• Article  

      Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation 

      Kirmizis, Antonis; Santos-Rosa, H.; Penkett, C. J.; Singer, M. A.; Vermeulen, M.; Mann, M.; Bähler, J.; Green, R. D.; Kouzarides, T. (2007)
      Modifications on histones control important biological processes through their effects on chromatin structure. Methylation at lysine 4 on histone H3 (H3K4) is found at the 5′ end of active genes and contributes to ...
    • 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  

      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  

      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  

      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 ...
    • 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  

      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) ...
    • Article  

      Fluctuations in biological and bioinspired electron-transfer reactions 

      Skourtis, Spiros S.; Waldeck, D. H.; Beratan, David N. (2010)
      Central to theories of electron transfer (ET) is the idea that nuclear motion generates a transition state that enables electron flow to proceed, but nuclear motion also induces fluctuations in the donor-acceptor (DA) ...
    • Article  

      Free energy simulations come of age: Protein-ligand recognition 

      Simonson, T.; Archontis, Georgios Z.; Karplus, M. (2002)
      In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
    • Article  

      Genomic approaches that aid in the identification of transcription factor target genes 

      Kirmizis, Antonis; Farnham, P. J. (2004)
      It is well-established that deregulation of the transcriptional activity of many different genes has been causatively linked to human diseases. In cancer, altered patterns of gene expression are often the result of the ...
    • 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  

      Making the Connection: Ciliary Adhesion Complexes Anchor Basal Bodies to the Actin Cytoskeleton 

      Antoniades, Ioanna; Stylianou, Panayiota; Skourides, Paris A. (2014)
      Cilia have been associated with diverse developmental and physiological processes, and defects in cilia underlie a number of genetic conditions. Several lines of evidence support a critical role of the actin cytoskeleton ...
    • Article  

      Neuralized Encodes a Peripheral Membrane Protein Involved in Delta Signaling and Endocytosis 

      Pavlopoulos, Elias; Pitsouli, Chrysoula; Klueg, K. M.; Muskavitch, M. A. T.; Moschonas, Nicholas K.; Delidakis, Christos (2001)
      Activation of the Notch (N) receptor involves an intracellular proteolytic step triggered by shedding of the extracellular N domain (N-EC) upon ligand interaction. The ligand Dl has been proposed to effect this N-EC shedding ...
    • Article  

      Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins 

      Curry, W. B.; Grabe, M. D.; Kurnikov, I. V.; Skourtis, Spiros S.; Beratan, David N.; Regan, J. J.; Aquino, A. J. A.; Beroza, P.; Onuchic, J. N. (1995)
      The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces ...
    • Article  

      Photosynthesis from the protein's perspective 

      Skourtis, Spiros S.; Beratan, David N. (2007)
    • Article  

      The Polycomb Group Protein SUZ12 regulates histone H3 lysine 9 methylation and HP1α distribution 

      De La Cruz, C. C.; Kirmizis, Antonis; Simon, M. D.; Isono, K. -I; Koseki, H.; Panning, B. (2007)
      Regulation of histone methylation is critical for proper gene expression and chromosome function. Suppressor of Zeste 12 (SUZ12) is a requisite member of the EED/EZH2 histone methyltransferase complexes, and is required ...
    • Article  

      Polypeptide Amino Acid Composition and Isoelectric Point. 1. A Closed-Form Approximation 

      Patrickios, Costas S. (1995)
      Two analytical expressions correlating explicitly polyampholyte isoelectric point to acid-base composition are derived and presented. The utility and limitations of these equations for the determination of the isoelectric ...
    • Article  

      Protein complexation with acrylic polyampholytes 

      Patrickios, Costas S.; Hertler, Walter R.; Hatton, T. Alan (1994)
      The interaction of dilute mixtures of proteins and ABC triblock methacrylic polyampholytes at different values of pH was investigated turbidimetrically. The onset of interaction was manifested by large changes in turbidity ...