Browsing by Subject "Proteins"

Now showing items 1-20 of 64

    • Article  

      Addressing the Functional Determinants of FAK during Ciliogenesis in Multiciliated Cells 

      Antoniades, Ioanna; Stylianou, Panayiota; Christodoulou, Neophytos; Skourides, Paris A. (2017)
      We previously identified focal adhesion kinase (FAK) as an important regulator of ciliogenesis in multiciliated cells. FAK and other focal adhesion (FA) proteins associate with the basal bodies and their striated rootlets ...
    • Article  

      Autosomal dominant polycystic kidney disease: Molecular genetics and molecular pathogenesis 

      Koptides, Michael; Constantinou-Deltas, Constantinos D. (2000)
      Mutations in three different genes, PKD1, PKD2 and PKD3, can cause a very similar clinical picture of the autosomal dominant form of polycystic kidney disease (ADPKD). Apparently, mutations in the PKD3 gene, which is still ...
    • Article  

      BioTextQuest+: A knowledge integration platform for literature mining and concept discovery 

      Papanikolaou, Nikolas; Pavlopoulos, Georgios A.; Pafilis, Evangelos; Theodosiou, Theodosios G.; Schneider, R.; Satagopam, V. P.; Ouzounis, Christos A.; Eliopoulos, Aristides G.; Promponas, Vasilis J.; Iliopoulos, Ioannis Crete (2014)
      The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific ...
    • Article  

      Cationic double-hydrophilic model networks: Synthesis, characterization, modeling and protein adsorption studies 

      Loizou, Elena; Triftaridou, Aggeliki I.; Georgiou, Theoni K.; Vamvakaki, Maria; Patrickios, Costas S. (2003)
      Group transfer polymerization (GTP) was used for the preparation of eight networks based on two hydrophilic monomers, 2-(dimethylamino)ethyl methacrylate (DMAEMA) and poly(ethylene glycol) methacrylate (PEGMA). Ethylene ...
    • 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  

      A comparative study on filtering protein secondary structure prediction 

      Kountouris, P.; Agathocleous, Michalis; Promponas, Vasilis J.; Christodoulou, Georgia; Hadjicostas, S.; Vassiliades, Vassilis; Christodoulou, Chris C. (2012)
      Filtering of Protein Secondary Structure Prediction (PSSP) aims to provide physicochemically realistic results, while it usually improves the predictive performance. We performed a comparative study on this challenging ...
    • Article  

      Comparing intracellular stability and targeting of sulfobetaine quantum dots with other surface chemistries in live cells 

      Muro, E.; Fragola, A.; Pons, T.; Lequeux, N.; Ioannou, Androulla; Skourides, Paris A.; Dubertret, B. (2012)
      The in vivo labeling of intracellular components with quantum dots (QDs) is very limited because of QD aggregation in the cell cytoplasm and/or QD confinement into lysosomal compartments. In order to improve intracellular ...
    • Article  

      Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation 

      Kuzmichev, A.; Margueron, R.; Vaquero, A.; Preissner, T. S.; Scher, M.; Kirmizis, Antonis; Ouyang, X.; Brockdorff, N.; Abate-Shen, C.; Farnham, P.; Reinberg, D. (2005)
      Changes in the substrate specificities of factors that irreversibly modify the histone components of chromatin are expected to have a profound effect on gene expression through epigenetics. Ezh2 is a histone-lysine ...
    • Article  

      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 ...
    • Article  

      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 ...
    • Article  

      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 ...
    • Article  

      Detection of a novel nonsense mutation and an intragenic polymorphism in the PKD1 gene of a Cypriot family with autosomal dominant polycystic kidney disease 

      Neophytou, Pavlos; Constantinides, Rolandos; Lazarou, Akis; Pierides, Alkis M.; Constantinou-Deltas, Constantinos D. (1996)
      Mutations in the PKD1 gene on the short arm of chromosome 16 account for 85%-90% of polycystic kidney disease patients in the Caucasian population. After the recent characterization of the gene, we started a search for ...
    • 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  

      Discovery of old diseases: The molecular approach [1] 

      Constantinou-Deltas, Constantinos D. (2003)
    • Doctoral Thesis  Open Access

      Dissecting the role of histone N-Terminal acetyltransferase NAA40 in gene regulation, metabolism and cancer 

      Demetriadou, Christina P. (Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών / University of Cyprus, Faculty of Pure and Applied Sciences, 2021-11)
      Η Ν-άλφα-ακετυλτρανσφεράση 40 (ΝΑΑ40) καταλύει τη μεταφορά μιας ακετυλομάδας στο άλφα αμινοτελικό άκρο της σερίνης 1 (S1) στις ιστόνες Η4 και Η2Α. Παρόλο που προηγούμενες μελέτες έχουν συνδέσει την ΝΑΑ40 με τον καρκίνο, η ...
    • Article  

      Electron transfer contact maps 

      Skourtis, Spiros S.; Beratan, David N. (1997)
      An exact approach is introduced to establish and compare quantitative structure-function relationships in electron transfer proteins. The strategy is based on the idea of an electron transfer contact map and is motivated ...
    • Article  

      Electron transfer mechanisms 

      Beratan, David N.; Skourtis, Spiros S. (1998)
      The tunneling pathway framework description of protein electron transfer reactions has prompted a lively discussion of how structure and evolution influence electron transfer rates. Recent protein and model system experiments, ...
    • Article  

      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 ...
    • 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  

      Familial Mediterranean fever associated pyrin mutations in Greece 

      Print Email Konstantopoulos, Konstantinos; Kanta, Alexandra; Constantinou-Deltas, Constantinos D.; Atamian, V.; Mavrogianni, D.; Tzioufas, A. G.; Kollainis, I.; Ritis, K.; Moutsopoulos, H. M. (2003)
      Objective: To search for pyrin mutations associated with familial Mediterranean fever (FMF) in Greece. Patients and methods: 62 patients fulfilling the Tel Hashomer diagnostic criteria for definite (33) or probable (29) ...