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Browsing by Subject "Binding Sites"

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    • Article  

      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 ...

    • Article  

      Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations 

      Durdagi, S.; Mavromoustakos, Thomas M.; Chronakis, Nikos; Papadopoulos, Manthos G. (2008)
      A series of experimentally reported as well as computationally designed monoadducts and bisadducts of [60]fullerene analogues have been used in order to analyze the binding interactions between fullerene based inhibitors ...

    • Article  

      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 ...

    • Article  

      Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin 

      Ioannou, Androulla; Lambrou, Alexandra; Daskalakis, Vangelis; Pinakoulaki, Eftychia (2017)
      Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2 − cordination to the heme Fe in the O-binding nitrito (O1[sbnd]N[dbnd]O2) mode and to the heme 2-vinyl position. Nitrite is a powerful ...

    • Article  

      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 ...

    • Article  

      Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus 

      Pinakoulaki, Eftychia; Ohta, T.; Soulimane, T.; Kitagawa, T.; Varotsis, Constantinos (2005)
      Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a3 2+-NO ...

    • Article  

      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, ...

    • Article  

      Fourier transform infrared (FTIR) and step-scan time-resolved FTIR spectroscopies reveal a unique active site in cytochrome caa3 oxidase from Thermus thermophilus 

      Pinakoulaki, Eftychia; Soulimane, T.; Varotsis, Constantinos (2002)
      Fourier transform infrared (FTIR) and step-scan time-resolved FTIR difference spectra are reported for the [carbonmonoxy]cytochrome caa3 from Thermus thermophilus. A major C-O mode of heme a3 at 1958 cm-1 and two minor ...

    • Article  

      Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses 

      Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (2009)
      The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...

    • Article  

      Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses 

      Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (2009)
      The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...

    • Article  

      Inactivation of the glutamine/amino acid transporter ASCT2 by 1,2,3-dithiazoles: Proteoliposomes as a tool to gain insights in the molecular mechanism of action and of antitumor activity 

      Oppedisano, F.; Catto, M.; Koutentis, Panayiotis Andreas; Nicolotti, O.; Pochini, L.; Koyioni, Maria G.; Introcaso, A.; Michaelidou, Sophia S.; Carotti, A.; Indiveri, C. (2012)
      The ASCT2 transport system catalyses a sodium-dependent antiport of glutamine and other neutral amino acids which is involved in amino acid metabolism. A library of 1,2,3-dithiazoles was designed, synthesized and evaluated ...

    • Article  

      A miR-1207-5p binding site polymorphism abolishes regulation of HBEGF and is associated with disease severity in CFHR5 nephropathy 

      Papagregoriou, Gregory N.; Erguler, K.; Dweep, H.; Voskarides, Konstantinos; Koupepidou, P.; Athanasiou, Yiannis; Pierides, Alkis M.; Gretz, N.; Felekkis, Kyriacos N.; Constantinou-Deltas, Constantinos D. (2012)
      Heparin binding epidermal growth factor (HBEGF) is expressed in podocytes and was shown to play a role in glomerular physiology. MicroRNA binding sites on the 3′UTR of HBEGF were predicted using miRWalk algorithm and ...

    • Article  

      Molecular optimization using computational multi-objective methods 

      Nicolaou, Christos A.; Brown, N.; Pattichis, Constantinos S. (2007)
      Improving the profile of a molecule for the drug-discovery process requires the simultaneous optimization of numerous, often competing objectives. Traditionally, standard chemo-informatics methods ignored this problem and ...

    • Article  

      The origin of the Fe IV = O intermediates in cytochrome aa 3 oxidase 

      Pinakoulaki, Eftychia; Daskalakis, Vangelis; Varotsis, Constantinos (2012)
      The dioxygen reduction mechanism in cytochrome oxidases relies on proton control of the electron transfer events that drive the process. Proton delivery and proton channels in the protein that are relevant to substrate ...

    • Article  

      Polarized distribution of Bcr-Abl in migrating myeloid cells and co-localization of Bcr-Abl and its target proteins 

      Skourides, Paris A.; Perera, S. A.; Ren, R. (1999)
      Bcr-Abl plays a critical role in the pathogenesis of Philadelphia chromosome-positive leukemia. Although a large number of substrates and interacting proteins of Bcr-Abl have been identified, it remains unclear whether ...

    • Article  

      Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites 

      Ioannou, Androulla; Pinakoulaki, Eftychia (2017)
      Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). ...

    • Article  

      Proteus and the design of ligand binding sites 

      Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)
      This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...

    • Article  

      Recognition and discrimination of gases by the oxygen-sensing signal transducer protein HemAT as revealed by FTIR spectroscopy 

      Pinakoulaki, Eftychia; Yoshimura, H.; Yoshioka, S.; Aono, S.; Varotsis, Constantinos (2006)
      The determination of ligand binding properties is a key step in our understanding of gas sensing and discrimination by gas sensory proteins. HemAT is a newly discovered signal transducer heme protein that recognizes O 2 ...

    • Article  

      Recognition of ribonuclease A by 3′-5′-pyrophosphate-linked dinucleotide inhibitors: A molecular dynamics/continuum electrostatics analysis 

      Polydoridis, Savvas; Leonidas, Demetres D.; Oikonomakos, Nikos G.; Archontis, Georgios Z. (2007)
      The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic ...

    • Article  

      A residue-pairwise generalized born scheme suitable for protein design calculations 

      Archontis, Georgios Z.; Simonson, T. (2005)
      We describe an efficient generalized Born (GB) approximation for proteins, in which the interaction energy between two amino acids depends on the whole protein structure, but can be accurately computed from residue-pairwise ...

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