Comparing side chain packing in soluble proteins, protein‐protein interfaces, and transmembrane proteins

Autor: Alejandro Virrueta, Jennifer Gaines, Corey S. O'Hern, Mairead Butler, Sandra Acebes, Lynne Regan

Publikováno v: Gaines, J C, Acebes, S, Virrueta, A, Butler, M, Regan, L & O'Hern, C S 2018, ' Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins ', Proteins: Structure, Function, and Bioinformatics, vol. 86, no. 5, pp. 581-591 . https://doi.org/10.1002/prot.25479

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c13db29ffed2c0aef0c4c7b05880eaa7
https://doi.org/10.1002/prot.25479

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

Autor: M. Fátima Lucas, Sandra Acebes, Francisco J. Ruiz-Dueñas, Ángel T. Martínez, Mario Toubes, Marta Pérez-Boada, Verónica Sáez-Jiménez, Victor Guallar

Publikováno v: The Journal of Physical Chemistry B
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)
Recercat. Dipósit de la Recerca de Catalunya
instname

Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a316aef43f4fbb61f11b648e365f14fa

Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism

Autor: Adalgisa Sinicropi, Victor Guallar, Fátima Lucas, Elena Fernández-Fueyo, Vivian de los Ríos, Yuta Miki, Maria Camilla Baratto, Sandra Acebes, Francisco J. Ruiz-Dueñas, Rebecca Pogni, Ángel T. Martínez, María Isabel López Fernández, Kenneth E. Hammel, Riccardo Basosi

Publikováno v: Biochemical Journal

LiP (lignin peroxidase) from Trametopsis cervina has an exposed catalytic tyrosine residue (Tyr181) instead of the tryptophan conserved in other lignin-degrading peroxidases. Pristine LiP showed a lag period in VA (veratryl alcohol) oxidation. Howeve

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d02b1db35af6c0741ef19e8d408b262
https://doi.org/10.1042/bj20130251

Ecoupling server: A tool to compute and analyze electronic couplings

Autor: Israel, Cabeza de Vaca, Sandra, Acebes, Victor, Guallar

Publikováno v: Journal of computational chemistry. 37(18)

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electron

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::b60dd391f179a4883ae0abe5486959ae
https://pubmed.ncbi.nlm.nih.gov/27157013

Rational Enzyme Engineering Through Biophysical and Biochemical Modeling

Autor: David Almendral, Sandra Acebes, Ángel T. Martínez, Henrik Lund, M. Fátima Lucas, Victor Guallar, Emanuele Monza, Francisco J. Ruiz-Dueñas, Elena Fernández-Fueyo

Publikováno v: Recercat. Dipósit de la Recerca de Catalunya
instname
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)

Due to its importance in the pharmaceutical industry, ligand dynamic simulations have experienced a great expansion. Using all-atom models and cutting edge hardware, one can perform non-biased ligand migration, active site search and binding studies.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa3958af61a051dfb03a47fe1739f550
http://hdl.handle.net/2117/84341