bioweb: molecular modelling group / grupo de modelado molecular

http://www.cbm.csic.es/bioweb

 



Publications since 2004. / Publicaciones desde 2004. (PubMed/Medline)
(A: article/artículo; R: review/revisión; C: book chapter/capítulo de libro; O: other/otros)

 2017:
 
(A).-
Marcos-Alcalde, I., Mendieta-Moreno, J.I., Puisac, B., Gil-Rodríguez, M.C., Hernández-Marcos, M., Soler-Polo, D., Ramos, F.J., Ortega, J., Pié, J., Mendieta, J. & Gómez-Puertas, P. (2017). Two-step ATP-driven opening of cohesin head. Scientific Reports 7, 3266.  [PubMed]  [PDF]  [http://dx.doi.org/10.1038/s41598-017-03118-9]
(A).-
Buey, R.M., Fernández-Justel, D., Marcos-Alcalde. Í., Winter, G., Gómez-Puertas, P., de Pereda, J.M. & Revuelta, J.L. (2017). A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases. Scientific Reports 7, 2648.  [PubMed]  [PDF]  [http://dx.doi.org/10.1038/s41598-017-02805-x]
(A).-
Puisac, P., Teresa-Rodrigo, M.E., Hernández-Marcos, M., Baquero-Montoya, C., Gil-Rodríguez, M.C., Visnes, T., Bot, C., Gómez-Puertas, P., Kaiser, F.J., Ramos, F.J., Ström, L. & Pié, J. (2017). mRNA quantification of NIPBL isoforms A and B in adult and fetal human tissues, and a pathological variant affecting only isoform A in two patients with Cornelia de Lange Syndrome. International Journal of Molecular Sciences 18, 481.  [PubMed]  [PDF]  [http://dx.doi.org/10.3390/ijms18030481]

 2016:
 
(A).-
Mendieta-Moreno, J., Trabada, D., Mendieta, J., Lewis, J., Gómez-Puertas, P. & Ortega, J. (2016). Quantum Mechanics / Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer. Journal of Physical Chemistry Letters 7, 4391–4397.  [PubMed]  [PDF]  [http://dx.doi.org/10.1021/acs.jpclett.6b02168]
(A).-
Aguilera Rossi, C.A., Gómez-Puertas, P. & Ayala Serrano, J.A. (2016). In vivo functional and molecular characterization of the Penicillin-Binding Protein 4 (DacB) of Pseudomonas aeruginosa. BMC Microbiology 16, 234.  [PubMed]  [PDF]  [http://dx.doi.org/10.1186/s12866-016-0853-x]
(R).-
Pié, J., Puisac, B., Hernández-Marcos, M., Teresa-Rodrigo, M.E., Gil-Rodríguez, M.C., Baquero-Montoya, C., Bernal, M.L., Bueno, I., Gómez-Puertas, P. & Ramos, F.J. (2016). Special cases in Cornelia de Lange Syndrome: the Spanish experience. American Journal of Medical Genetics Part C 172C, 198-205  [PubMed]  [PDF]  [http://dx.doi.org/10.1002/ajmg.c.31501]

 2015:
 
(A).-
Marcos-Alcalde, I., Setoain, J., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2015). MEPSA: minimum energy pathway analysis for energy landscapes. Bioinformatics 31, 3853-3855.  [PubMed]  [PDF]  [http://dx.doi.org/10.1093/bioinformatics/btv453]
(A).-
Salvarelli, E., Krupka, M., Rivas, G., Mingorance, J., Gómez-Puertas, P., Alfonso, C. & Rico, A.I. (2015). The Cell Division Protein FtsZ from Streptococcus pneumoniae Exhibits a GTPase Activity Delay. Journal of Biological Chemistry 290, 25081–25089.  [PubMed]  [PDF]  [http://dx.doi.org/10.1074/jbc.M115.650077]
(A).-
Mendieta-Moreno, J.I., Marcos-Alcalde, I., Trabada, D.G., Gómez-Puertas, P., Ortega, J. & Mendieta, J. (2015). A practical Quantum Mechanics Molecular Mechanics method for the dynamical study of reactions in biomolecules. Advances in Protein Chemistry and Structural Biology 100, 67-88.  [PubMed]  [PDF]  [http://dx.doi.org/10.1016/bs.apcsb.2015.06.003]
(A).-
Valdivieso, E., Perteguer, M.J., Hurtado, C., Campioli, P., Rodríguez, E., Saborido, A., Martínez-Sernández, V., Gómez-Puertas, P., Ubeira, F.M. & Gárate, T. (2015). ANISERP: a new serpin from the parasite Anisakis simplex. Parasites & Vectors 8, 399.  [PubMed]  [PDF]  [http://dx.doi.org/10.1186/s13071-015-1006-z]
(A).-
Martín-García, F., Papaleo, E., Gómez-Puertas, P., Boomsma, W. & Lindorff-Larsen, K. (2015). Comparing molecular dynamics force fields in the essential subspace. Plos ONE 10, e0121114.  [PubMed]  [PDF]  [http://dx.doi.org/10.1371/journal.pone.0121114]
(A).-
Gil-Rodríguez, M.C., ... , Marcos-Alcalde, I., Wesselink, J-J., Lusa-Bernal, S., ... , Gómez-Puertas, P., ..., & Pié, J. (2015). De novo Heterozygous Mutations in SMC3 Cause a Range of Cornelia De Lange Syndrome-Overlapping Phenotypes. Human Mutation 36, 454-462.  [PubMed]  [PDF]  [http://dx.doi.org/10.1002/humu.22761]

 2014:
 
(A).-
Baquero-Montoya, C., Gil-Rodríguez, M.C., Hernández-Marcos, M., Teresa-Rodrigo, M.E., Vicente-Gabas, A., Bernal, M.L., Casale, C.H., Bueno-Lozano, G., Bueno-Martínez, I., Queralt, E., Villa, O., Hernando-Davalillo, C., Armengol, L., Gómez-Puertas, P., Puisac, B., Selicorni, A., Ramos, F.J. & Pié, J. (2014). Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation. European Journal of Medical Genetics 57, 503-509.  [PubMed]  [PDF]  [http://dx.doi.org/10.1016/j.ejmg.2014.05.006]
(A).-
Mendieta-Moreno, J.I., Walker, R., Lewis, J., *Gómez-Puertas, P., ^Mendieta, J. & *^Ortega, J. (*Corresponding authors; ^Co-last authors) (2014). FIREBALL/AMBER: An efficient local-orbital DFT QM/MM method for biomolecular systems. Journal of Chemical Theory and Computation 10, 2185–2193.  [PDF]  [http://dx.doi.org/10.1021/ct500033w]
(R).-
Iozzo, P., Holmes, M., Schmidt, M.V., Cirulli, F., Guzzardi, M.A., Berry, A., Balsevich, G., Andreassi, M.G., Wesselink J.J., Liistro, T. Gómez-Puertas, P., Eriksson, J.G. & Seckl, J. (2014). Developmental ORIgins of Healthy and Unhealthy AgeiNg: The Role of Maternal Obesity - Introduction to DORIAN. Obesity Facts 7, 130-151.  [PDF]  [http://dx.doi.org/10.1159/000362656]
(A).-
López-Camacho, E., Rentero, Z., Ruiz-Carrascoso, G., Wesselink, J-J., Pérez-Vázquez, M., Lusa-Bernal, S., Gómez-Puertas, P., Kingsley, R.A., Gómez-Sánchez, P., Campos, J., Oteo, J. & Mingorance, J. (2014). Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens. Clinical Microbiology and Infection 20, O891-O893.  [PubMed]  [PDF - manuscript]  [http://dx.doi.org/10.1111/1469-0691.12616]
(A).-
Betancor, G., ,Nevot, M., Mendieta, J., Gómez-Puertas, P., Martínez, M.A. & Menéndez-Arias, L. (2014). Molecular basis of the association of H208Y and thymidine analogue resistance mutations M41L, L210W and T215Y in the HIV-1 reverse transcriptase of treated patients. Antiviral Research 106, 42-52.  [PubMed]  [PDF]  [Supplementary Info PDF]  [http://dx.doi.org/10.1016/j.antiviral.2014.03.004]
(A).-
Baquero-Montoya, C., Gil-Rodríguez, M.C., Braunholz D., Teresa-Rodrigo, M.E., Obieglo C., Gener, B., Schwarzmayr, T., Strom, T.M., Gómez-Puertas, P., Puisac, B., Gillessen- Kaesbach, G., Musio, A., Ramos, F.J., Kaiser, F.J. & Pié, J. (2014). Somatic mosaicism in a Cornelia de Lange syndrome patient with NIPBL mutation identified by different Next Generation Sequencing approaches. Clinical Genetics 86, 595–597.  [PubMed]  [PDF]  [http://dx.doi.org/10.1111/cge.12333]
(A).-
Gonzalez de Prado Salas, P., Hörger, I., Martín-García, F., Mendieta, J., Alonso, A., Encinar, M., Gómez-Puertas, P., Vélez, M. & Tarazona, P. (2014). Torsion and curvature of FtsZ filaments. Soft Matter 10, 1977-1986.  [PubMed]  [PDF]  [Supplementary Info PDF]  [http://dx.doi.org/10.1039/c3sm52516c]

 2013:
 
(A).-
Reis, F.P., Barbas, A., Klauer, A.A., Schaeffer, D., López-Viñas, E., Gómez-Puertas, P., van Hoof, A. & Arraiano, C.M. (2013). Modulating the RNA processing and decay by the exosome: altering Rrp44/Dis3 activity and end-product. PLoS ONE 8(11): e76504.  [PubMed]  [PDF]  [http://dx.doi.org/10.1371/journal.pone.0076504]
(A).-
Ramos, M., Menao, S., Arnedo, M., Puisac, B., Gil-Rodríguez, M.C., Teresa-Rodrigo, M.E., Hernández-Marcos, M., Pierre, G., Ramaswami, U., Baquero-Montoya, C., Bueno, G., Casale, C., Hegardt, F.G, Gómez-Puertas, P. & Pié, J. (2013). New case of Mitochondrial HMG-CoA Synthase deficiency. Functional analysis of eight mutations. European Journal of Medical Genetics 56, 411-415.  [PubMed]  [PDF]  [http://dx.doi.org/10.1016/j.ejmg.2013.05.008]
(A).-
Puisac, B., Teresa-Rodrigo, M.E., Arnedo, M., Gil-Rodríguez, M.C., Pérez-Cerdá, C., Ribes, A., Pié, A., Bueno, G., Gómez-Puertas, P. & Pié, J. (2013). Analysis of aberrant splicing and nonsense-mediated decay of the stop codon mutations c.109G>T and c.504_505delCT in 7 patients with HMG-CoA lyase deficiency. Molecular Genetics and Metabolism 108, 232-240.  [PubMed]  [PDF]  [http://dx.doi.org/10.1016/j.ymgme.2013.01.019]
(A).-
Martín-García, F., Mendieta-Moreno, J.I., Marcos-Alcalde, I, *Gómez-Puertas, P. & Mendieta, J. (* Corresponding author). (2013). Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: An alternative role for ß-Glu 188. Biochemistry 52, 959-966.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [Supp. video. AVI]  [http://dx.doi.org/10.1021/bi301109x]
(A).-
Perteguer, M.J., Gómez-Puertas, P., Cañavate, C., Dagger, F., Gárate, T. & Valdivieso, E. (2013). Ddi1-like protein from Leishmania major is an active Aspartyl-Proteinase. Cell Stress & Chaperones 18, 171–181.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [cover paper / artículo de portada]  [http://dx.doi.org/10.1007/s12192-012-0368-9]
(A).-
Rodríguez, J.M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.J., López, G., Valencia, A. & Tress, M. (2013). APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research 41(Database issue), D110-D117.  [PubMed]  [http://dx.doi.org/10.1093/nar/gks1058]

 2012:
 
(A).-
Wesselink, J.J., López-Camacho, E., De la Peña, S., Ramos-Ruiz, R., Ruiz-Carrascoso, G., Lusa-Bernal, S., Fernández-Soria, V., Gómez-Gil, R., *Gómez-Puertas, P. & *Mingorance, J. (* Corresponding authors). (2012). Genome sequence of OXA-48 carbapenemase producing Klebsiella pneumoniae KpO3210. Journal of Bacteriology 194, 6981.  [PubMed]  [PDF]  [http://dx.doi.org/10.1128/JB.01897-12]
(A).-
Arnedo, M., Menao, S., Puisac, B., Teresa-Rodrigo, M., Gil-Rodríguez, M., López-Viñas, E., Gómez-Puertas, P., Casals, N., Casale, C.H., Hegardt, F.G. & Pie, J. (2012). Characterization of a novel HMG-CoA Lyase enzyme with a dual location in endoplasmic reticulum and cytosol. Journal of Lipid Research 53, 2046-2056.  [PubMed]  [PDF]  [http://dx.doi.org/10.1194/jlr.M025700]
(A).-
Ahijado-Guzmán, R., Gómez-Puertas, P., Alvarez-Puebla, R.A., Rivas, G. & Liz-Marzán, L.M. (2012). SERS-based detection of the interactions between the essential cell division FtsZ protein and bacterial membrane elements. ACS Nano 6, 7514-7520.  [PubMed]  [PDF]  [http://dx.doi.org/10.1021/nn302825u]
(A).-
González-Magaldi, M., Postigo, R., de la Torre, B.G., Vieira, Y.A, López-Viñas, E., Gómez-Puertas, P., Andreu, D., Kremer, L., Rosas, M.F. & Sobrino, F. (2012). Mutations that hamper dimerization of foot-and-mouth disease virus 3A protein are detrimental for infectivity. Journal of Virology 86, 11013-11023.  [PubMed]  [PDF]  [http://dx.doi.org/10.1128/JVI.00580-12]
(A).-
Mendieta, J., Pérez-Lago, L., Salas, M., & Camacho A. (2012). Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove. Journal of Bacteriology 194, 4727-35.  [PubMed]  [PDF - manuscript]  [http://dx.doi.org/10.1128/JB.00677-12]
(A).-
Matos, R.G., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2012). The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes. Biochimica et Biophysica Acta (BBA) - General Subjects 1820, 1543–1552.  [PubMed]  [PDF]  [http://dx.doi.org/10.1016/j.bbagen.2012.06.009]
(A).-
Martín-García, F., Salvarelli, E., Mendieta-Moreno, J.I., Vicente, M., Mingorance, J., Mendieta, J. & Gómez-Puertas, P. (2012). Molecular dynamics simulation of GTPase activity in polymers of the cell division protein FtsZ. FEBS Letters 586, 1236–1239.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [Supp. video. AVI]  [Supp. video. MOV -HD-]  [http://dx.doi.org/10.1016/j.febslet.2012.03.042]
(A).-
Martín-García, F., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2012). Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion. Biochemical and Biophysical Research Communications 420, 42-47.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [http://dx.doi.org/10.1016/j.bbrc.2012.02.112]
(A).-
Martín-García, F., Mendieta-Moreno, J.I., López-Viñas, E., *Gómez-Puertas, P. & *Mendieta, J. (* Co-last authors) (2012). The Role of Gln(61) in HRas GTP Hydrolysis: A Quantum Mechanics/Molecular Mechanics Study. Biophysical Journal 102, 152-157.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [Supp. video. AVI]  [Supp. video. AVI -HD-]  [http://dx.doi.org/10.1016/j.bpj.2011.11.4005]
(A).-
Puisac, B., Ramos, M., Arnedo, M., Menao, S., Gil-Rodríguez, M.C., Teresa-Rodrigo, M.E., Pié, A., de Karam, J.C., Wesselink, J.J., Giménez, I., Ramos, F.J., Casals, N., Gómez-Puertas, P., Hegardt, F.G. & Pié, J. (2012). Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway. Molecular Biology Reports 39, 4777-4785.  [PubMed]  [PDF]  [http://dx.doi.org/10.1007/s11033-011-1270-8]

 2011:
 
(A).-
López, E., Wesselink, J.J., López, I., Mendieta, J., *Gómez-Puertas, P. & *Muñoz, S.R. (* Co-last authors) (2011). Technical phosphoproteomic and bioinformatic tools useful in cancer research. Journal of Clinical Bioinformatics 1, 26.  [PubMed]  [PDF]
(A).-
Kisic, M., Matamoros, T., Nevot, M., Mendieta, J., Martínez-Picado, J., Martínez, M.A. & Menéndez-Arias, L. (2011). Thymidine analogue excision and discrimination modulated by mutational complexes including single amino acid deletions of Asp-67 or Thr-69 in HIV-1 reverse transcriptase. Journal of Biological Chemistry 286, 20615-20624.  [PubMed]  [PDF]
(A).-
Matos, R.G., Barbas, A, Gómez-Puertas, P. & Arraiano, C.M. (2011). Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade dsRNA. PROTEINS: Structure, Function, and Bioinformatics 79, 1853-1867.  [PubMed]  [PDF]  [Supp. Inf. PDF]
(A).-
Oroz, J., Valbuena, A., Vera, A.M., Mendieta, J., Gómez-Puertas, P. & Carrión-Vázquez M. (2011). Nanomechanics of the cadherin ectodomain: 'canalization' by Ca2+ binding results in a new mechanical element. Journal of Biological Chemistry 286, 9405-9418.  [PubMed]  [PDF]
(R).-
López, E., Matthiesen, R., Mendieta, J., Wesselink, J.J., Gómez-Puertas, P. & Ferreira, A. (2011). Functional phosphoproteomics tools for current immunological disorders research. Journal of Integrated -OMICS 1, 1-16.  [Journal]  [PDF]
(A).-
Hurtado, C., Bustos, M.J., Granja, A.G., de León, P., Sabina, P., López-Vinas, E., Gómez-Puertas, P., Revilla, Y. & Carrascosa, A.L. (2011). The African swine fever virus lectin EP153R modulates the surface membrane expression of MHC class I antigens. Archives of Virology 156, 219-234.  [PubMed]  [PDF]

 2010:
 
(R).-
Mingorance, J., Rivas, G., Vélez, M., Gómez-Puertas, P. & Vicente, M. (2010). Strong FtsZ is with the force: mechanisms to constrict bacteria. Trends in Microbiology 18, 348-356.  [PubMed]  [PDF]
(A).-
Magro, M., Andreu, D., Gómez-Puertas, P., Melero, J.A. & Palomo, C. (2010). Neutralization of Human Respiratory Syncytial Virus Infectivity by Antibodies and Low Molecular Weight Compounds Targeted Against the Fusion (F) Glycoprotein. Journal of Virology 84, 7970-7982.  [PubMed]  [PDF]
(R).-
Romanelli, V., Belinchón, A., Benito-Sanz, S., Martínez-Glez, V., Gracia-Bouthelier, R., Heath, K.E., Campos-Barros, A., García-Miñaur, S., Fernández, L., Meneses, H., López-Siguero, J.P., Guillén-Navarro, E., Gómez-Puertas, P., Wesselink, J.J., Mercado, G., Esteban-Marfil, V., Palomo, R., Mena, R., Sánchez, A., del Campo, M. & Lapunzina, P. (2010). CDKN1C (p57Kip2) Analysis in Beckwith-Wiedemann syndrome (BWS) Patients: Genotype-Phenotype Correlations, Novel Mutations, and Polymorphisms. American Journal of Medical Genetics Part A 152A, 1390-1397.  [PubMed]  [PDF]
(A).-
Pié, J., Gil-Rodríguez, M.C., Ciero, M., López-Viñas, E., Ribate, M.P., Arnedo, M., Deardorff, M.A., Puisac, B., Legarreta, J., de Karam, J.C., Rubio, E., Bueno, I., Baldellou, A., Calvo, M.T., Casals, N., Olivares, J.L., Losada, A., Hegardt, F.G., Krantz, I.D., Gómez-Puertas, P. & Ramos F.J. (2010). Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. American Journal of Medical Genetics. Part A. 152A, 924-929.  [PubMed]  [PDF]  [Suppl.Material. PDF]

 2009:
 
(A).-
Mendieta, J., Rico, A.I., López-Viñas, E., Vicente, M., Mingorance, J. & Gómez-Puertas, P. (2009). Structural and Functional Model for Ionic (K+/Na+) and pH Dependence of GTPase Activity and Polymerization of FtsZ, the Prokaryotic Ortholog of Tubulin. Journal of Molecular Biology 390, 17-25.  [PubMed]  [PDF]
(A).-
Barbas, A., Matos, R.G., Amblar, M., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2009). Determination of key residues for catalysis and RNA-cleavage specificity: one mutation turns RNase II into a "super"-enzyme. Journal of Biological Chemistry 284, 20486-20498.  [PubMed]  [PDF]
(A).-
Menao, S., López-Viñas, E., Mir, C., Puisac, B., Gratacós, E., Arnedo, M., Carrasco, P., Moreno, S., Ramos, M., Gil, M.C., Pié, A., Ribes, A., Pérez-Cerda, C., Ugarte, M., Clayton, P.T., Korman, S.H., Serra, D., Asins, G., Ramos, F.J., Gómez-Puertas, P., Hegardt, F.G., Casals, N. & Pié, J. (2009). Ten novel HMGCL mutations in 24 patients of different origin with 3-hydroxy-3-methyl-glutaric aciduria. Human Mutation 30, E520-9.  [PubMed]  [PDF]
(A).-
Mera, P., Bentebibel, A., López-Viñas, E., Cordente, A.G., Gurunathan, C., Sebastián, D., Ariza, X., Gómez-Puertas, P., Asins, G., Serra, D., García, J. & Hegardt, F.G. (2009). C75 is Converted to C75-CoA in the Hypothalamus, where it Inhibits Carnitine Palmitoyltransferase 1 and Decreases Food Intake and Body Weight. Biochemical Pharmacology 77, 1084-1095.  [PubMed]  [PDF]

 2008:
 
(A).-
Cuellar, J., Martin-Benito, J., Scheres, S.H.W., Sousa, R., Moro, F., Lopez-Viñas, E., Gomez-Puertas, P., Muga, A., Carrascosa, J.L. & Valpuesta, J.M. (2008). The structure of a CCT:Hsc70NBD complex suggests a mechanism for Hsp70 delivery of substrates to the chaperonin. Nature Structural & Molecular Biology 15, 858-864.  [PubMed]  [PDF]  [Suppl.Info-PDF]
(A).-
Kisic, M., Mendieta, J., Puertas, M.C., Parera, M., Martínez, M.A., Martínez-Picado, J. & Menéndez-Arias, L. (2008). Mechanistic Basis of Zidovudine Hypersusceptibility and Lamivudine Resistance Conferred by the Deletion of Codon 69 in the HIV-1 Reverse Transcriptase Coding Region. Journal of Molecular Biology 382, 327-341.  [PubMed]  [PDF]
(A).-
Barbas, A., Matos, R.G., Amblar, M., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2008). New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end-product. Journal of Biological Chemistry 283, 13070-13076.  [PubMed]  [PDF]
(A).-
Llorente, M.T., Taylor, I.A., López-Viñas, E., Gómez-Puertas, P., Calder, L.J., García-Barreno, B. & Melero, J.A. (2008). Structural properties of the human respiratory syncytial virus P protein: Evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase co-factors. PROTEINS: Structure, Function and Bioinformatics 72, 946-958.  [PubMed]  [PDF]
(A).-
Asenjo, A., Mendieta, J., Gómez-Puertas, P. & Villanueva, N. (2008). Residues in human Respiratory syncytial virus P protein that are essential for its activity on RNA viral synthesis. Virus Research 132, 160-173.  [PubMed]  [PDF]
(A).-
Mendieta, J., Cases-González, C.E., Matamoros, T., Ramírez, G. & Menéndez-Arias, L. (2008). A Mg(2+)-induced conformational switch rendering a competent DNA polymerase catalytic complex. PROTEINS: Structure, Function and Bioinformatics 71, 565-574.  [PubMed]  [PDF]
(A).-
López-Viñas, E.*, Atrian, S.*, Gomez-Puertas, P., Chabás, A., Vilageliu, L. & Grinberg, D. (2008). An evolutionary and structure-based docking model for glucocerebrosidase-saposin C and glucocerebrosidase-substrate interactions. Relevance for Gaucher disease. PROTEINS: Structure, Function and Bioinformatics 70, 882-891.  [PubMed]  [PDF]
(* Co-first authors)

  2007:
 
(A).-
Blas-Galindo, E., Cava, F., López-Viñas, E., Mendieta, J. & Berenguer, J. (2007). Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus. Applied and Environmental Microbiology 73, 5138-5145.  [PubMed]  [PDF]  [Suppl. Mat.]
(R).-
Pié J., López-Viñas, E., Puisac, B., Menao, S., Pié A., Casale, C., Ramos, F., Hegardt, F.G., Gómez-Puertas, P. & Casals, N. (2007). Molecular genetics of HMG-CoA lyase deficiency. Molecular Genetics and Metabolism 92, 198-209.  [PubMed]  [PDF]
(A).-
López-Viñas, E., Bentebibel, A., Gurunathan, C., Morillas, M., De Arriaga, D., Serra, D., Asins, G., Hegardt, F. & Gómez-Puertas, P. (2007). Definition by functional and structural analysis of two malonyl-CoA sites in carnitine palmitoyltransferase 1A. Journal of Biological Chemistry 282, 18212-18224.  [PubMed]  [PDF]
(A).-
Mendieta, J., Pérez-Lago, J., Salas, M. & Camacho, A. (2007). DNA sequence-specific recognition by a transcripcional regulator requires indirect readout of A-tracts. Nucleic Acids Research 35, 3252-3261.  [PubMed]  [PDF]
(A).-
Carrasco, P., Menao, S., López-Viñas, E., Santpere, G., Clotet, J., Sierra, A.Y., Gratacos, E., Puisac, B., Gomez-Puertas, P., Hegardt, F.G., Pie, J. & Casals, N. (2007). C-Terminal End and Aminoacid Lys48 in HMG-Coa Lyase Are Involved in Substrate Binding and Enzyme Activity. Molecular Genetics and Metabolism 91, 120-127.  [PubMed]  [PDF] (cover paper / artículo de portada).
(A).- Agirrezabala, X., Velázquez-Muriel, J.A., Gomez-Puertas, P., Scheres, S.H.W., Carazo, J.M., & Carrascosa, J.L. (2007). Quasi-Atomic Model of Bacteriophage T7 Procapsid Shell:  Insights into the Structure and Evolution of a Basic Fold. Structure 15, 461-472.  [PubMed]  [PDF]
(A).- Cava, F., Laptenko, O., Borukhov, S., Chahlafi, Z., Blas-Galindo, E., Gomez-Puertas, P., & Berenguer, J. (2007). Control of the Respiratory Metabolism of Thermus thermophilus by the Conjugative Respiration Element NCE. Molecular Microbiology 64, 630-646.  [PubMed]  [PDF]
(A).-
Contreras, L., Gomez-Puertas, P., Iijima, M., Kobayashi, K., Saheki, T., & Satrústegui, J. (2007). Ca2+ Activation Kinetics of the Two Aspartate-glutamate Mitochondrial Carriers Aralar and Citrin: Role in Heart Malate-aspartate NADH Shuttle. Journal of Biological Chemistry 282, 7098-7106.  [PubMed]  [PDF]
(A).- Amblar, M., Barbas, A., Gomez-Puertas, P., & Arraiano, C. (2007). The role of the S1 domain in Exoribonucleolytic Activity: Substrate Specificity and Multimerization. RNA 13, 317-327.  [PubMed]  [PDF]
(A).- Martin-Benito, J., Gomez-Reino, J., Stirling, P.C., Lundin, V.F., Gomez-Puertas, P., Boskovic, J., Chacon, P., Fernandez, J.J., Berenguer, J., Leroux, M.R. & Valpuesta, J.M. (2007). Divergent substrate-binding mechanisms reveal an evolutionary specialization of eukaryotic prefoldin compared to its archaeal counterpart. Structure 15, 101-110.  [PubMed]  [PDF] (cover paper / artículo de portada).

  2006:
 
(A).-
Cordente, A.G., Lopez-Viñas, E., Vazquez, M.I., Gomez-Puertas, P., Asins, G., Serra, D. & Hegardt, F.G. (2006). Mutagenesis of specific amino acids converts carnitine  acetyltransferase into carnitine palmitoyltransferase. Biochemistry 45,6133-6141.  [PubMed]  [PDF]
(A).- Rodriguez-Pombo, P., Navarrete, R., Merinero, B., Gomez-Puertas, P. & Ugarte, M. (2006). Mutational Spectrum of Maple Syrup Urine Disease in Spain. Human Mutation 27, 715.  [PubMed]  [PDF]
(A).-
Bentebibel, A., Sebastian, D., Herrero, L., Lopez-Viñas, E., Serra, D., Asins, G., Gomez-Puertas, P. & Hegardt, F.G. (2006).  Novel effect of C75 on Carnitine Palmitoyltransferase I activity and palmitate oxidation. Biochemistry 45, 4339-4350.  [PubMed]  [PDF]
(A).-
Mir, C., Lopez-Viñas, E., Aledo, R., Puisac, B., Rizzo, C., Dionisi-Vici, C., Deodato, F., Pie, J., Gomez-Puertas, P., Hegardt, F.G. & Casals, N. (2006).  A single residue mutation, G203E, causes 3-hydroxy-3-methylglutaric aciduria by occluding the substrate channel in the 3D structural model of HMG-CoA lyase -Review. Journal of Inherited Metabolic Disease 29, 64-70.  [PubMed]  [PDF]
(R).-
Ortiz, A.R., Gomez-Puertas, P., Leo-Macias, A., Lopez-Romero, P., Lopez-Viñas, E., Morreale, A., Murcia, M., & Wang, K. (2006) Computational approaches to model ligand selectivity in drug design. Current Topics in Medicinal Chemistry 6, 41-55.  [PubMed]  [PDF]

  2005:
 
(A).-
Mendieta, J., Gago, F. & Ramirez, G. (2005). Binding of 5'-GMP to the GluR2 AMPA receptor: Insight from targeted molecular dynamics simulation. Biochemistry. 44:14470-14476.  [PubMed]  [PDF]
(O).-
Lopez-Viñas, E. & Gomez-Puertas, P. (2005) -Scientific divulgation-. Bioinformatica, la informacion al servicio de la ciencia (Bioinformatics, information in the service of science). Journal of the Official College of Physicists of Spain: Fisica y Sociedad 16, 46-50. [PDF]
(A).-
Mendieta, J., Fuertes, M.A., Kunchitapatham, R., Santa-María, I., Moreno, F.J., Alonso, C., Gago, F., Muñoz, V., Avila J. & Hernández, F.. (2005). Phosphorylation modulates the alpha helical structure and polymerization of a peptide from the third tau microtubule-binding repeat. Biochim Biophys Acta. 1721:16-26.  [PubMed]  [PDF]
(R).-
Perez, B., Desviat, L.R., Gomez-Puertas, P., Martinez, A., Stevens, R.C. & Ugarte, M. (2005). Kinetic and stability analysis of PKU mutations identified in BH(4)-responsive patients - Review. Molecular Genetics and Metabolism 86, S11-S16.  [PubMed]  [PDF]
(A).-
Tress, M., de Juan, D., Graña, O., Gomez, M.J., Gomez-Puertas, P., Gonzalez, J.M., Lopez, G. & Valencia, A. (2005). Scoring docking models with evolutionary information. PROTEINS: Structure, Function, and Bioinformatics 60, 275-280.  [PubMed]  [PDF]
(A).-
Puisac, B., Lopez-Viñas, E., Moreno, S., Mir, C., Perez-Cerda, C., Menao, S., Lluch, D., Pie, A., Gomez-Puertas, P., Casals, N., Ugarte, M., Hegardt, F.G. & Pie, J. (2005). Skipping of exon 2 and exon 2 plus 3 of HMG-CoA lyase (HL) gene produces the loss of beta sheets 1 and 2 in the recently proposed (beta-alpha)8 TIM barrel model of HL. Biophysical Chemistry 115, 241-245.  [PubMed]  [PDF]

  2004:
 
(C).-
Lopez-Viñas, E. & Gomez-Puertas, P. (2004). Sequence and structural alignments of eukaryotic and procaryotic cytoskeletal proteins. Chapter for "Molecules in time and space: Bacterial shape, division and phylogeny." M. Vicente, J. Tamames, A. Valencia & J. Mingorance (Eds.) Kluwer Academic/Plenum Publishers. 
(A).-
Mendieta, J. & Gago, F. (2004). In silico activation of Src tyrosine kinase reveals the molecular basis for intramolecular autophosphorylation. J. Mol. Graph. Model. 23:189-198.  [PubMed]  [PDF]
(A).-
Mendieta, J., Martin-Santamaria, S., Priego, E.M., Balzarini, J., Camarasa, E M.J., Perez-Perez M.J. & Gago, F. (2004). Role of histidine-85 in the catalytic mechanism of thymidine phosphorylase as assessed by targeted molecular dynamics simulations and quantum mechanical calculations. Biochemistry. 43:405-414.  [PubMed]  [PDF]
(A).-
Cordente, A.G., Lopez-Viñas, E., Vazquez, M.I., Swiegers, J.H., Pretorius, I.S., Gomez-Puertas, P., Hegardt, F.G., Asins, G. & Serra, D. (2004). Redesign of carnitine acetyltransferase specificity by protein engineering. Modification of methionine564 broadens the specificity to longer acyl-CoAs as substrates. Journal of Biological Chemistry 279, 33899-33908.  [PubMed]  [PDF]
(C).-
Mingorance, J., Rico, A. & Gomez-Puertas, P. (2004). Bacterial morphogenes. Chapter for "Molecules in time and space: Bacterial shape, division and phylogeny." M. Vicente, J. Tamames, A. Valencia & J. Mingorance (Eds.) Kluwer Academic/Plenum Publishers. 
(A).-
Gil, J., García, M.A., Gomez-Puertas, P., Guerra, S., Rullas, J., Nakano, H., Alcami, A. & Esteban, M. (2004). TRAF family proteins link PKR with NF-kB activation. Molecular and Cellular Biology 24, 4502-4512.  [PubMed]  [PDF]
(A).-
Morillas, M., Lopez-Viñas, E., Valencia, A., Serra, D., Gomez-Puertas, P., Hegardt, F.G. & Asins, G. (2004). Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal. Biochemical Journal 379, 777-784.  [PubMed]  [PDF]
(R).-
Gomez-Puertas, P., Martin-Benito, J., Carrascosa, J.L., Willison, K.R. & Valpuesta, J.M. (2004). The substrate recognition mechanisms in chaperonins - Review. Journal of Molecular Recognition 17, 85-94.  [PubMed]  [PDF]
(A).-
Falcon, A.M., Marion, R.M., Zurcher, T., Gomez-Puertas, P., Portela, A., Nieto, A. & Ortin, J. (2004). Defective RNA replication and late gene expression in temperature-sensitive (A/Victoria/3/75) Influenza viruses expressing deleted forms of NS1 protein. Journal of Virology 78, 3880-3888.  [PubMed]  [PDF]
(C).-
Lopez-Romero, P., Gomez, M.J., Gomez-Puertas, P. & Valencia, A. (2004). Prediction of functional sites in proteins by evolutionary methods. Chapter for "Principles and Practice. Methods in Proteome and Protein Analysis". R.M. Kamp, J. Calvete & T. Choli-Papadopoulou (Eds.) Springer-Verlag, Berlin Heidelberg.



BIOWEB: MOLECULAR MODELLING GROUP
Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM).
http://www.cbm.csic.es/bioweb
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28049 Madrid. Spain
Tel: (+34) 91 196 4662 / 4663
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