Literature DB >> 20119480

Computational molecular biology approaches to ligand-target interactions.

Paola Lupieri, Chuong Ha Hung Nguyen, Zhaleh Ghaemi Bafghi, Alejandro Giorgetti, Paolo Carloni.   

Abstract

Binding of small molecules to their targets triggers complex pathways. Computational approaches are keys for predictions of the molecular events involved in such cascades. Here we review current efforts at characterizing the molecular determinants in the largest membrane-bound receptor family, the G-protein-coupled receptors (GPCRs). We focus on odorant receptors, which constitute more than half GPCRs. The work presented in this review uncovers structural and energetic aspects of components of the cellular cascade. Finally, a computational approach in the context of radioactive boron-based antitumoral therapies is briefly described.

Entities:  

Year:  2009        PMID: 20119480      PMCID: PMC2799985          DOI: 10.2976/1.3092784

Source DB:  PubMed          Journal:  HFSP J        ISSN: 1955-205X


  92 in total

Review 1.  G-protein-coupled receptors at a glance.

Authors:  Wesley K Kroeze; Douglas J Sheffler; Bryan L Roth
Journal:  J Cell Sci       Date:  2003-12-15       Impact factor: 5.285

2.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

Review 3.  Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function.

Authors:  Kurt Kristiansen
Journal:  Pharmacol Ther       Date:  2004-07       Impact factor: 12.310

Review 4.  Receptor-mediated activation of heterotrimeric G-proteins: current structural insights.

Authors:  Christopher A Johnston; David P Siderovski
Journal:  Mol Pharmacol       Date:  2007-04-12       Impact factor: 4.436

5.  The G226A mutant of Gs alpha highlights the requirement for dissociation of G protein subunits.

Authors:  E Lee; R Taussig; A G Gilman
Journal:  J Biol Chem       Date:  1992-01-15       Impact factor: 5.157

6.  Hidden Markov models in computational biology. Applications to protein modeling.

Authors:  A Krogh; M Brown; I S Mian; K Sjölander; D Haussler
Journal:  J Mol Biol       Date:  1994-02-04       Impact factor: 5.469

7.  Structure of a type II thymidine kinase with bound dTTP.

Authors:  Markus S Birringer; Michael T Claus; Gerd Folkers; Daniel P Kloer; Georg E Schulz; Leonardo Scapozza
Journal:  FEBS Lett       Date:  2005-02-28       Impact factor: 4.124

8.  Structure and Raman spectrum of clavulanic acid in aqueous solution.

Authors:  Andrea Miani; Simone Raugei; Paolo Carloni; Marion S Helfand
Journal:  J Phys Chem B       Date:  2007-02-16       Impact factor: 2.991

9.  Evaluation of human thymidine kinase 1 substrates as new candidates for boron neutron capture therapy.

Authors:  Ashraf S Al-Madhoun; Jayaseharan Johnsamuel; Rolf F Barth; Werner Tjarks; Staffan Eriksson
Journal:  Cancer Res       Date:  2004-09-01       Impact factor: 12.701

10.  Temporal development of cyclic nucleotide-gated and Ca2+ -activated Cl- currents in isolated mouse olfactory sensory neurons.

Authors:  Anna Boccaccio; Anna Menini
Journal:  J Neurophysiol       Date:  2007-04-25       Impact factor: 2.714

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  4 in total

1.  Vibrationally assisted electron transfer mechanism of olfaction: myth or reality?

Authors:  Ilia A Solov'yov; Po-Yao Chang; Klaus Schulten
Journal:  Phys Chem Chem Phys       Date:  2012-08-17       Impact factor: 3.676

2.  GOMoDo: A GPCRs online modeling and docking webserver.

Authors:  Massimo Sandal; Tran Phuoc Duy; Matteo Cona; Hoang Zung; Paolo Carloni; Francesco Musiani; Alejandro Giorgetti
Journal:  PLoS One       Date:  2013-09-06       Impact factor: 3.240

3.  How Far Does a Receptor Influence Vibrational Properties of an Odorant?

Authors:  Anna Reese; Nanna Holmgaard List; Jacob Kongsted; Ilia A Solov'yov
Journal:  PLoS One       Date:  2016-03-25       Impact factor: 3.240

4.  Odorant receptors of Drosophila are sensitive to the molecular volume of odorants.

Authors:  Majid Saberi; Hamed Seyed-Allaei
Journal:  Sci Rep       Date:  2016-04-26       Impact factor: 4.379

  4 in total

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