{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:36:54Z","timestamp":1740123414473,"version":"3.37.3"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2017,7,29]],"date-time":"2017-07-29T00:00:00Z","timestamp":1501286400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2017,9]]},"DOI":"10.1007\/s10822-017-0045-2","type":"journal-article","created":{"date-parts":[[2017,7,29]],"date-time":"2017-07-29T09:25:52Z","timestamp":1501320352000},"page":"841-854","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics"],"prefix":"10.1007","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2427-6098","authenticated-orcid":false,"given":"Golfo G.","family":"Kordopati","sequence":"first","affiliation":[]},{"given":"Haralambos","family":"Tzoupis","sequence":"additional","affiliation":[]},{"given":"Anastassios N.","family":"Troganis","sequence":"additional","affiliation":[]},{"given":"Gerasimos M.","family":"Tsivgoulis","sequence":"additional","affiliation":[]},{"given":"Simona","family":"Golic Grdadolnik","sequence":"additional","affiliation":[]},{"given":"Carmen","family":"Simal","sequence":"additional","affiliation":[]},{"given":"Theodore V.","family":"Tselios","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,7,29]]},"reference":[{"key":"45_CR1","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0092-8674(00)81107-1","volume":"85","author":"L Steinman","year":"1996","unstructured":"Steinman L (1996) Multiple sclerosis: a coordinated immunological attack against myelin in the central nervous system. Cell 85:299\u2013302","journal-title":"Cell"},{"key":"45_CR2","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1056\/NEJM200009283431307","volume":"343","author":"JH Noseworthy","year":"2000","unstructured":"Noseworthy JH, Lucchinetti C, Rodriguez M, Weinshenker BG (2000) Multiple sclerosis. N Engl J Med 343:938\u2013952","journal-title":"N Engl J Med"},{"key":"45_CR3","doi-asserted-by":"crossref","first-page":"829129","DOI":"10.1155\/2011\/829129","volume":"2011","author":"N Shahrizaila","year":"2011","unstructured":"Shahrizaila N, Yuki N (2011) Guillain-barr\u00e9 syndrome animal model: the first proof of molecular mimicry in human autoimmune disorder. J Biomed Biotechnol 2011:829129","journal-title":"J Biomed Biotechnol"},{"key":"45_CR4","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1084\/jem.188.8.1511","volume":"188","author":"KJ Smith","year":"1998","unstructured":"Smith KJ, Pyrdol J, Gauthier L, Wiley DC, Wucherpfennig KW (1998) Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein. J Exp Med 188:1511\u20131520","journal-title":"J Exp Med"},{"key":"45_CR5","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s12035-009-8071-2","volume":"40","author":"O Jahn","year":"2009","unstructured":"Jahn O, Tenzer S, Werner HB (2009) Myelin proteomics: molecular anatomy of an insulating sheath. Mol Neurobiol 40:55\u201372","journal-title":"Mol Neurobiol"},{"key":"45_CR6","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1146\/annurev.iy.08.040190.003051","volume":"8","author":"SS Zamvil","year":"1990","unstructured":"Zamvil SS, Steinman L (1990) The T lymphocyte in experimental allergic encephalomyelitis. Annu Rev Immunol 8:579\u2013621","journal-title":"Annu Rev Immunol"},{"key":"45_CR7","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1177\/135245859600100503","volume":"1","author":"CM Pelfrey","year":"1996","unstructured":"Pelfrey CM, Tranquill LR, Vogt AB, McFarland HF (1996) T cell response to two immunodominant proteolipid protein (PLP) peptides in multiple sclerosis patients and healthy controls. Mult Scler 1:270\u2013278","journal-title":"Mult Scler"},{"key":"45_CR8","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/S0896-6273(00)81107-1","volume":"24","author":"L Steinman","year":"1999","unstructured":"Steinman L (1999) Assessment of animal models for MS and demyelinating disease in the design of rational therapy. Neuron 24:511\u2013514","journal-title":"Neuron"},{"key":"45_CR9","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1084\/jem.191.5.761","volume":"191","author":"AC Anderson","year":"2000","unstructured":"Anderson AC, Nicholson LB, Legge KL, Turchin V, Zaghouani H, Kuchroo VK (2000) High frequency of autoreactive myelin proteolipid protein\u2013specific T cells in the periphery of naive mice. J Exp Med 191:761\u2013770","journal-title":"J Exp Med"},{"key":"45_CR10","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.2174\/092986706777935113","volume":"13","author":"M Katsara","year":"2006","unstructured":"Katsara M, Tselios T, Deraos S, Deraos G, Matsoukas M-T, Lazoura E, Matsoukas J, Apostolopoulos V (2006) Round and round we go: cyclic peptides in disease. Curr Med Chem 13:2221\u20132232","journal-title":"Curr Med Chem"},{"key":"45_CR11","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.4049\/jimmunol.142.5.1523","volume":"142","author":"VK Tuohy","year":"1989","unstructured":"Tuohy VK, Lu Z, Sobel RA, Laursen RA, Lees MB (1989) Identification of an encephalitogenic determinant of myelin proteolipid protein for SJL mice. J Immunol 142:1523\u20131157","journal-title":"J Immunol"},{"key":"45_CR12","doi-asserted-by":"crossref","first-page":"783","DOI":"10.4049\/jimmunol.149.3.783","volume":"149","author":"JM Greer","year":"1992","unstructured":"Greer JM, Kuchroo VK, Sobel R a, Lees MB (1992) Identification and characterization of a second encephalitogenic determinant of myelin proteolipid protein (residues 178\u2013191) for SJL mice. J Immunol 149:783\u2013788","journal-title":"J Immunol"},{"key":"45_CR13","doi-asserted-by":"crossref","first-page":"371","DOI":"10.4049\/jimmunol.156.1.371","volume":"156","author":"JM Greer","year":"1996","unstructured":"Greer JM, Sobel RA, Sette A, Southwood S, Lees MB, Kuchroo VK (1996) Immunogenic and encephalitogenic epitope clusters of myelin proteolipid protein. J Immunol 156:371\u2013379","journal-title":"J Immunol"},{"key":"45_CR14","doi-asserted-by":"crossref","first-page":"3326","DOI":"10.4049\/jimmunol.153.7.3326","volume":"153","author":"VK Kuchroo","year":"1994","unstructured":"Kuchroo VK, Greer JM, Kaul D, Ishioka G, Franco A, Sette A, Sobel RA, Lees MB (1994) A single TCR antagonist peptide inhibits experimental allergic encephalomyelitis mediated by a diverse T cell repertoire. J Immunol 153:3326\u20133336","journal-title":"J Immunol"},{"key":"45_CR15","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1021\/jm040849g","volume":"48","author":"J Matsoukas","year":"2005","unstructured":"Matsoukas J, Apostolopoulos V, Kalbacher H, Papini A-M, Tselios T, Chatzantoni K, Biagioli T, Lolli F, Deraos S, Papathanassopoulos P, Troganis A, Mantzourani E, Mavromoustakos T, Mouzaki A (2005) Design and synthesis of a novel potent myelin basic protein epitope 87\u201399 cyclic analogue: enhanced stability and biological properties of mimics render them a potentially new class of immunomodulators. J Med Chem 48:1470\u20131480","journal-title":"J Med Chem"},{"key":"45_CR16","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1007\/s10822-011-9467-4","volume":"25","author":"C Potamitis","year":"2011","unstructured":"Potamitis C, Matsoukas M-T, Tselios T, Mavromoustakos T, Goli\u010d Grdadolnik S (2011) Conformational analysis of the \u039c\u0392\u03a183\u201399 (Phe91) and \u039c\u0392\u03a183\u201399 (Tyr91) peptide analogues and study of their interactions with the HLA-DR2 and human TCR receptors by using molecular dynamics. J Comput Aided Mol Des 25:837\u2013853","journal-title":"J Comput Aided Mol Des"},{"key":"45_CR17","doi-asserted-by":"crossref","first-page":"17968","DOI":"10.3390\/molecules191117968","volume":"19","author":"T Tselios","year":"2014","unstructured":"Tselios T, Aggelidakis M, Tapeinou A, Tseveleki V, Kanistras I, Gatos D, Matsoukas J (2014) Rational design and synthesis of altered peptide ligands based on human myelin oligodendrocyte glycoprotein 35\u201355 epitope: inhibition of chronic experimental autoimmune encephalomyelitis in mice. Molecules 19:17968\u201317984","journal-title":"Molecules"},{"key":"45_CR18","doi-asserted-by":"crossref","first-page":"709","DOI":"10.2217\/imt.14.42","volume":"6","author":"M Katsara","year":"2014","unstructured":"Katsara M, Deraos S, Tselios T V, Pietersz G, Matsoukas J, Apostolopoulos V (2014) Immune responses of linear and cyclic PLP 139\u2013151 mutant peptides in SJL\/J mice: peptides in their free state versus mannan conjugation. Immunotherapy 6:709\u2013724","journal-title":"Immunotherapy"},{"key":"45_CR19","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1002\/bip.22669","volume":"104","author":"A Tapeinou","year":"2015","unstructured":"Tapeinou A, Matsoukas M-T, Simal C, Tselios T (2015) Cyclic peptides on a merry-go-round; towards drug design. Biopolymers 104:453\u2013461","journal-title":"Biopolymers"},{"key":"45_CR20","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1002\/bip.21476","volume":"94","author":"S Namjoshi","year":"2010","unstructured":"Namjoshi S, Benson HAE (2010) Cyclic peptides as potential therapeutic agents for skin disorders. Biopolymers 94:673\u2013680","journal-title":"Biopolymers"},{"key":"45_CR21","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1007\/s00726-008-0079-9","volume":"35","author":"X Li","year":"2008","unstructured":"Li X, Peterkofsky A, Wang G (2008) Solution structure of NPr, a bacterial signal-transducing protein that controls the phosphorylation state of the potassium transporter-regulating protein IIANtr. Amino Acids 35:531\u2013539","journal-title":"Amino Acids"},{"key":"45_CR22","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/nrd2606","volume":"7","author":"M Pellecchia","year":"2008","unstructured":"Pellecchia M, Bertini I, Cowburn D, Dalvit C, Giralt E, Jahnke W, James TL, Homans SW, Kessler H, Luchinat C, Meyer B, Oschkinat H, Peng J, Schwalbe H, Siegal G (2008) Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov 7:738\u2013745","journal-title":"Nat Rev Drug Discov"},{"key":"45_CR23","doi-asserted-by":"crossref","first-page":"6683","DOI":"10.1021\/jm060040z","volume":"49","author":"ED Mantzourani","year":"2006","unstructured":"Mantzourani ED, Tselios TV, Grdadolnik SG, Platts JA, Brancale A, Deraos GN, Matsoukas JM, Mavromoustakos TM (2006) Comparison of proposed putative active conformations of myelin basic protein epitope 87\u201399 linear altered peptide ligands by spectroscopic and modelling studies: the role of positions 91 and 96 in T-cell receptor activation. J Med Chem 49:6683\u20136691","journal-title":"J Med Chem"},{"key":"45_CR24","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.jmgm.2007.02.004","volume":"26","author":"ED Mantzourani","year":"2007","unstructured":"Mantzourani ED, Platts JA, Brancale A, Mavromoustakos TM, Tselios TV (2007) Molecular dynamics at the receptor level of immunodominant myelin basic protein epitope 87\u201399 implicated in multiple sclerosis and its antagonists altered peptide ligands: triggering of immune response. J Mol Graph Model 26:471\u2013481","journal-title":"J Mol Graph Model"},{"key":"45_CR25","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.1016\/j.bmc.2007.11.083","volume":"16","author":"ED Mantzourani","year":"2008","unstructured":"Mantzourani ED, Blokar K, Tselios TV, Matsoukas JM, Platts JA, Mavromoustakos TM, Grdadolnik SG (2008) A combined NMR and molecular dynamics simulation study to determine the conformational properties of agonists and antagonists against experimental autoimmune encephalomyelitis. Bioorg Med Chem 16:2171\u20132182","journal-title":"Bioorg Med Chem"},{"key":"45_CR26","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.jmgm.2016.06.005","volume":"68","author":"MP Yannakakis","year":"2016","unstructured":"Yannakakis MP, Tzoupis H, Michailidou E, Mantzourani E, Simal C, Tselios T (2016) Molecular dynamics at the receptor level of immunodominant myelin oligodendrocyte glycoprotein 35\u201355 epitope implicated in multiple sclerosis. J Mol Graph Model 68:78\u201386","journal-title":"J Mol Graph Model"},{"key":"45_CR27","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1111\/j.1399-3011.1991.tb00769.x","volume":"37","author":"K Barlos","year":"1991","unstructured":"Barlos K, Chatzi O, Gatos D, Stavropoulos G (1991) 2-Chlorotrityl chloride resin: studies on anchoring of Fmoc-amino acids and peptide cleavage. Int J Pept Protein Res 37:513\u2013520","journal-title":"Int J Pept Protein Res"},{"key":"45_CR28","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1021\/jm980250e","volume":"42","author":"T Tselios","year":"1999","unstructured":"Tselios T, Probert L, Daliani I, Matsoukas E, Troganis A, Gerothanassis IP, Mavromoustakos T, Moore GJ, Matsoukas JM (1999) Design and synthesis of a potent cyclic analogue of the myelin basic protein epitope MBP 72\u201385: importance of the Ala 81 carboxyl group and of a cyclic conformation for induction of experimental allergic encephalomyelitis. J Med Chem 42:1170\u20131177","journal-title":"J Med Chem"},{"key":"45_CR29","doi-asserted-by":"crossref","first-page":"2713","DOI":"10.1016\/S0960-894X(00)00556-4","volume":"10","author":"T Tselios","year":"2000","unstructured":"Tselios T, Daliani I, Deraos S, Thymianou S, Matsoukas E, Troganis A, Gerothanassis I, Mouzaki A, Mavromoustakos T, Probert L, Matsoukas J (2000) Treatment of experimental allergic encephalomyelitis (EAE) by a rationally designed cyclic analogue of myelin basic protein (MBP) epitope 72\u201385. Bioorg Med Chem Lett 10:2713\u20132717","journal-title":"Bioorg Med Chem Lett"},{"key":"45_CR30","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1002\/bip.22710","volume":"104","author":"M Ieronymaki","year":"2015","unstructured":"Ieronymaki M, Androutsou ME, Pantelia A, Friligou I, Crisp M, High K, Penkman K, Gatos D, Tselios T (2015) Use of the 2-chlorotrityl chloride resin for microwave-assisted solid phase peptide synthesis. Biopolymers 104:506\u2013514","journal-title":"Biopolymers"},{"key":"45_CR31","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1021\/jm0102147","volume":"45","author":"T Tselios","year":"2002","unstructured":"Tselios T, Apostolopoulos V, Daliani I, Deraos S, Grdadolnik S, Mavromoustakos T, Melachrinou M, Thymianou S, Probert L, Mouzaki A, Matsoukas J (2002) Antagonistic effects of human cyclic MBP 87\u201399 altered peptide ligands in experimental allergic encephalomyelitis and human T-cell proliferation. J Med Chem 45:275\u2013283","journal-title":"J Med Chem"},{"key":"45_CR32","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612","journal-title":"J Comput Chem"},{"key":"45_CR33","volume-title":"AMBER 2015","author":"DA Case","year":"2015","unstructured":"Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham, III TE, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz KM, Monard P, Needham HT, Nguyen H, Omelyan I, Onufriev A, Roe DR, Roitberg A, Salomon-Ferrer R, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, York DM, Kollman P (2015) AMBER 2015. University of California, San Francisco"},{"key":"45_CR34","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696\u20133713","journal-title":"J Chem Theory Comput"},{"key":"45_CR35","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926\u2013935","journal-title":"J Chem Phys"},{"key":"45_CR36","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1063\/1.1332996","volume":"114","author":"JA Izaguirre","year":"2001","unstructured":"Izaguirre JA, Catarello DP, Wozniak JM, Skeel RD (2001) Langevin stabilization of molecular dynamics. J Chem Phys 114:2090\u20132098","journal-title":"J Chem Phys"},{"key":"45_CR37","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"J-P Ryckaert","year":"1977","unstructured":"Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327\u2013341","journal-title":"J Comput Phys"},{"key":"45_CR38","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N \u22c5log(N) method for Ewald sums in large systems. J Chem Phys 98:10089\u201310092","journal-title":"J Chem Phys"},{"key":"45_CR39","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084\u20133095","journal-title":"J Chem Theory Comput"},{"key":"45_CR40","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1021\/ct700119m","volume":"3","author":"J Shao","year":"2007","unstructured":"Shao J, Tanner SW, Thompson N, Cheatham TE (2007) Clustering molecular dynamics trajectories: 1. characterizing the performance of different clustering algorithms. J Chem Theory Comput 3:2312\u20132334","journal-title":"J Chem Theory Comput"},{"key":"45_CR41","doi-asserted-by":"crossref","first-page":"6039","DOI":"10.1021\/jm070770m","volume":"50","author":"Z Spyranti","year":"2007","unstructured":"Spyranti Z, Dalkas GA, Spyroulias GA, Mantzourani ED, Mavromoustakos T, Friligou I, Matsoukas JM, Tselios TV (2007) Putative bioactive conformations of amide linked cyclic myelin basic protein peptide analogues associated with experimental autoimmune encephalomyelitis. J Med Chem 50:6039\u20136047","journal-title":"J Med Chem"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-017-0045-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0045-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0045-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,25]],"date-time":"2024-06-25T21:25:44Z","timestamp":1719350744000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-017-0045-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,29]]},"references-count":41,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2017,9]]}},"alternative-id":["45"],"URL":"https:\/\/doi.org\/10.1007\/s10822-017-0045-2","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2017,7,29]]}}}