Journal of Molecular Recognition

Cover image for Vol. 26 Issue 2

February 2013

Volume 26, Issue 2

Pages 59–120

  1. Issue Information

    1. Top of page
    2. Issue Information
    3. Research Articles
    1. Issue Information (pages i–iii)

      Article first published online: 21 JAN 2013 | DOI: 10.1002/jmr.2226

  2. Research Articles

    1. Top of page
    2. Issue Information
    3. Research Articles
    1. Protein–cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles (pages 59–66)

      Ranajay Saha, Surajit Rakshit, Pramod Kumar Verma, Rajib Kumar Mitra and Samir Kumar Pal

      Article first published online: 7 JAN 2013 | DOI: 10.1002/jmr.2246

      Thumbnail image of graphical abstract

      Schematic representations of riboflavin electron transfer in the protein nanospace, under the spatial confinement of reverse micelles of different surfactant charge. The study shows that both the hydration and the surface charge of the confining volume largely determines the biochemical reactions dynamics like ultrafast electron transfer, in real biological cells.

    2. Ligand binding and self-association cooperativity of β-lactoglobulin (pages 67–75)

      Gabriel Gutiérrez-Magdaleno, Martiniano Bello, M. Carmen Portillo-Téllez, Adela Rodríguez-Romero and Enrique García-Hernández

      Article first published online: 7 JAN 2013 | DOI: 10.1002/jmr.2249

      Thumbnail image of graphical abstract

      Because of their complex structural dynamics, oligomeric lipocalins are expected to show intermolecular binding cooperativity. β-lactoglobulin evidenced homodimerization and dodecyl sulfate binding reciprocal effects. The X-ray structure of the complex revealed structural basis of the interaction. Determination of cooperative effects allows a better understanding of the behavior of lipocalin homomers.

    3. Mapping of heparin/heparan sulfate binding sites on αvβ3 integrin by molecular docking (pages 76–85)

      Lionel Ballut, Nicolas Sapay, Émilie Chautard, Anne Imberty and Sylvie Ricard-Blum

      Article first published online: 21 JAN 2013 | DOI: 10.1002/jmr.2250

      Thumbnail image of graphical abstract

      The two major conclusions drawn from this study are (i) the predicted binding sites differ in the RGD-dependent and RGD-independent integrin subfamilies and (ii) the binding sites identified are compatible with the formation at the cell surface of ternary complexes comprising integrin, protein ligand and heparan sulfate. Furthermore, this work would be helpful to design future site-directed mutagenesis experiments aiming at confirming experimentally the location of binding site(s) on the integrin surface.

    4. Prediction of amino acid residues participated in substrate recognition by cytochrome P450 subfamilies with broad substrate specificity (pages 86–91)

      Maria S. Zharkova, Boris N. Sobolev, Nina Yu. Oparina, Alexander V. Veselovsky and Alexander I. Archakov

      Article first published online: 7 JAN 2013 | DOI: 10.1002/jmr.2251

      Thumbnail image of graphical abstract

      Analysis of six cytochrome P450 subfamilies with the broad and cross-substrate specificity enables to select the sets of amino acid residues located at the entrance of active sites. It was suggested that they can form the primary binding site for substrates and participate in their recognition.

    5. Allostery mediates ligand binding to Grb2 adaptor in a mutually exclusive manner (pages 92–103)

      Caleb B. McDonald, Jimmy El Hokayem, Nawal Zafar, Jordan E. Balke, Vikas Bhat, David C. Mikles, Brian J. Deegan, Kenneth L. Seldeen and Amjad Farooq

      Article first published online: 11 JAN 2013 | DOI: 10.1002/jmr.2256

      Thumbnail image of graphical abstract


      • Binding of Grb2 to both Gab1 and Sos1 is governed by 2:1 stoichiometry
      • Binding of Gab1 to Grb2 sterically blocks the binding of Sos1 and vice versa
      • Such competitive binding results in the formation of two binary complexes in lieu of a composite ternary complex
      • Ligand binding to Grb2 appears to be under tight allosteric control
    6. Protein stabilization with a dipeptide-mimic triazine-scaffolded synthetic affinity ligand (pages 104–112)

      I. T. Sousa, N. M. T. Lourenço, C. A. M. Afonso and M. A. Taipa

      Article first published online: 11 JAN 2013 | DOI: 10.1002/jmr.2252

      Thumbnail image of graphical abstract

      The potential of selective biomimetic ligands to act as “extrinsic artificial amino acids” in the stabilization of proteins was assessed. Significant stabilization at elevated temperatures (60 °C–80 °C) was achieved through specific binding of a solid-phase bifunctional triazine-scaffolded affinity ligand to a model enzyme protein. It is predictable that the dipeptide mimic binds to eligible complementary sites on the enzyme surface by intermolecular interactions similar to those responsible for maintenance of protein's structure, thus restricting molecular motions for unfolding and enhancing thermostability.

    7. Asymmetric structure and domain binding interfaces of human tyrosyl-tRNA synthetase studied by molecular dynamics simulations (pages 113–120)

      Oleksandr V. Savytskyi, Semen O. Yesylevskyy and Alexander I. Kornelyuk

      Article first published online: 11 JAN 2013 | DOI: 10.1002/jmr.2259

      Thumbnail image of graphical abstract

      HsTyrRS in solution consists of a number of compact asymmetric conformations, which differ significantly by their rigidity, internal mobility and orientation of C-terminal modules. Distinct interfaces of domain binding were obtained. Formation of the hydrogen bonds between R93 residue of the ELR cytokine motif and the residues A340 and E479 in the C-module was observed. It is suggested that the lack of cytokine activity in the full-length HsTyrRS is explained by blocking the ELR motif by C-modules.