Browsing by Author "Archontis, Georgios Z."
Now showing items 1-20 of 54
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The 1.76 Å resolution crystal structure of glycogen phosphorylase b complexed with glucose, and CP320626, a potential antidiabetic drug
Oikonomakos, Nikos G.; Zographos, Spyros E.; Skamnaki, Vicky T.; Archontis, Georgios Z. (2002)CP320626, a potential antidiabetic drug, inhibits glycogen phosphorylase in synergism with glucose. To elucidate the structural basis of synergistic inhibition, we determined the structure of muscle glycogen phosphorylase ...
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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 ...
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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. ...
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Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field based on drude oscillators
Archontis, Georgios Z.; Leontidis, Epameinondas; Andreou, Georgia (2005)Recent theoretical and experimental studies have shown that polarizable anions, such as iodide and bromide, preferentially accumulate close to the surface of electrolyte solutions. This finding is in sharp contrast to the ...
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Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
Archontis, Georgios Z.; Simonson, T.; Karplus, M. (2001)Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...
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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, ...
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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 ...
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Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase
Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...
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Computational protein design: The proteus software and selected applications
Simonson, Thomas; Gaillard, Thomas; Mignon, David; Schmidt, am Busch; Lopes, Anne; Amara, Najette; Polydorides, Savvas; Sedano, Audrey; Druart, Karen; Archontis, Georgios Z. (2013)
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Computational protein design: The proteus software and selected applications
Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (2013)We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...
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Computational sidechain placement and protein mutagenesis with implicit solvent models
Lopes, A.; Alexandrov, A.; Bathelt, C.; Archontis, Georgios Z.; Simonson, T. (2007)Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement ...
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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 ...
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Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
Simonson, T.; Archontis, Georgios Z.; Karplus, M. (1997)A method is proposed to include long-range electrostatic interactions in free energy calculations that involve the creation or deletion of net charges in a macromolecule. The vicinity of the mutation site is treated ...
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Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis
Van Heemst, J.; Jansen, D. T. S. L.; Polydorides, Savvas; Moustakas, Antonis K.; Bax, M.; Feitsma, A. L.; Bontrop-Elferink, D. G.; Baarse, M.; Van Der Woude, D.; Wolbink, G. -J; Rispens, T.; Koning, F.; De Vries, R. R. P.; Papadopoulos, George K.; Archontis, Georgios Z.; Huizinga, T. W.; Toes, R. E. (2015)The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA) + rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we ...
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Crystallographic and computational studies on 4-phenyl-N-(β-D- glucopyranosyl)-1H-1,2, 3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with α-D-glucose, N-acetyl-β-D- glucopyranosylamine and N-benzoyl-N′-β-D-glucopyranosyl urea binding
Alexacou, Kyra Melinda; Hayes, Joseph M.; Tiraidis, Costas; Zographos, Spyros E.; Leonidas, Demetres D.; Chrysina, Evangelia D.; Archontis, Georgios Z.; Oikonomakos, Nikos G.; Paul, J. V.; Varghese, B.; Loganathan, D. (2008)4-Phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its ...
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Cumulant expansion of the free energy: Application to free energy derivatives and component analysis
Archontis, Georgios Z.; Karplus, M. (1996)The free-energy change in a system represented by an empirical energy function, when calculated by thermodynamic integration from the initial to the final state, can be expressed as a sum of "free-energy components," that ...
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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 ...
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Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model
Archontis, Georgios Z.; Simonson, T. (2001)Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, ...
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Dissecting the stabilization of iodide at the air-water interface into components: A free energy analysis
Archontis, Georgios Z.; Leontidis, Epameinondas (2006)Recent experiments and simulations show that large chaotropic anions favor solvation at the water surface, mainly due to induction interactions dominated by ionic polarizabilities. We compare the solvation free-energy ...
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Electron transfer through fluctuating bridges: On the validity of the superexchange mechanism and time-dependent tunneling matrix elements
Skourtis, Spiros S.; Archontis, Georgios Z.; Xie, Q. (2001)An attempt is made to find the most general description of the superexchange mechanism that is valid for time-dependent donor-bridge-acceptor systems. Time-dependent electron-transfer probabilities that involve single MD ...