Alejandro Giorgetti

Alejandro Giorgetti

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Alejandro Giorgetti

Publications by authors named "Alejandro Giorgetti"

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MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics.

Nucleic Acids Res 2019 Jul;47(W1):W456-W461

Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy.

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http://dx.doi.org/10.1093/nar/gkz416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602572PMC
July 2019

Dual binding mode of "bitter sugars" to their human bitter taste receptor target.

Sci Rep 2019 Jun 11;9(1):8437. Epub 2019 Jun 11.

Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany.

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http://dx.doi.org/10.1038/s41598-019-44805-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560132PMC
June 2019

Orthosteric and benzodiazepine cavities of the αβγ GABA receptor: insights from experimentally validated in silico methods.

J Biomol Struct Dyn 2019 Apr 4;37(6):1597-1615. Epub 2018 May 4.

a Departamento de Física, Instituto de Física del Sur (IFISUR) , Universidad Nacional del Sur (UNS), CONICET , Bahía Blanca , Argentina.

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http://dx.doi.org/10.1080/07391102.2018.1462733DOI Listing
April 2019

Multiscale simulations on human Frizzled and Taste2 GPCRs.

Curr Opin Struct Biol 2019 04 29;55:8-16. Epub 2019 Mar 29.

Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.02.009DOI Listing
April 2019

GABA receptor family: overview on structural characterization.

Future Med Chem 2019 Feb 25. Epub 2019 Feb 25.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, I-37134 Verona, Italy.

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http://dx.doi.org/10.4155/fmc-2018-0336DOI Listing
February 2019

Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study.

Molecules 2018 Oct 12;23(10). Epub 2018 Oct 12.

Institute of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich, Germany.

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http://www.mdpi.com/1420-3049/23/10/2616
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http://dx.doi.org/10.3390/molecules23102616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222423PMC
October 2018

Evidence of Alternative Splicing as a Regulatory Mechanism for Kissr2 in Pejerrey Fish.

Front Endocrinol (Lausanne) 2018 17;9:604. Epub 2018 Oct 17.

Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (CONICET-UNSAM), Buenos Aires, Argentina.

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http://dx.doi.org/10.3389/fendo.2018.00604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200147PMC
October 2018

Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics.

Int J Mol Sci 2018 Aug 31;19(9). Epub 2018 Aug 31.

Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.

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http://dx.doi.org/10.3390/ijms19092588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165245PMC
August 2018

Allosteric sodium binding cavity in GPR3: a novel player in modulation of Aβ production.

Sci Rep 2018 07 23;8(1):11102. Epub 2018 Jul 23.

Department of Neurosciences, Biomedicine and Movement Sciences-University of Verona, Verona, Italy.

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http://www.nature.com/articles/s41598-018-29475-7
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http://dx.doi.org/10.1038/s41598-018-29475-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056553PMC
July 2018

MIRATE: MIps RATional dEsign Science Gateway.

J Integr Bioinform 2018 Jun 13;15(4). Epub 2018 Jun 13.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.

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http://dx.doi.org/10.1515/jib-2017-0075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348745PMC
June 2018

Conserved charged amino acids are key determinants for fatty acid binding proteins (FABPs)-membrane interactions. A multi-methodological computational approach.

J Biomol Struct Dyn 2018 03 16;36(4):861-877. Epub 2017 Mar 16.

a Departamento de Física, Grupo de Biofísica - UNS , IFISUR, Universidad Nacional del Sur, CONICET , Bahía Blanca , Argentina.

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http://dx.doi.org/10.1080/07391102.2017.1301271DOI Listing
March 2018

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations.

Biochem Biophys Res Commun 2018 03 2;498(2):366-374. Epub 2018 Feb 2.

Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0006291X183018
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http://dx.doi.org/10.1016/j.bbrc.2018.01.160DOI Listing
March 2018

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme.

J Chem Theory Comput 2017 Nov 27;13(11):5647-5657. Epub 2017 Oct 27.

Department of Physics, Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal-Straße, 52074 Aachen, Germany.

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http://dx.doi.org/10.1021/acs.jctc.7b00508DOI Listing
November 2017

Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis.

Front Mol Biosci 2017 6;4:63. Epub 2017 Sep 6.

Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.

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http://dx.doi.org/10.3389/fmolb.2017.00063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592726PMC
September 2017

Identification of new BMP6 pro-peptide mutations in patients with iron overload.

Am J Hematol 2017 Jun 29;92(6):562-568. Epub 2017 Apr 29.

Department of Medicine, Section of Internal Medicine, University of Verona, Verona, Italy; Veneto Region Referral Center for Iron Disorders, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy.

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http://doi.wiley.com/10.1002/ajh.24730
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http://dx.doi.org/10.1002/ajh.24730DOI Listing
June 2017

Structural heterogeneity of the μ-opioid receptor's conformational ensemble in the apo state.

Sci Rep 2017 04 3;8:45761. Epub 2017 Apr 3.

Laboratory of Computational Biophysics, German Research School for Simulation Sciences GmbH, Joint venture of RWTH Aachen University and Forschungszentrum Jülich, 52425 Jülich, Germany.

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http://dx.doi.org/10.1038/srep45761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377942PMC
April 2017

Bioinformatics Applications in Life Sciences and Technologies.

Biomed Res Int 2016 4;2016:3603827. Epub 2016 May 4.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany.

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http://dx.doi.org/10.1155/2016/3603827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870335PMC
February 2017

Effects of interface mutations on the dimerization of alanine glyoxylate aminotransferase and implications in the mistargeting of the pathogenic variants F152I and I244T.

Biochimie 2016 Dec 5;131:137-148. Epub 2016 Oct 5.

Department of Neurosciences, Biomedicine and Movement Sciences (Section of Biological Chemistry), University of Verona, Verona, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2016.10.001DOI Listing
December 2016

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.

Int J Biochem Cell Biol 2016 08 19;77(Pt B):264-74. Epub 2016 Apr 19.

Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biomedicine, Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.biocel.2016.04.004DOI Listing
August 2016

A Multimodal Approach for Protein Remote Homology Detection.

IEEE/ACM Trans Comput Biol Bioinform 2015 Sep-Oct;12(5):1193-8

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http://dx.doi.org/10.1109/TCBB.2015.2424417DOI Listing
July 2016

Residues in the Distal Heme Pocket of Arabidopsis Non-Symbiotic Hemoglobins: Implication for Nitrite Reductase Activity.

Int J Mol Sci 2016 Apr 28;17(5). Epub 2016 Apr 28.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.

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http://dx.doi.org/10.3390/ijms17050640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881466PMC
April 2016

Molecular characterization of HIV-1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays.

Sci Rep 2016 Mar 1;6:22319. Epub 2016 Mar 1.

Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy.

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http://dx.doi.org/10.1038/srep22319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772117PMC
March 2016

Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects.

Chembiochem 2015 Dec 6;16(18):2633-45. Epub 2015 Nov 6.

Department of Biotechnology, Biomolecular NMR Laboratory, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.

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http://dx.doi.org/10.1002/cbic.201500451DOI Listing
December 2015

Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins.

Arch Biochem Biophys 2015 Sep 19;582:91-100. Epub 2015 Mar 19.

Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany.

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http://dx.doi.org/10.1016/j.abb.2015.03.011DOI Listing
September 2015

Apparent Mineralocorticoid Excess by a Novel Mutation and Epigenetic Modulation by HSD11B2 Promoter Methylation.

J Clin Endocrinol Metab 2015 Sep 30;100(9):E1234-41. Epub 2015 Jun 30.

Departments of Medicine (F.P., S.F., F.M., C.Z., S.U., O.O.) Life and Reproduction Sciences (F.A., A.Ga., P.C.), Pathology and Diagnostics (G.S.), and Biotechnology (A.Gi., G.S.), University of Verona, 37134 Verona, Italy; Chaum Life Center (S.-W.C.), CHA University, 135-081 Seoul, Korea; and Friedman School of Nutrition Science and Policy (S.-W.C.), Tufts University, Boston, Massachusetts 02111.

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http://dx.doi.org/10.1210/jc.2015-1760DOI Listing
September 2015

Evidence for a Transient Additional Ligand Binding Site in the TAS2R46 Bitter Taste Receptor.

J Chem Theory Comput 2015 Sep 24;11(9):4439-49. Epub 2015 Aug 24.

Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE) , Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany.

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http://dx.doi.org/10.1021/acs.jctc.5b00472DOI Listing
September 2015

Role of active-site residues Tyr55 and Tyr114 in catalysis and substrate specificity of Corynebacterium diphtheriae C-S lyase.

Proteins 2015 Jan 18;83(1):78-90. Epub 2014 Nov 18.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona, Italy.

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http://dx.doi.org/10.1002/prot.24707DOI Listing
January 2015

Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase-an enzyme used in bioremediation.

J Mol Model 2014 Dec 30;20(12):2531. Epub 2014 Nov 30.

Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada le Grazie 15, 37134, Verona, Italy.

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http://dx.doi.org/10.1007/s00894-014-2531-yDOI Listing
December 2014

Characterization of C-S Lyase from C. diphtheriae: a possible target for new antimicrobial drugs.

Biomed Res Int 2013 11;2013:701536. Epub 2013 Sep 11.

Department of Biotechnology, University of Verona, 15 Strada Le Grazie, 37134 Verona, Italy.

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http://dx.doi.org/10.1155/2013/701536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784150PMC
June 2014

Identification of aldolase and ferredoxin reductase within the dbt operon of Burkholderia fungorum DBT1.

J Basic Microbiol 2014 May 17;54(5):464-9. Epub 2013 May 17.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.

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http://dx.doi.org/10.1002/jobm.201200408DOI Listing
May 2014

Chemosensorial G-proteins-coupled receptors: a perspective from computational methods.

Adv Exp Med Biol 2014 ;805:441-57

Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), Trieste, Italy.

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http://dx.doi.org/10.1007/978-3-319-02970-2_18DOI Listing
May 2014

Structure/function relationships of phospholipases C Beta.

Curr Protein Pept Sci 2013 Dec;14(8):650-7

Department of Biotechnology, University of Verona, Ca' Vignal 1: strada le Grazie 15, I-37134 Verona, Italy.

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http://dx.doi.org/10.2174/13892037113146660085DOI Listing
December 2013

Genome-wide Membrane Protein Structure Prediction.

Curr Genomics 2013 Aug;14(5):324-9

Applied Bioinformatics Group, Dept. of Biotechnology, University of Verona, strada Le grazie 15, 37134, Verona, Italy; ; German Research School for Simulation Sciences, Juelich, Germany; ; Center for Biomedical Computing (CBMC), University of Verona, strada Le grazie 8, 37134, Verona, Italy.

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http://dx.doi.org/10.2174/13892029113149990009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763683PMC
August 2013

A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations.

J Chem Theory Comput 2013 Feb 16;9(2):1240-6. Epub 2013 Jan 16.

CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, 34165 Trieste, Italy.

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http://dx.doi.org/10.1021/ct3008233DOI Listing
February 2013

Structural requirements for cooperativity in ileal bile acid-binding proteins.

J Biol Chem 2011 Nov 14;286(45):39307-17. Epub 2011 Sep 14.

Department of Biotechnology, University of Verona, 37134 Verona, Italy.

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http://dx.doi.org/10.1074/jbc.M111.261099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234755PMC
November 2011

Nicotine blocks the hyperpolarization-activated current Ih and severely impairs the oscillatory behavior of oriens-lacunosum moleculare interneurons.

J Neurosci 2010 Aug;30(32):10773-83

Neurobiology Department and Italian Institute of Technology Unit, International School for Advanced Studies (SISSA), 34014 Trieste, Italy.

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http://dx.doi.org/10.1523/JNEUROSCI.2446-10.2010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634696PMC
August 2010

Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor.

PLoS One 2010 Aug 25;5(8):e12394. Epub 2010 Aug 25.

Statistical and Biological Physics, International School for Advanced Studies and DEMOCRITOS Modeling, Center for Research in Atomistic Simulations, Trieste, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012394PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928277PMC
August 2010

Mutation analysis of violaxanthin de-epoxidase identifies substrate-binding sites and residues involved in catalysis.

J Biol Chem 2010 Jul 27;285(31):23763-70. Epub 2010 May 27.

Dipartimento di Biologia, Università di Padova, Via Ugo Bassi 58 B, 35121 Padova, Italy.

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http://dx.doi.org/10.1074/jbc.M110.115097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911307PMC
July 2010

NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.

Nucleic Acids Res 2010 Jul 31;38(Web Server issue):W628-32. Epub 2010 May 31.

Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 1, 37134 Verona, Italy.

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http://dx.doi.org/10.1093/nar/gkq484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896076PMC
July 2010

Gating in CNGA1 channels.

Pflugers Arch 2010 Mar 7;459(4):547-55. Epub 2009 Nov 7.

CBM S.c.r.l, Area Science Park SS 14 Km 163.5, 34012, Basovizza (TS), Trieste, Italy.

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http://dx.doi.org/10.1007/s00424-009-0751-2DOI Listing
March 2010

Site-directed enzymatic PEGylation of the human granulocyte colony-stimulating factor.

FEBS J 2009 Nov 16;276(22):6741-50. Epub 2009 Oct 16.

Bio-Ker Srl, c/o Sardegna Ricerche Scientific Park, Pula, Cagliari, Italy.

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http://doi.wiley.com/10.1111/j.1742-4658.2009.07387.x
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http://dx.doi.org/10.1111/j.1742-4658.2009.07387.xDOI Listing
November 2009

Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase Itch and the E2 UbcH7.

Biochem Pharmacol 2008 Dec 31;76(11):1620-7. Epub 2008 Aug 31.

Department of Biochemical Sciences "Rossi-Fanelli", University of Rome "La Sapienza", P.le Aldo Moro 5, Rome, Italy.

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http://linkinghub.elsevier.com/retrieve/pii/S000629520800593
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http://dx.doi.org/10.1016/j.bcp.2008.08.026DOI Listing
December 2008

The evaluation of protein structure prediction results.

Mol Biotechnol 2008 May 11;39(1):1-8. Epub 2007 Dec 11.

Department of Biochemical Sciences Rossi Fanelli, University of Rome La Sapienza, P. le A. Moro, 5, 00185, Rome, Italy.

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http://dx.doi.org/10.1007/s12033-007-9023-6DOI Listing
May 2008

Automatic procedure for using models of proteins in molecular replacement.

Proteins 2007 Feb;66(3):689-96

Department of Biochemical Sciences, University of Rome La Sapienza, P.le Aldo Moro, 5-00185 Rome, Italy.

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http://dx.doi.org/10.1002/prot.21225DOI Listing
February 2007

Locking CNGA1 channels in the open and closed state.

Biophys J 2006 May 2;90(10):3599-607. Epub 2006 Mar 2.

International School for Advanced Studies and Instituto Nazionale Fisica della Materia, I-34014 Trieste, Italy.

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http://dx.doi.org/10.1529/biophysj.105.073346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440740PMC
May 2006

Evaluating the usefulness of protein structure models for molecular replacement.

Bioinformatics 2005 Sep;21 Suppl 2:ii72-6

Department of Biochemical Sciences, University of Rome La Sapienza, Rome, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bti1112DOI Listing
September 2005

Structural basis of gating of CNG channels.

FEBS Lett 2005 Mar;579(9):1968-72

Istituto Nazionale per la Fisica della Materia and International School for Advanced Studies, Via Beirut 4, 34014 Trieste, Italy.

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http://dx.doi.org/10.1016/j.febslet.2005.01.086DOI Listing
March 2005

Molecular modeling of ion channels: structural predictions.

Curr Opin Chem Biol 2003 Feb;7(1):150-6

International School for Advanced Studies, via Beirut 2, 34014 Trieste, Italy.

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http://dx.doi.org/10.1016/s1367-5931(02)00012-1DOI Listing
February 2003