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Browsing by Subject "Peptides"

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    • Article  

      Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations 

      Tamamis, Phanourios; Archontis, Georgios Z. (2011)
      Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling ...

    • Article  

      Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: Insights from molecular dynamics simulations 

      Tamamis, Phanourios; Kasotakis, E.; Mitraki, A.; Archontis, Georgios Z. (2009)
      The self-assembly of peptides and proteins into nanostructures is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. ...

    • Article  

      Analgesic tolerance and cross-tolerance to i.c.v. endomorphin-1, endomorphin-2, and morphine in mice; 15276249 

      Soignier, R. D.; Vaccarino, A. L.; Fanti, Kostas A.; Wilson, A. M.; Zadina, J. E. (2004)
      The present study examined the development of analgesic tolerance to endomorphin-1 (EM1), endomorphin-2 (EM2), and morphine, and cross-tolerance among these drugs. Male Swiss Webster mice were injected i.c.v. with EM1, ...

    • Article  

      CHARMM: The biomolecular simulation program 

      Brooks, B. R.; Brooks III, C. L.; Mackerell Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, Georgios Z.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009)
      CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...

    • Article  

      Chiral separations using a polypeptide and polymeric dipeptide surfactant polyelectrolyte multilayer coating in open-tubular capillary electrochromatography 

      Kamande, M. W.; Zhu, X.; Kapnissi‐Christodoulou, Constantina P.; Warner, I. M. (2004)
      A polyelectrolyte multilayer (PEM) coating consisting of the polypeptide, poly(L-lysine) hydrobromide, poly(L-lysine) and the polymeric dipeptide surfactant, poly(sodium undecanoyl-L-leutcyl-alaninate), poly(L-SULA), is ...

    • Article  

      Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides 

      Tamamis, Phanourios; Kasotakis, E.; Archontis, Georgios Z.; Mitraki, A. (2014)
      Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. Their ability to form biocompatible ...

    • Doctoral Thesis  Open Access

      Computational study of ionic effects on the conformational stability and the helix/coil equilibrium of model oligopeptides 

      Ioannou, Filippos D. (Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών / University of Cyprus, Faculty of Pure and Applied Sciences, 2013-01)
      Η παρούσα διδακτορική διατριβή είναι μια υπολογιστική μελέτη της επίδρασης των αλάτων στη στερεοδιαταξική σταθερότητα και την ισορροπία έλικας/τυχαίου σπειρώματος ολιγοπεπτιδίων, με στόχο τη διαφώτιση του μηχανισμού της ...

    • Article  

      Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water 

      Tamamis, Phanourios; Skourtis, Spiros S.; Morikis, D.; Lambris, J. D.; Archontis, Georgios Z. (2007)
      The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist ...

    • Article  

      Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin 

      Tamamis, Phanourios; Pierou, P.; Mytidou, C.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (2011)
      The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive ...

    • Article  

      Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics 

      Lazaridis, T.; Archontis, Georgios Z.; Karplus, M. (1995)
      This chapter discusses published analyses of protein stability based on model compound data and outlines the assumptions that have been made. The enthalpy of protein folding is considered and a thermodynamic cycle is used ...

    • Article  

      Fragment orbital based description of charge transfer in peptides including backbone orbitals 

      Heck, A.; Woiczikowski, P. B.; Kubař, T.; Welke, K.; Niehaus, T.; Giese, B.; Skourtis, Spiros S.; Elstner, M.; Steinbrecher, T. B. (2014)
      Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult ...

    • Article  

      Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulations 

      Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)
      Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...

    • Article  

      Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulationsAAA 

      Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)
      Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...

    • Article  

      In vivo, site-specific, covalent conjugation of quantum dots to proteins via split-intein splicing 

      Charalambous, Anna; Andreou, Maria I.; Antoniades, Ioanna; Christodoulou, Neophytos; Skourides, Paris A. (2012)
      The ability to target proteins with nanostructures and/or nanodevices in vivo is important for understanding and controlling their biological function. Quantum dots (QDs) serve as an ideal model nanostructure due to their ...

    • Article  

      Model investigations for vanadium-protein interactions: Vanadium(III) compounds with dipeptides and their oxovanadium(IV) analogues 

      Tasiopoulos, Anastasios J.; Tolis, Evangelos I.; Tsangaris, John Michael; Evangelou, Angelos M.; Woollins, J. D.; Slawin, A. M. Z.; Pessoa, J. C.; Correia, I.; Kabanos, Themistoklis A. (2002)
      The reaction of VCl3 with 1,10-phenanthroline and a series of dipeptides (H2dip), having aliphatic as well as aromatic side chains, in methyl alcohol and in the presence of triethylamine affords vanadium(III) compounds of ...

    • Article  

      Models of oxovanadium(IV)-protein interactions: The first oxovanadium(IV) complexes with dipeptides 

      Tasiopoulos, Anastasios J.; Vlahos, Antonis T.; Keramidas, Anastasios D.; Kabanos, Themistoklis A.; Deligiannakis, Yiannis G.; Raptopoulou, Catherine P.; Terzis, Aris (1996)

    • Article  

      Reviewprobing protein electron transfer mechanisms from the molecular to the cellular length scales1 

      Skourtis, Spiros S.; Maran, Flavio; Toniolo, Claudio (2013)

    • Article  

      Self-assembly of an aspartate-rich sequence from the adenovirus fiber shaft: Insights from molecular dynamics simulations and experiments 

      Tamamis, Phanourios; Terzaki, K.; Kassinopoulos, Marios; Mastrogiannis, L.; Mossou, E.; Forsyth, V. T.; Mitchell, E. P.; Mitraki, A.; Archontis, Georgios Z. (2014)
      The self-assembly of short peptides into fibrous nanostructures (such as fibrils and tubes) has recently become the subject of intense theoretical and experimental scrutiny, as such assemblies are promising candidates for ...

    • Article  

      Specific antibody to Cryptococcus neoformans glucurunoxylomannan antagonizes antifungal drug action against cryptococcal biofilms in vitro 

      Martinez, Luis R.; Christaki, Eirini; Casadevall, Arturo (2006)
      The fungus Cryptococcus neoformans possesses a polysaccharide capsule and can form biofilms on medical devices. We investigated the efficacy that the combination of a specific antibody to the capsular polysaccharide and ...

    • Article  

      Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamics 

      Ioannou, F.; Archontis, Georgios Z.; Leontidis, Epameinondas (2011)
      We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space ...

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