Browsing by Subject "Peptides"

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 ...