bilayer (POPC) and in POPC/cholesterol/sphingomyelin bilayer, which resembles the raft membrane microdomain supposed to be the site of the signal transducing machinery. Both POPC and raft-like environment produce significant alterations in structure and flexibility of the CD3 zeta zeta with respect to nuclear magnetic resonance (NMR) model: the dimer is more compact, its secondary structure is slightly less ordered, the arrangement-of the Asp6 pair, which is important for binding to the Arg residue in the alpha chain of the T cell receptor (TCR), is stabilized by water molecules. Different interactions of charged residues with lipids at the lipid-cytoplasm boundary occur when the two environments are compared. Furthermore, in contrast to what is observed in POPC, in the raft-like environment correlated motions between transmembrane and cytoplasmic regions are observed. Altogether the data suggest that when the TCR complex resides in the raft domains, the CD3 zeta zeta dimer assumes a specific conformation probably necessary to the correct signal transduction. (C) 2013 Elsevier B. V. All rights reserved
The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study
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The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study
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Russo Krauss I, Merlino A, Vergara A, Sica F
* An overview of biological macromolecule crystallization (918 views)
Int J Mol Sc (ISSN: 1422-0067, 1661-6596, 1422-0067electronic), 2013 May 31; 14(6): 11643-11691.
Impact Factor: 2.339
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Esposito L, Balasco N, De Simone A, Berisio R, Vitagliano L
* Interplay between peptide bond geometrical parameters in nonglobular structural contexts (407 views)
Biomed Res Int (ISSN: 2314-6133, 2314-6141, 2314-6141electronic), 2013; 2013: N/D-N/D.
Impact Factor: 2.13
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Berisio R
* Learning from pathogens: Exploiting host-pathogen liaison for therapeutic development (364 views)
Curr Protein Pept Sci (ISSN: 1389-2037, 1389-2037linking), 2012 Dec; 13(8): 697-698.
Impact Factor: 2.326
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Galdiero S, Falanga A, Cantisani M, Tarallo R, della Pepa ME, D'Oriano V, Galdiero M
* Microbe-Host Interactions: Structure and Role of Gram-Negative Bacterial Porins (430 views)
Curr Protein Pept Sci (ISSN: 1389-2037, 1389-2037linking), 2012 Dec; 13(8): 843-854.
Impact Factor: 2.326
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Galdiero S, Russo L, Falanga A, Cantisani M, Vitiello M, Fattorusso R, Malgieri G, Galdiero M, Isernia C
* Structure and Orientation of the gH625-644 Membrane Interacting Region of Herpes Simplex Virus Type 1 in a Membrane Mimetic System (331 views)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2012 Apr 10; 51(14): 3121-3128.
Impact Factor: 3.377
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Esposito C, Cantisani M, D'Auria G, Falcigno L, Pedone E, Galdiero S, Berisio R
* Mapping key interactions in the dimerization process of HBHA from Mycobacterium tuberculosis, insights into bacterial agglutination (396 views)
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2012 Mar 23; 586(6): 659-667.
Impact Factor: 3.582
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Galdiero S, Vitiello M, Falanga A, Cantisani M, Incoronato N, Galdiero M
* Intracellular Delivery: Exploiting Viral Membranotropic Peptides (650 views)
Current Drug Metabolism (ISSN: 1389-2002), 2012 Jan; 13(1): 93-104.
Impact Factor: 4.405
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Barile E, Leone M, Barile E, Dahl R, Pellecchia M
* Design and NMR Studies of Cyclic Peptides Targeting the N-Terminal Domain of the Protein Tyrosine Phosphatase YopH (2165 views)
Chem Biol Drug Des (ISSN: 1747-0277, 1747-0285), 2011 Jan; 77(1): 12-19.
Impact Factor: 2.282
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Verardi R, Traaseth NJ, Shi L, Porcelli F, Monfregola L, De Luca S, Amodeo P, Veglia G, Scaloni A
* Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers (468 views)
Bba-Gen Subjects (ISSN: 0005-2736, 0006-3002, 0925-4439), 2011 Jan; 1808(1): 34-40.
Impact Factor: 3.99
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Varriale S, Merlino A, Coscia MR, Mazzarella L, Oreste U
* An evolutionary conserved motif is responsible for Immunoglobulin heavy chain packing in the B cell membrane (325 views)
Molecular Phylogenetics And Evolution (ISSN: 1055-7903), 2010 Dec; 57(3): 1238-1244.
Impact Factor: 3.889
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Leone M, Barile E, Vazquez J, Mei A, Guiney D, Dahl R, Pellecchia M
* NMR-based design and evaluation of novel bidentate inhibitors of the protein tyrosine phosphatase YopH (440 views)
Chem Biol Drug Des (ISSN: 1747-0277, 1747-0285), 2010 Jul; 76(1): 10-16.
Impact Factor: 2.527
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Napolitano M, Ottaiano A, Mauro F, Ieranò C, Satriano R, Pacelli R, Franco R, De Angelis V, Castello G, Scala S
* CD4(+)CD45RA(+)CXCR4(+) lymphocytes are inversely associated with progression in stages I-III melanoma patients (351 views)
Cancer Immunol Immunother (ISSN: 0340-7004, 0340-7004linking), 2010 Apr; 59(4): 511-517.
Impact Factor: 4.293
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Calvanese L, Saporito A, Oliva R, D'Auria G, Pedone C, Paolillo L, Ruvo M, Marasco D, Falcigno L
* Structural insights into the interaction between the Cripto CFC domain and the ALK4 receptor (438 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009 Mar; 15(3): 175-183.
Impact Factor: 1.807
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Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Janis J, Valjakka J, Pastorekova S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S
* Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes (419 views)
Jbc Papers (ISSN: 0021-9258, 1083-351x, 0021-9258linking), 2008 Oct 10; 283(41): 27799-27809.
Impact Factor: 5.52
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Merlino A, Varriale S, Coscia MR, Mazzarella L, Oreste U
* Structure and dimerization of the teleost transmembrane immunoglobulin region (336 views)
Journal Of Molecular Graphics & Modelling (ISSN: 1093-3263), 2008 Oct; 27(3): 401-407.
Impact Factor: 2.347
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Goldfine ID, Maddux BA, Youngren JF, Reaven G, Accili D, Trischitta V, Vigneri R, Frittitta L
* The role of membrane glycoprotein plasma cell antigen 1 ectonucleotide pyrophosphatase phosphodiesterase 1 in the pathogenesis of insulin resistance and related abnormalities (590 views)
Endocrine Reviews (ISSN: 0163-769x), 2008 Feb; 29(1): 62-75.
Impact Factor: 18.562
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Galdiero S, Falanga A, Vitiello M, D'Isanto M, Collins C, Orrei V, Browne H, Pedone C, Galdiero M
* Evidence for a role of the membrane-proximal region of herpes simplex virus type 1 glycoprotein H in membrane fusion and virus inhibition (551 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2007 May 25; 8(8): 885-895.
Impact Factor: 3.446
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis (396 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
Impact Factor: 4.472
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Galdiero S, Galdiero M, Pedone C
* Beta-Barrel Membrane Bacterial Proteins: Structure, Function, Assembly And Interaction With Lipids (399 views)
Curr Protein Pept Sci (ISSN: 1389-2037, 1389-2037linking), 2007 Feb; 8(1): 63-82.
Impact Factor: 3.259
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Calvanese L, Saporito A, Marasco D, D'Auria G, Minchiotti G, Pedone C, Paolillo L, Falcigno L, Ruvo M
* Solution structure of mouse Cripto CFC domain and its inactive variant Trp107Ala (349 views)
J Med Chem (ISSN: 0022-2623, 1520-4804, 0022-2623print), 2006 Nov 30; 49(24): 7054-7062.
Impact Factor: 5.115
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Amit M, Berisio R, Baram D, Harms J, Bashan A, Yonath A
* A crevice adjoining the ribosome tunnel: Hints for cotranslational folding (375 views)
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2005 Jun 13; 579(15): 3207-3213.
Impact Factor: 3.415
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Galdiero S, Gouaux E
* High Resolution Crystallographic Studies Of Alpha-Hemolysin-Phospholipid Complexes Define Heptamer-Lipid Head Group Interactions: Implication For Understanding Protein-Lipid Interactions (309 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2004 Jun; 13(6): 1503-1511.
Impact Factor: 4.116
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Galdiero M, Vitiello M, Galdiero S
* Eukaryotic cell signaling and transcriptional activation induced by bacterial porins (402 views)
Fems Microbiology Letters (ISSN: 0378-1097), 2003 Sep 12; 226(1): 57-64.
Impact Factor: 1.932
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Galdiero S, Capasso D, Vitiello M, D'Isanto M, Pedone C, Galdiero M
* Protein P2 from Haemophilus influenzae: The role of its surface exposed loops on the mitogen-activated protein kinase cascade (350 views)
Infection And Immunity (ISSN: 0019-9567), 2003 May; 71(5): 2798-2809.
Impact Factor: 3.875
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Cardone L, de Cristofaro T, Affaitati A, Garbi C, Ginsberg MD, Saviano M, Varrone S, Rubin CS, Gottesman ME, Avvedimento EV, Feliciello A
* A-kinase anchor protein 84/121 are targeted to mitochondria and mitotic spindles by overlapping amino-terminal motifs (457 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2002 Jul 12; 320(3): 663-675.
Impact Factor: 5.359
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Del Vecchio S, Ciarmiello A, Salvatore M
Clinical imaging of multidrug resistance in cancer (351 views)
Q J Nucl Med (ISSN: 1124-3937, 1125-0135), 1999 Jun; 43(2): 125-131.
Impact Factor: 2.125
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Scala S, Pacelli R, Iaffaioli RV, Normanno N, Pepe S, Frasci G, Genua G, Tsuruo T, Tagliaferri P, Bianco AR
Reversal of adriamycin resistance by recombinant α-interferon in multidrug-resistant human colon carcinoma LoVo-doxorubicin cells (551 views)
Cancer Res (ISSN: 0008-5472, 1538-7445, 1538-7445electronic), 1991 Sep 15; 51(18): 4898-4902.
Impact Factor: 8.426
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39 Records (38 excluding Abstracts).
Total impact factor: 230.343 (221 excluding Abstracts).
Total 5 year impact factor: 234.965 (225.344 excluding Abstracts).
Total impact factor: 230.343 (221 excluding Abstracts).
Total 5 year impact factor: 234.965 (225.344 excluding Abstracts).
406 views. Last view on Tuesday 20 September 2022, 18:44:31
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