Jesus Mendieta

• Doctor of Science
• Francisco de Vitoria University

The quest to understand and mimic proton translocation mechanisms in natural channels has driven the development of peptide‐based artificial channels facilitating efficient proton transport across nanometric membranes. It is demonstrated here that hierarchical peptide self‐assembly can form micrometers‐long proton nanochannels. The fourfold symmetr...

Coupled with PCR, reverse transcriptases (RTs) have been widely used for RNA detection and gene expression analysis. Increased thermostability and nucleic acid binding affinity are desirable RT properties to improve yields and sensitivity of these applications. The effects of amino acid substitutions in the RT RNase H domain were tested in an engin...

A double proton transfer reaction in a Guanine-Cytosine (GC) base pair has been proposed as a possible mechanism for rare tautomer (G*C*) formation and thus a source of spontaneous mutations. We analyze this system with free energy calculations based on extensive Quantum Mechanics / Molecular Mechanics simulations to properly consider the influence...

Nucleoside reverse transcriptase (RT) inhibitors (NRTIs) are the backbone of current antiretroviral treatments. However, emergence of viral resistance against NRTIs is a major threat to their therapeutic effectiveness. In HIV-1, NRTI resistance-associated mutations either reduce RT-mediated incorporation of NRTI triphosphates (discrimination mechan...

DNA-water interactions have revealed as very important actor in DNA mechanics, from the molecular to the macroscopic scale. Given the particularly useful properties of DNA molecules to engineer novel materials through self-assembly and by bridging organic and inorganic materials, the interest in understanding DNA elasticity has crossed the boundari...

The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the “head” structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms o...

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics / molecular mechanics (QM/MM) techniques...

From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this paper we present MEPSA (Minimum Energy Path Surface Analysis), a cross-plat...

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance betwe...

Thymidine analogue resistance mutations (TAMs) in HIV-1 reverse transcriptase (RT) associate in two clusters: (i) TAM1 (M41L, L210W and T215Y) and TAM2 (D67N, K70R, K219E/Q, and sometimes T215F). The amino acid substitution H208Y shows increased prevalence in patients treated with nucleoside analogues and is frequently associated with TAM1 mutation...

In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Be...

FtsZ filaments participate in bacterial cell division, but it is still not clear how their dynamic polymerization and shape exert force on the underlying membrane. We present a theoretical description of individual filaments that incorporates information from molecular dynamic simulations. The structure of the crystallized Methanococcus jannaschii...

The use of quantum mechanics/molecular mechanics (QM/MM) simulations to study the free energy landscape of the water activation at the catalytic site of mitochondrial F1-ATPase affords us insight into the generation of the nucleophile OH- prior to the ATP hydrolysis. As a result, the ATP molecule was found to be the final proton acceptor. In the si...

A bacteriophage Ø29 transcriptional regulator, protein p4, interacts with its DNA target by employing two mechanisms: by direct readout of the chemical signatures of only one DNA base and by inducing local modification on the topology of short A tracts (indirect readout). p4 binds as a dimer to targets consisting of imperfect inverted repeats. Here...

FtsZ, the prokaryotic ortholog of tubulin, assembles into polymers in the bacterial division ring. The interfaces between monomers contain a GTP molecule, but the relationship between polymerization and GTPase activity is not unequivocally proven. A set of short FtsZ polymers were modelled and the formation of active GTPase structures was monitored...

Activation of the water molecule involved in GTP hydrolysis within the HRas·RasGAP system is analyzed using a tailored approach based on hybrid quantum mechanics/molecular mechanics (QM/MM) simulation. A new path emerges: transfer of a proton from the attacking water molecule to a second water molecule, then a different proton is transferred from t...

ABSTRACT: Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs...

Single amino acid deletions in the β3-β4 hairpin loop of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) have been identified in heavily treated patients. The deletion of Asp-67 together with mutations T69G and K70R (Δ67 complex) are usually associated with thymidine analog resistance mutations (TAMs) (e.g. M41L, T215Y, etc.)...

Cadherins form a large family of calcium-dependent cell-cell adhesion receptors involved in development, morphogenesis, synaptogenesis, differentiation, and carcinogenesis through signal mechanotransduction using an adaptor complex that connects them to the cytoskeleton. However, the molecular mechanisms underlying mechanotransduction through cadhe...

Signaling networks are key elements in all major aspects of cellular life, playing a major role in inter- and intracellular communications. They are involved in diverse processes such as cell-cycle progression, cellular metabolism, cell-cell communication and appropriate response to the cellular environment. The latter comprises a whole range of ne...

Signaling networks are key elements in all major aspects of cellular life, playing a major role in inter-and intracellular communications. They are involved in diverse processes such as cell-cycle progression, cellular metabolism, cell-cell communication and appropriate response to the cellular environment. The latter comprises a whole range of net...

Cadherins form a large family of calcium-dependent cell-cell adhesion receptors involved in development, morphogenesis, synaptogenesis, differentiation, and carcinogenesis through signal mechanotransduction using an adaptor complex that connects them to the cytoskeleton. However, the molecular mechanisms underlying mechanotransduction through cadhe...

Bacterial cell division occurs through the formation of a protein ring (division ring) at the site of division, with FtsZ being its main component in most bacteria. FtsZ is the prokaryotic ortholog of eukaryotic tubulin; it shares GTPase activity properties and the ability to polymerize in vitro. To study the mechanism of action of FtsZ, we used mo...

Deletions in the beta 3-beta 4 hairpin loop of human immunodeficiency virus type 1 reverse transcriptase (RT) are associated with the emergence of multidrug resistance. Common mutational patterns involve the deletion of Asp67 (Delta 67) and mutations such as K70R and T215F or T215Y, or the deletion of Thr69 (Delta 69) and mutations of the Q151M com...

The structural and dynamical changes occurring before nucleotide addition were studied using molecular dynamics (MD) simulations of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexes containing one or two Mg2+ ions in the presence of dNTP. Our models revealed that the formation of a catalytically competent DNA polymera...

Human respiratory syncytial virus (HRSV) P protein, 241 amino acid long, is a structural homotetrameric phosphoprotein. Viral transcription and replication processes are dependent on functional P protein interactions inside viral ribonucleoprotein complexes (RNPs). Binding capacity to RNPs proteins and transcription and replication complementation...

The bacteriophage Ø29 transcriptional regulator p4 binds to promoters of different intrinsic activities. The p4–DNA complex contains two identical protomers that make similar interactions with the target sequence 5′-AACTTTTT-15 bp-AAAATGTT-3′. To define how the various elements in the target sequence contribute to p4's affinity, we studied p4 bindi...

A spontaneous rpsL mutant of Thermus thermophilus was isolated in a search for new selection markers for this organism. This new allele, named rpsL1, encodes a K47R/K57E double mutant S12 ribosomal protein that confers a streptomycin-dependent (SD) phenotype to T. thermophilus. Models built on the available three-dimensional structures of the 30S r...

Guanine nucleotides behave as competitive antagonists at ionotropic glutamate receptors and show neuroprotective activity in different experimental excitotoxicity paradigms, both in vivo and in cultured cell preparations. Taking 5'-GMP as the reference nucleotide, we have tried to understand how these molecules interact with the agonist-binding sit...

Paired helical filaments (PHFs) isolated from patients with Alzheimer's disease (AD) mainly consist of the microtubule-associated protein tau in a hyperphosphorylated form. It has been found that PHFs are the first example of pathological protein aggregation associated with formation of alpha-helices [Biochemistry (2002) 41, 7150-5]. In an effort t...

Structural data suggest that important hinge-bending motions of the two lobes that shape the catalytic domain of Src tyrosine kinase, together with reorganization of an alpha helix (helix C), are needed for the activation loop to adopt the catalytically competent conformation. The phosphorylation of a Tyr residue (Tyr-416) in this loop also seems t...

Computational studies have been conducted to built a closed form of TPase and to characterize the transition state of the phosphorylisis reaction catalyzed by TPase. The results obtained point to a crucial role of His-85 and the O2 of thymine in the catalysis. This modelled transition state forms the basis for the design of new TPase inhibitors.

The structural changes taking place in the enzyme thymidine phosphorylase (TPase, also known as PD-ECGF) that are required to achieve catalytic competence upon binding thymidine and phosphate have been simulated by means of targeted molecular dynamics (tMD). The hinge regions were characterized by structural homology comparisons with pyrimidine nuc...

The antitumor ecteinascidin ET743 has been shown to inhibit the transcriptional activation of a number of genes at nanomolar concentrations. Cell sensitivity to subnanomolar concentrations of the drug has also been shown to specifically depend on the transcription-coupled nucleotide excision repair system. ET743 is known to bind covalently to the m...

The complexation of the hexapeptide Lys-Cys-Thr-Cys-Cys-Ala (FT), peptidic fragment {56–61} of mouse liver metallothionein MT I, in the presence of both Cd(II) and Zn(II) is investigated as a model to understand the metal-binding properties of natural MT's, in which Cd and Zn are simultaneously present. The influence of Cd(II) or Zn(II) on the comp...

Excitatory synaptic transmission is mediated by ionotropic glutamate receptors (iGluRs) through the induced transient opening of transmembrane ion channels. The three-dimensional structure of the extracellular ligand-binding core of iGluRs shares the overall features of bacterial periplasmic binding proteins (PBPs). In both families of proteins, th...

The Zn(2+)-glutathione system is studied as a model for metal-peptide systems where some critical factors must be considered when using voltammetric techniques for the determination of stability constants. These factors are the presence of side reactions (in this case, both the protonation of glutathione and the hydrolysis of Zn(2+)), the associati...

Multivariate curve resolution is applied to cyclic voltammetry (CV) data obtained in the study of Cd(II) complexation by glutathione (GSH). The relatively poor resolution of CV hinders the direct interpretation of raw data. The use of CV is improved by the combination of several chemometric techniques based on factor analysis:  singular-value decom...

The cadmium-binding properties of the C-terminal hexapeptide of mouse metallothionein I, Lys-Cys-Thr-Cys-Cys-Ala, were studied by circular dichroism spectroscopy (CD), differential pulse polarography (DPP) and magnetic resonance (NMR).The structure of the multiple cadmium binding sites could not be determined by because of the insolubility of the C...

The zinc-binding properties of the C-terminal hexapeptide of mouse metallothionein I, Lys–Cys–Thr–Cys–Cys–Ala, were studied by differential pulse polarography (DPP) with a recently proposed multivariate curve resolution (MCR) method, based on factor analysis techniques, which allows the identification of the signal corresponding to different metal...

The trifluoroethanol-dependent induction of the nonnative α-helical form of β-lactoglubulin has been studied by circular dichroism spectroscopy. Data analysis is performed by factor analysis and multivariate curve resolution. An intermediate form in the induction of the α-helical form of the β-lactoglobulin has been identified at low TFE concentrat...

Different multivariate data analysis techniques based on factor analysis and multivariate curve resolution are shown for the study of biochemical evolutionary processes like conformational changes and protein folding. Several simulated CD spectral data sets describing different hypothetical protein folding pathways are analyzed and discussed in rel...

The complexation between Zn2+ and glutathione (GSH), in borate buffer, is studied by Differential Pulse Polarography (DPP). Data obtained at pH 8.5 from a titration of Zn2+ by GSH, i.e. at different GSH-to-Zn2+concentration ratios have been analyzed by a recently proposed multivariate curve resolution method. DPP signals obtained within a wide pH r...

The complexation of glutathione (GSH) by Cd2+ has been investigated as a model for the coordination chemistry of Cd2+ by thiol-containing peptides. Experimental data obtained by differential pulse polarography (DPP) for different Cd2+-to-GSH concentration ratios at fixed pH have been globally analyzed by the recently proposed multivariate curve res...

Circular dichroism (CD) spectroscopy is a useful tool for the detection of changes in both the secondary and tertiary structure of proteins induced by processes such as, protein folding. Despite the big amount of information that the CD spectra contain, these changes are monitored using a selected and limited number of wavelengths. The choosing of...

Metallothioneins (MT) are a class of proteins with a high content in cysteine, which provides them with an especial ability to bind metal ions which is the responsible of its physiological roles like the sequestering of toxic metals1The metal-thiolate stoichiometry and the structure of the protein are dependent on the size, charge and coordination...

The complexation of Cd2+ by glutathione (GSH), in 0.13 m borate buffer at pH 9.5, was studied by differential pulse polarography (DPP) and multivariate curve resolution. The Cd-GSH system has been chosen as a model to check the possibilities of this new polarographic approach to the study of metal ion complexation by peptides. Experimental data obt...

An electrochemical study, using differential pulse polarography, of the binding properties of the peptide Lys-Cys-Thr-Cys-Cys-Ala Thionein Fragment [56–61] MT I (FT) with cadmium and zinc was performed. This molecule, intrinsic to the metallothionein structure, was chosen as a model of the Cd, Zn Metallothioneins ion exchange and binding properties...

In order to obtain a better understanding of the electrochemical behavior of the Metallothionein (MT), the peptidic fragment Lys–Cys–Thr–Cys–Cys–Ala [56–61] MT I (FT) compound constitutive of the proteic structure has been studied. The elucidation of the electrochemical mechanism at the electrode could be reached from comparison with other mechanis...

The electrochemical behaviour of Cd,Zn thioneins (MT) from rabbit liver and horse kidney with respect to solution pH at the dropping mercury electrode was studied using differential pulse polarography. The equilibrium M + T ⇆ MT concerning the formation of metallothionein from their metal depleted form for assessing the possibility of reproducing t...

Rat bone marrow cell populations, containing different proportions of erythroid cells, have been fractionated by counter-current distribution in the non-charge-sensitive dextran/polyethyleneglycol two-phase systems on the basis of hydrophobic cell surface properties. Cell fractions with a low distribution coefficient, which contain non-erythroid ce...

The transferrin-binding capacity of rat bone marrow cells and different erythroid-enriched populations from rat bone marrow has been studied and compared with that previously reported for pure reticulocyte populations. Two components with different transferrin-binding capacities were found. The one with higher affinity was present mainly in erythro...

We have previously reported the possibility of modifying the electrical properties of cells by means of their interaction with a specific ligand carrying a polyelectrolyte (Anal Biochem 200: 280-285). This selective modification of receptor-containing cells changed their partition in a charge-sensitive aqueous two-phase system. We here present the...

Counter-current distribution in non charge-sensitive aqueous poly(ethylene glycol)-dextran two phase systems allows the fractionation of rat bone marrow cells into two broad cell subpopulations with different distribution coefficients in a relatively short time. Morphological identification and enzymatic studies suggest that erythroid cells are mai...

The partitioning of rat reticulocytes in poly(ethylene glycol) (PEG)-dextran two-phase systems increases into the PEG-rich top phase when the cells are incubated with transferrin covalently modified with monomethoxy-PEG (MPEG-transferrin) prior to partitioning. Two observations support the suggestion that such an increase in top-phase partitioning...

Polylysine has been covalently bound to human transferrin in a 1:1 molar ratio over a disulfide bond that can be easily split by reducing agents such as dithiothreitol. The association constant for the binding of the transferrin-polylysine derivative to transferrin receptors present on rat erythroblasts and the number of binding sites were identica...

A decrease in the number of binding sites for 125I-transferrin, without an apparent modification of the association constant, has been observed during the maturation of reticulocytes into erythrocytes. As an experimental model, different red cell populations from phenylhydrazinic anaemic rates (95% to 12% reticulocyte-rich) have been used. The frac...