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  • Equilibrium and dynamic studies for adsorption of boron on calcium alginate gel beads using principal component analysis (PCA) and partial least squares (PLS)

     Ruiz Planas, Montserrat; Roset Calzada, M. Lourdes; Demey Cedeño, Hary; Castro, S.; Sastre Requena, Ana Maria; Perez Gonzalez, Juan Jesus
    Materialwissenschaft und Werkstofftechnik
    Date of publication: 2013-05-29
    Journal article

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    In this paper, boron removal from aqueous solutions by adsorption on calcium alginate gel beads was investigated. Based on the batch tests, calcium alginate gel beads demonstrated a good capacity of adsorption; the maximum capacity obtained was 121 mg/g at pH 6. The aim of this paper is the study of analytical tools for extracting more analytical information from a few experiments. Principal component analysis (PCA) was employed to perform a comparative analysis between different isotherms obtained by varying the percentage of alginate on the adsorbent beads. The calculated fraction of the cumulative sum of squares for all the components (R2X(cum)) and the predictive reliability model based on the value of the correlation coefficient of cross validation (Q2 (cum)) obtained were 0.9639 and 0.8523, respectively. Dynamic system study using 20 different columns was carried out. Partial least squares (PLS) modeling are applied to characterize the effect of the experimental variables on the adsorption process. Some of the descriptors studied were the initial boron concentration (Co), adsorbent mass (m), pH, column diameter (dc), column depth (Z) and superficial flow velocity (U0). Experimental adsorptions were compared against predicted adsorptions and a correlation coefficient (r2) of 0.9927 was obtained.

  • Computational study of substrates and mediators features of lacasses

     Delavari, Azar; Perez Gonzalez, Juan Jesus
    Journal of biomolecular structure and dynamics
    Date of publication: 2013-06-10
    Journal article

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    The catalytic cycle of lacasses consists in the oxidation of the substrate with the concomitant reduction of molecular oxygen to water. In the process the substrate is converted to a free radical, that can oxidize larger substrates acting as a mediator or it can undergo polymerization. The goal of the present work is to characterize the laccase binding pocket of different species in order to establish their common pharmacophoric characteristics. For this purpose we have carried out docking studies with a subset of substrates, covering the diversity of substrates using the Glide program. We have rationalized the differential values of Km found among diverse species for a specific substrate.

  • Amygdalin analogs for the treatment of psoriasis

     Perez Gonzalez, Juan Jesus
    Future Medicinal Chemistry
    Date of publication: 2013-06-01
    Journal article

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    Psoriasis is one of the most prevalent autoimmune illness worldwide. Several treatments are available depending on the extension of the psoriatic lesion. Among the topical treatments corticoids, vitamin D3 analogs and retinoids are commonly used. These treatments may have adverse effects in the long-term. On the other hand, systemic conventional treatments include immunosupresors like cyclosporine or methotrexate associated with high toxicity levels. Biologicals are alternative therapeutical agents introduced in the last ten years. However, due to recent knowledge on the etiology of the disease, diverse new small molecules have appeared as promising alternatives for the treatment of psoriasis. In this line the inhibitors of Janus kinase 3, inhibitors of phosphodiestearse 4 and amygdalin analogs. The latter are promising molecules presently in preclinical studies which are the object of the present report.

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    Molecular determinants of the bacterial resistance to fluoroquinolones: A computational study  Open access

     Lupala, Cecylia Severin; Gomez Gutierrez, Patricia; Perez Gonzalez, Juan Jesus
    Current Computer-Aided Drug Design
    Date of publication: 2013-06-13
    Journal article

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    We carried out docking studies of fifteen diverse quinolones to the cleaved topoisomerase IV-DNA complex. Arg117 has not been described to be involved in resistance, since it is putatively involved in the enzymatic reaction and its mutation would be lethal for the organism. Mutants of Ser79 exhibit resistance to quinolones which can be explained by the loss of an important anchoring point. Interestingly, quinolone resistance observed in Asp83 mutants cannot be explained directly on the basis of the loss of a direct interaction, but could be explained on the basis of its involvement at the entrance of the ligands to their binding pocket since the residue is located at the mouth of the pocket. The results of the present study suggest that a Mg2+ is bound to quinolones before binding to the cleaved topoisomarase IV-DNA complex and use Asp83 for entry into the binding pocket.

    Abstract: Quinolones constitute a large class of antibacterial agents whose action is mediated through the formation of a ternary complex with DNA and either, DNA Gyrase or topoisomerase IV, resulting in the inhibition of DNA replication. In order to get a deeper insight into the features of the complex formation, we carried out docking studies of fifteen diverse quinolones to the cleaved topoisomerase IV-DNA complex. Docking studies were performed using the crystal structures of the cleaved complex with levofloxacin and moxifloxacin (pdb entries 3K9F and 2XKK, respectively) using the GOLD software. Ligands dock in positions similar to those of the crystal structures. Analysis of the results reveals that bound quinolones appear intercalated between the two nucleotides that are involved in the DNA cleavage and exhibit hydrogen bonds with Arg117 and, the latter mediated though a water molecule. Arg117 has not been described to be involved in resistance, since it is putatively involved in the enzymatic reaction and its mutation would be lethal for the organism. Mutants of Ser79 exhibit resistance to quinolones which can be explained by the loss of an important anchoring point. Interestingly, quinolone resistance observed in Asp83 mutants cannot be explained directly on the basis of the loss of a direct interaction, but could be explained on the basis of its involvement at the entrance of the ligands to their binding pocket since the residue is located at the mouth of the pocket. The results of the present study suggest that the 4-keto and 3-carboxyl groups of the fluoroquinolones bind a Mg2+ before binding to the cleaved topoisomarase IV-DNA complex and use Asp83 for entry into the binding pocket. Accordingly, mutations that do not conserve the binding capacity for the quinolone-Mg2+ complex will prevent the binding of this class of ligands. The results we present here are also compared with the structure of PD0305970 a 2,4-dione active against the Ser79 and Asp83 mutants.

  • Conformational diversity in contryphans from conus venom: Cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop

     Sonti, Rajesh; Gowd, Konkallu Hanumae; Rao, K. N Shashanka; Ragothama, Srinivasarao; Rodríguez García, Alejandro; Perez Gonzalez, Juan Jesus; Balaram, Padmanabhan
    Chemistry: a european journal
    Date of publication: 2013-11-05
    Journal article

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    Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCVDLYPWC* (In936) and Conus loroisii, GCPDWDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis¿ trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds. Flexibility in rigid structures: The ability of nature to synthesize constrained disulfide-bonded cyclic molecules which adopt well-defined multiple conformational states is highlighted. Aromatic/proline interactions modulate cis-trans equilibria about Xxx-Pro bonds in the 23-membered heterocyclic ring of the contryphans isolated from cone snail venom (see figure).

  • Amygdalin analogues inhibit INF-gamma signalling reducing inflammatory response in human keratinocytes (HaCat)

     Paoletti, Iole; De Gregorio, Vicenza; Baroni, Adone; Tufano, Maria Antonieta; Donnarumma, Giovanna; Perez Gonzalez, Juan Jesus
    Inflammation
    Date of publication: 2013-12-02
    Journal article

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    Peptide T (PT), an octapeptide fragment located in the V2 region of the HIV-1 gp120-coating protein, appears to be beneficial in the treatment of psoriasis. Our previous investigationssuggest that keratinocytes play a key role in conditioning the therapeutic effects of PT in psoriasis. The aim of this study was to explore the effects of PT and the peptidomimetic natural products,Dhurrin and Prunasin, on the expression of the IL-6, IL-8, IL-23, HSP70 and ICAM-1 on IFN-¿ and TNF-a-NHEK activated cells. Moreover, we analysed the interference of PT and its analogues through STAT-3 activation. Our results show that the analogues tested exhibit the beneficial biological effects of PT, suggesting the primary role of keratinocytes upon which PT and the peptidomimetics act directly, by reducing proinflammatory responses. Its reduction appears to be important for therapeutic approach in psoriasis pathogenesis.

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    Synthesis, Langmuir and Langmuir-Blodgett films of a calix[7]arene ethyl ester  Open access

     Torrent Burgues, Juan; Vocanson, Francis; Perez Gonzalez, Juan Jesus; Errachid, Abdelhamid
    Colloids and surfaces A: physicochemical and engineering aspects
    Date of publication: 2012
    Journal article

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    Postprint (author’s final draft)

  • Modelización de receptores acoplados a proteinas G y diseño de ligandos

     Roset Calzada, M. Lourdes; Perez Gonzalez, Juan Jesus
    Participation in a competitive project

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  • Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site

     Martinez Archundia, Marlet; Cordomí Montoya, Arnau; Garriga Sole, Pere; Perez Gonzalez, Juan Jesus
    Journal of biomedicine and biotechnology
    Date of publication: 2012
    Journal article

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  • Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics

     Sharma, Parul; Singh, Parvesh; Bisetty, Krishna; Rodríguez García, Alejandro; Perez Gonzalez, Juan Jesus
    Journal of peptide science
    Date of publication: 2011-03
    Journal article

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    Rational design of new class of BH3-mimetics as inhibitors of the Bcl-X(L) protein  Open access

     Pinto Manresa, Marta; Orzaez, Maria del Mar; Delgado-Soler, L.; Perez Gonzalez, Juan Jesus; Rubio Martinez, Jaime
    Journal of chemical information and modeling
    Date of publication: 2011-06
    Journal article

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    The Bcl-2 family of proteins plays an important role in the intrinsic pathway of cell apoptosis. Overexpression of prosurvival members of this family of proteins is often associated with the development of many types of cancer and confers resistance against conventional therapeutic treatments. Accordingly, antagonism of its protective function has emerged as an encouraging anticancer strategy. In the present work, we use a pharmacophore for describing interaction between the BH3 domain of different pro-apoptotic members and the pro-survival protein Bcl-xL in order to identify new lead compounds. In the strategy followed in the present work, the harmacophore was derived from molecular dynamics studies of different Bcl-xL/BH3 complexes. This pharmacophore was later used as query for 3D database screening. Hits obtained from the search were computationally assessed, and a subset proposed for in vitro testing. Two of the 15 compounds assayed were found able to disrupt the Bcl-xL/Bak(BH3) complex with IC50 values in the lower micromolar range. Finally, docking studies were performed to explore the binding mode of these compounds to Bcl-xL for further modifications.

  • A computational study of Neuromedin B

     Sharma, Parul; Singh, Parvesh; Bisetty, Krishna; Perez Gonzalez, Juan Jesus
    Computational and theoretical chemistry
    Date of publication: 2011-09-15
    Journal article

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    A methodological study has been undertaken to assess the conformational profile of Neuromedin B (NMB) using classical molecular dynamics simulations (MD) and replica exchange molecular dynamics (REMD) simulations under generalized Born (GB) solvent conditions. Comparison of the results obtained from these simulations suggests that the peptide has a propensity to adopt both b-turns and a-helical conformations regardless of the simulation protocols used. However, the conformations adopted more helical character under REMD conditions and showed good agreement with the NMR supported structure reported in the literature.

  • Is the folding topology of a protein related to its amino acid occurrence?

     Perez Gonzalez, Juan Jesus
    Journal of biomolecular structure and dynamics
    Date of publication: 2011-02
    Journal article

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  • Molecular mechanisms of disease for mutations at Gly-90 in rhodopsin

     Toledo, Darwin; Ramon Portés, Eva; Aguila Cerda, Mónica; Cordomí Montoya, Arnau; Perez Gonzalez, Juan Jesus; Mendes, H.F.; Cheetham, Michael E; Garriga Sole, Pere
    Journal of biological chemistry
    Date of publication: 2011-11-18
    Journal article

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  • Structural and Stability Studies of Class A G-protein coupled receptors

     Reyes Alcaraz, Arfaxad
    Defense's date: 2011-07-08
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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  • Estudi de la utilització dels mapes de potencial electrostàtic i de polarització com a descriptors moleculars  Open access

     Roset Calzada, M. Lourdes
    Defense's date: 2011-11-18
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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    La Ingeniería molecular se basa en el conocimiento de las características estereoelectrónicas que definen el reconocimiento molecular, que es el resultado de una complementariedad, tanto geométrica como electrónica, entre diferentes entidades moleculares. La importancia de las diferentes contribuciones electrostáticas nos permite realizar un estudio teórico de predicción de la reactividad y otras propiedades moleculares a partir de cálculos de potencial electrostático y de polarización moleculares. El presente trabajo se basa en el estudio de la utilización de los mapas de potencial electrostático y de potencial de polarización como descriptores moleculares. En primer lugar se realiza un estudio del efecto de la base y de la metodología empleada en el cálculo de propiedades eléctricas de primer y segundo orden. El análisis se lleva a cabo con las moléculas de cianuro de hidrógeno, formaldehído y urea. Las bases utilizadas son del tipo doble zeta estándar, a las cuales se han añadido funciones de polarización y difusas. En particular, se han utilizado la base doble zeta 6-31G(d), les bases doble zeta aumentadas con uno o dos conjuntos de funciones de polarización : 6-31G(d,p) , 6-31G(2d,2p) y también se ha utilizado la base 6-311G++(2d,2p), que incluye funciones difusas. Los diferentes niveles de cálculo utilizan metodologías Hartree-Fock, MÆller-Plesset de segundo y cuarto orden y teoría del funcional de la densidad (DFT) : SCF, MP2, MP4, BLYP i B3LYP. Se analiza el efecto de los diferentes conjuntos de base a la contribución de la polarización a la energía de interacción, calculando para cada sistema propiedades de primer orden, como son los momentos dipolares y los momentos cuadrupolares, y propiedades de segundo orden, como la polarizabilidad y hiperpolarizabilidad moleculares. Seguidamente se evalúa el efecto de la base y el método de cálculo en la obtención de potenciales electrostáticos y de polarización moleculares. Se realiza un estudio comparativo de los mapas calculados con diferentes bases y metodologías, en concreto un estudio de la distribución espacial y un análisis de correlación entre las diferentes bases y metodologías. Un análisis de los mapas de polarización molecular a partir del cálculo de las diferencias de polarización relativas y las desviaciones estándar correspondientes nos permite un estudio comparativo de las diferentes metodologías y bases utilizadas. En particular se realiza un análisis comparativo entre diferentes métodos de cálculo con la base 6-311G++(2d,2p), tomando como referencia el cálculo MP4. Finalmente, se utilizan los mapas de potencial electrostático, de polarización y de interacción para el análisis de las características de reconocimiento molecular de un conjunto de compuestos bioactivos, a fin de analizar la importancia de la contribución de la polarización. Por este motivo, se elige para el estudio un conjunto de moléculas con una alta polarizabilidad, y en concreto, dos familias de compuestos con abundantes átomos de cloro y con una actividad tóxica definida, que forman parte de los grupos de dioxinas y furanos. Para ello se realiza el estudio de la inclusión de la polarización molecular como descriptor en la predicción de la actividad biológica de dioxinas y furanos, realizando el cálculo de potenciales electrostáticos y de polarización, un análisis de los mapas de potencial, y definiendo las principales zonas de interacción electrostática y de polarización molecular a partir de cálculos de componentes principales (PCA), así como la predicción de la actividad biológica en base a un estudio realizado mediante cálculos de mínimos cuadrados parciales (PLS).

    Molecular engineering is based on the knowledge of the stereoelectronic features that define the molecular recognition, which is the result of the complementarity of geometric and electronic features between two different molecular entities. The importance of different electrostatic contributions allows us to make a theoretical prediction of molecular properties, from calculations of electrostatic potential and molecular polarization. This work is based on the study of the use of maps of electrostatic potential and polarization potential as molecular descriptors. First there is a study of the effect of the basis set and the methodology used in the calculation of first and second order electrical properties. The analysis was carried out with the molecules of hydrogen cyanide, formaldehyde and urea. The base sets used are the standard double-zeta, to which were added polarization and diffuse functions. In particular, we have used the double zeta basis 6-31G (d), double zeta basis augmented with one or two sets of polarization functions: 6-31G (d, p), 6-31G (2d, 2p) and also used the base 6-311G + + (2d, 2p), which includes diffuse functions. The different levels of calculation methodologies used Hartree-Fock, Moller-Plesset second and fourth order and the theory of density functional (DFT): SCF, MP2, MP4, BLYP B3LYP i. We analyze the effect of different sets based on the contribution of polarization to the interaction energy, calculated for each system of first order properties, such as dipolar moments and quadrupolar moments, and second order properties such as polarizability and molecular hyperpolarizability. Further, the effect of the basis and method on the calculation of the electrostatic potential and molecular polarization potentials is evaluated. For this purpose we performed a comparative study of the maps calculated with different basis sets and methodologies, in particular a study of the spatial distribution and correlation analysis between the different data bases and methodologies was done. An analysis of molecular polarization maps by calculating the differences in polarization and relative standard deviation allows for a comparative study of different methodologies and bases used. Specifically, a comparative analysis between different methods of calculating the base 6-311G + + (2d, 2p), calculated by reference to the MP4 was done. We use maps of electrostatic, polarization and interaction potentials for the analysis of molecular recognition features of a set of bioactive compounds, to discuss the importance of the contribution of polarization. For this reason, we choose to study a set of molecules with high polarizability, specifically, two families of compounds with heavy atoms of chlorine and defined toxic activity, which are part of groups of dioxins and furans. A study of the polarization maps as indicators of biological activity of dioxins and furans, based on the best methodology is done. The inclusion of polarization as a molecular descriptor for predicting biological activity of dioxins and furans was studied from the calculation of electrostatic potentials and polarization, an analysis of the potential maps, and defining the main areas of interaction molecular electrostatic and polarization interaction from calculations of principal components (PCA) and the prediction of biological activity based on a study by calculation of partial least squares (PLS).

  • Study of the M3 muscarinic acetylcholine receptor by molecular dynamics simulations and site-directed mutagenesis

     Martínez Archundia, Marlet Themis
    Defense's date: 2011-04-14
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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    Randomized tree construction algorithm to explore energy landscapes  Open access

     Jaillet, Leonard Georges; Corcho Sanchez, Francisco Jose; Perez Gonzalez, Juan Jesus; Cortés, Juan
    Journal of computational chemistry
    Date of publication: 2011-12
    Journal article

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    We report in the present work a new method for exploring conformational energy landscapes. The method, called T-RRT, combines ideas from statistical physics and robot path planning algorithms. A search tree is constructed on the conformational space starting from a given state. The tree expansion is driven by a double strategy: on the one hand, it is naturally biased towards yet unexplored regions of the space; on the other, a Monte Carlo-like transition test guides the expansion toward energetically favorable regions. The balance between these two strategies is automatically achieved thanks to a self-tuning mechanism. The method is able to efficiently find both, energy minima and transition paths between them. As a proof of concept, the method is applied to two academic benchmarks and to the alanine dipeptide.

    Postprint (author’s final draft)

  • Assessment of the performace of the functional density theory to compute molecular polarizabilities using molecular polarization maps

     Perez Gonzalez, Juan Jesus; Roset Calzada, M. Lourdes
    Journal of Computational Methods in Sciences and Engineering
    Date of publication: 2011-03-01
    Journal article

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  • Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent

     Rodríguez García, Alejandro; Mokoema, Pol; Corcho Sanchez, Francisco Jose; Bisetty, Krishna; Perez Gonzalez, Juan Jesus
    Journal of physical chemistry B
    Date of publication: 2010-02-17
    Journal article

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    The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.

  • Interactions of fatty acids with phosphatidylethanolamine membranes: X-ray diffraction and molecular dynamics studies

     Cordomi Montoya, Arnau; Prades, Jesus; Frau, Juan; Voegler, Oliver; Funari, Sergio S.; Perez Gonzalez, Juan Jesus; Escriba, Pablo V.; Barcelo, Francisca
    Journal of lipid research
    Date of publication: 2010-05
    Journal article

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  • Design of peptidomimetics

     Perez Gonzalez, Juan Jesus; Corcho Sanchez, Francisco Jose; Rubio Martinez, Jaime
    Date of publication: 2010-09-15
    Book chapter

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  • New insights into the molecular mechanisms of rhodopsin retinitis pigmentosa

     Aguila Cerda, Mónica
    Defense's date: 2010-12-21
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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  • Conformational profile of bombesin assessed using different computational protocols

     Sharma, Parul; Parvesh, Singha; Bisettya, Krishna; Corcho Sanchez, Francisco Jose; Perez Gonzalez, Juan Jesus
    Journal of molecular graphics and modeling
    Date of publication: 2010-12-31
    Journal article

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  • Molecular dynamics simulations of Ac-3Aib-Cage-3Aib-NHMe

     Singh, Parvesh; Sharma, Parul; Bisetty, Krishna; Perez Gonzalez, Juan Jesus
    Molecular simulation
    Date of publication: 2010
    Journal article

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  • Structural characterization of a zinc high-affinity binding site in rhodopsin

     Darwin, Toledo; Cordomí, Arnau; Proietti, Maria Grazia; Maurizio, Benfatto; Del Valle Mendoza, Luis Javier; Perez Gonzalez, Juan Jesus; Garriga Sole, Pere; Sepulcre Sanchez, Francesc
    Photochemistry and photobiology
    Date of publication: 2009-02
    Journal article

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  • Molecular Dynamics (MD) Simulations of VIP and PACAP27

     Corcho Sanchez, Francisco Jose; Mokoena, P; Bisetty, K; Perez Gonzalez, Juan Jesus
    Biopolymers
    Date of publication: 2009-05
    Journal article

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  • Conformational study of the pcu cage monopeptide: a key role of some force-field parameters

     Bisetty, K; Perez Gonzalez, Juan Jesus
    Journal of physical chemistry B
    Date of publication: 2009-03
    Journal article

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  • Analysis of the basis set and correlation effects on the computation of molecular polarizabilities using molecular polarization maps

     Roset Calzada, M. Lourdes; Rubio-Martinez, J; Perez Gonzalez, Juan Jesus
    Theoretical chemistry accounts
    Date of publication: 2009-05
    Journal article

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  • Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers

     Cordomi, A; Edholm, O; Perez Gonzalez, Juan Jesus
    Journal of chemical theory and computation
    Date of publication: 2009-08
    Journal article

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  • Computational investigation of the conformational profile of the four stereomers of Ac-L-Pro-c(3)Phe-NHMe (c(3)Phe= 2,3-methanophenylalanine)

     Rodríguez García, Alejandro; Canto Silva, Josep; Corcho Sanchez, Francisco Jose; Perez Gonzalez, Juan Jesus
    Biopolymers
    Date of publication: 2009
    Journal article

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    The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace-Pro-c3Phe-NMe, previously reported to exhibit b-turn structures in dichloromethane with different type I/type II b-turn profiles. Molecular systems were represented at the molecular mechanics level using the parm96 parameterization of the AMBER force field. Calculations were carried out in dichloromethane using an implicit solvent approach. Characterization of the conformational features of the peptide analogs was carried out using simulated annealing (SA), molecular dynamics (MD) and replica exchange molecular dynamics (REMD). Present results show that MD calculations do not provide a reasonable sampling after 300 ns. In contrast, both SA and REMD provide similar results and agree well with experimental observations.

  • MODELIZACIÓN MOLECULAR DE RECEPTORES ACLOPADOS A PROTEINAS G

     Roset Calzada, M. Lourdes; Perez Gonzalez, Juan Jesus
    Participation in a competitive project

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  • STRUCTURE-BASED DISCOVERY OF NEW SMALL-MOLECULE INHIBITORS OF THE ANTIAPOPTOTIC PROTEIN Bcl-x(L)

     Pinto Manresa, Marta; Orzaez, Maria del Mar; Perez Paya, Enrique; Perez Gonzalez, Juan Jesus; Rubio Martinez, Jaime
    Drugs of the future
    Date of publication: 2009-10
    Journal article

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  • Key Interactions responsible of molecular recognition process between MKK-Derived D-SITE peptides and MAPKs

     Perez Gonzalez, Juan Jesus
    Drugs of the future
    Date of publication: 2009-10
    Journal article

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  • Erratum: Complete maps of molecular-loop conformational spaces (Journal of Computational Chemistry (2007) 28 (2170))

     Porta, J M; Ros, Ll; Thomas, F; Corcho Sanchez, Francisco Jose; Canto Silva, Josep; Perez Gonzalez, Juan Jesus
    Journal of computational chemistry
    Date of publication: 2008-01
    Journal article

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  • Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. A molecular dynamics simulation study

     Cordomi Montoya, Arnau; Edholm, O; Perez Gonzalez, Juan Jesus
    Journal of physical chemistry B
    Date of publication: 2008-02
    Journal article

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  • A proposed bioactive form of peptide T and the design of peptidomimetics

     Centeno, N B; Perez Gonzalez, Juan Jesus
    Journal of computer-aided molecular design
    Date of publication: 2008-01
    Journal article

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  • Molecular dynamics simulations of rhodopsin point mutants at the cytoplasmic side of helices 3 and 6

     Cordomi Montoya, Arnau; Ramon, E; Garriga Sole, Pere; Perez Gonzalez, Juan Jesus
    Journal of biomolecular structure and dynamics
    Date of publication: 2008-06
    Journal article

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  • Molecular dynamics simulations of seven-transmembrane receptors  Open access

     Cordomi Montoya, Arnau
    Defense's date: 2008-03-11
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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    Seven transmembrane (7-TM) G protein coupled receptors (GPCR) constitute the largest family of integral membrane proteins in eukaryotes with more than 1000 members and encoding more than 2% of the human genome. These proteins play a key role in the transmission and transduction of cellular signals responding to hormones, neurotransmitters, light and other agonists, regulating basic biological processes. Their natural abundance together with their localization in the cell membrane makes them suitable targets for therapeutic intervention. Consequently, GPCR are proteins with enormous pharmacologic interest, representing the targets of about 50% of the currently marketed drugs. The current limitations in the experimental techniques necessary for microscopic studies of the membrane as well as membrane proteins emerged the use of computational methods and specifically molecular dynamics simulations. The lead motif of this thesis is the study of GPCR by means of this technique, with the ultimate goal of developing a methodology that can be generalized to the study of most 7-TM as well as other membrane proteins. Since the bovine rhodopsin was the only protein of the GPCR family with a known threedimensional structure at an atomic level until very recently, most of the effort is centered in the study of this receptor as a model of GPCR.The scope of this thesis is twofold. On the one hand it addresses the study of the simulation conditions, including the procedure as well as the sampling box to get optimal results, and on the other, the biological implications of the structural and dynamical behavior observed in the simulations. Specifically, regarding the methodological aspects of the work, the bovine rhodopsin has been studied using different treatments of long-range electrostatic interactions and sampling conditions, as well as the effect of sampling the protein embedded in different one-component lipid bilayers. The binding of ions to lipid bilayers in the absence of the protein has also been investigated. Regarding the biological consequences of the analysis of the MD trajectories, it has been carefully addressed the binding site of retinal and its implications in the process of isomerization after photon uptake, the alteration a group of residues constituting the so-called electrostatic lock between helices TM3 and TM6 in rhodopsin putatively used as common activation mechanism of GPCR, and the structural effects caused by the dimerization based on a recent semi-empirical model. Finally, the specific binding of ions to bacteriorhodopsin has also been studied. The main conclusion of this thesis is provide support to molecular dynamics as technique capable to provide structural and dynamical informational about membranes and membrane proteins, not currently accessible from experimental methods). Moreover, the use of an explicit lipidic environment is crucial for the study the membrane protein dynamics as well as for the protein-protein and lipidprotein interactions.

  • Diseño asistido por ordenador de inhibidores de las dianas terapéuticas Bcl-xl/Bcl-2 y TTR

     Pinto Manresa, Marta
    Defense's date: 2008-07-28
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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  • Complete maps of molecular-loop conformational spaces

     Porta Pleite, Josep M.; Ros, L; Thomas, F; Corcho Sanchez, Francisco Jose; Canto Silva, Josep; Perez Gonzalez, Juan Jesus
    Journal of computational chemistry
    Date of publication: 2007-10
    Journal article

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  • Structural Analysis of Substance P Using Molecular Dynamics and NMR Spectroscopy

     Corcho Sanchez, Francisco Jose; Salvatella, X; Canto Silva, Josep; Giralt, E; Perez Gonzalez, Juan Jesus
    Journal of peptide science
    Date of publication: 2007-11
    Journal article

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  • Access to the full text
    Complete maps of molecular-loop conformational spaces  Open access

     Porta Pleite, Josep M.; Ros Giralt, Lluis; Thomas Arroyo, Federico; Corcho Sanchez, Francisco Jose; Canto Silva, Josep; Perez Gonzalez, Juan Jesus
    Journal of computational chemistry
    Date of publication: 2007-01
    Journal article

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    This paper presents a numerical method to compute all possible conformations of distance-constrained molecular loops, i.e., loops where some interatomic distances are held fixed, while others can vary. The method is general (it can be applied to single or multiple intermingled loops of arbitrary topology) and complete (it isolates all solutions, even if they form positive-dimensional sets). Generality is achieved by reducing the problem to finding all embeddings of a set of points constrained by pairwise distances, which can be formulated as computing the roots of a system of Cayley-Menger determinants. Completeness is achieved by expressing these determinants in Bernstein form and using a numerical algorithm that exploits such form to bound all root locations at any desired precision. The method is readily parallelizable, and the current implementation can be run on single- or multiprocessor machines. Experiments are included that show the method's performance on rigid loops, mobile loops, and multiloop molecules. In all cases, complete maps including all possible conformations are obtained, thus allowing an exhaustive analysis and visualization of all pseudo-rotation paths between different conformations satisfying loop closure.

  • Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers

     Cordomi Montoya, Arnau; Perez Gonzalez, Juan Jesus
    Journal of physical chemistry B
    Date of publication: 2007-06
    Journal article

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  • A molecular dynamics study of the pentacyclo-undecane (PCU) cage polypeptides of the type Ac-3Ala-Cage-3Ala-NHMe

     Bisetty, K; Kruger, H G; Perez Gonzalez, Juan Jesus
    Molecular simulation
    Date of publication: 2007-10
    Journal article

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  • Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer

     Cordomi Montoya, Arnau; Edholm, O; Perez Gonzalez, Juan Jesus
    Journal of computational chemistry
    Date of publication: 2007-04
    Journal article

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  • Marine paint formulations: conducting polymers as anticorrosive additives

     Armelin Diggroc, Elaine; Oliver Pujol, Ramon; Liesa Mestres, Francisco; Iribarren Laco, Jose Ignacio; Estrany Coda, Francisco; Aleman Llanso, Carlos Enrique; Perez Gonzalez, Juan Jesus; Pinto Manresa, Marta; Zanuy Gomara, David
    Progress in organic coatings
    Date of publication: 2007-04
    Journal article

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  • Critical role of electrostatic interactions of amino acids at the cytoplasmic region of helices 3 and 6 in rhodopsin conformational properties and activation.

     Ramon, E; Cordomi Montoya, Arnau; Bosch, L; Zernii, Ey; Perez Gonzalez, Juan Jesus; Garriga Sole, Pere
    Journal of biological chemistry
    Date of publication: 2007-05
    Journal article

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  • X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

     Sepulcre Sanchez, Francesc; Cordomi Montoya, Arnau; Proietti, M G; Perez Gonzalez, Juan Jesus; Garcia Strino, Joaquim; Querol, Enric; Padrós, Esteve
    Proteins: structure, function, and bioinformatics
    Date of publication: 2007-05
    Journal article

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  • A theoretical study of the pentacyclo-undecane cage peptides of the type (Ac-X-Y-NHMe)

     Krishna, Bisetty; Corcho Sanchez, Francisco Jose; Joseph, Canto; Canto Silva, Josep; Perez Gonzalez, Juan Jesus
    Journal of peptide science
    Date of publication: 2006-06
    Journal article

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