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Biomedical subjects

M J Ramos

Publications and source records attributed to M J Ramos.

At least 19 recordsLinked to original sources
PubMed2006

Detailed microscopic study of the full zipA:FtsZ interface.

Protein-protein interaction networks are very important for a wide range of biological processes. Crystallographic structures and mutational studies have generated a large number of information that allowed the discovery of energetically important determinants of specificity at intermolecular protein interfaces and the understanding of the structural and energetic characteristics of the binding hot spots. In this study we have used the improved MMPB/SA (molecular mechanics/Poisson-Boltzmann surface area) approach that combining molecular mechanics and continuum solvent permits to calculate the free energy differences upon alanine mutation. For a better understanding of the binding determinants of the complex formed between the FtsZ fragment and ZipA we extended the alanine scanning mutagenesis study to all interfacial residues of this complex. As a result, we present new mutations that allowed the discovery of residues for which the binding free energy differences upon alanine mutation are higher than 2.0 kcal/mol. We also observed the formation of a hydrophobic pocket with a high warm spot spatial complementarity between FtsZ and ZipA. Small molecules could be designed to bind to these amino acid residues hindering the binding of FtsZ to ZipA. Hence, these mutational data can be used to design new drugs to control more efficiently bacterial infections.

Alanine↗
PubMed2006

Molecular dynamics model of unliganded HIV-1 reverse transcriptase.

HIV-1 RT is one of the most important antiviral targets in the treatment of acquired immunodeficiency syndrome (AIDS). Several crystallographic structures are available for this enzyme, mostly with bound inhibitors. Despite their importance for structure based drug design towards new anti-HIV retrovirals, the X-ray structures of the unliganded enzyme could only be obtained incomplete, with a low resolution and until recently even the conformation of the p66 thumb was controversial. In this work we have aligned different X-ray RT structures, and built up a computational model of RT using homology modeling, which was afterwards refined and validated through MD simulations with explicit solvent. The model enzyme was structurally stable through the whole MD simulation, showing a RMSD of 2 Angstrom from the starting geometry. The Ramanchandram plot has improved along the simulation. Both intra-domain and interdomain movements were observed. The thumb kept its closed conformation through the whole simulation. A contact map, hydration sites study and a detailed analysis of the solvation of the nucleotide binding site are also presented.

Binding Sites↗
PubMed2005

NF-kappaB in human disease: current inhibitors and prospects for de novo structure based design of inhibitors.

Nuclear-Factor kappa B (NF-kappaB) is an inducible transcription factor of the Rel family, sequestered in the cytoplasm by the IkappaB family of proteins. NF-kappaB exists in several dimeric forms, but the p50/p65 heterodimer is the predominant one. Activation of NF-kappaB by a range of physical, chemical, and biological stimuli leads to phosphorylation and proteasome dependent degradation of IkappaB, leading to the release of free NF-kappaB. This free NF-kappaB then binds to its target sites (kappaB sites in the DNA), to initiate transcription. This transcription has been known to be involved in a number of diseases including cancer, AIDS, and inflammatory disorders. The present article focuses on two important issues of current and future interest- firstly a review of the main human diseases which are initiated due to NF-kappaB mediated transcription is presented. Next, comprehensive information on the current inhibitors which are targeted to interfere with the NF-kappaB pathway is provided. This latter section presents a critical review on different types of latest inhibitors targeting the complex NF-kappaB pathway at several stages. The inhibitors developed till date and still under investigation, include mainly those which interfere with the activation of NF-kappaB. Based on the complexity of NF-kappaB activation, and the current knowledge of the structural biology of NF-kappaB-DNA binding, finally it is proposed that a better approach to inhibit NF-kappaB induced transcription exists. In this context, a perspective is presented in the end, proposing de novo design of inhibitors which directly interact with the DNA Binding region of the free NF-kappaB (p50 subunit), so as to generate more specific and selective leads of NF-kappaB-DNA binding.

Antioxidants↗
PubMed2003

New designs for MRI contrast agents.

New designs for Magnetic Resonance Imaging contrast agents are presented. Essentially, they all are host-guest inclusion complexes between y-cyclodextrins and polyazamacrocycles of gadolinium (III) ion. Substitutions have been made to the host to optimise the host-guest association. Molecular mechanics calculations have been performed, using the UFF force field for metals, to decide on the suitability of the substitutions, and to evaluate the host-guest energies of association. Interesting general conclusions have been obtained, concerning the improvement of Magnetic Resonance Imaging contrast agents; namely, a set of rational methodologies have been deduced to improve the association between the gadolinium (III) chelates and the cyclodextrins, and their efficiency is demonstrated with a large set of substituted complexes, opening new doors to increase the diagnostic capabilities of Magnetic Resonance Imaging.

Contrast Media↗
PubMed2003

Nuclear factor kappa B: a potential target for anti-HIV chemotherapy.

The Nuclear Factor Kappa B (NF-kappaB) is a lymphoid-specific transcription factor, which is sequestered in the cytoplasm by the protein IkappaB. NF-kappaB plays a major role in the regulation of HIV-1 gene expression. Upon activation, NF-kappaB is released from IkappaB, moves to the nucleus, and binds to its sites on the HIV long terminal repeat to start transcription of integrated HIV genome. The present review focuses on the NF-kappaB as a potential target for the development of chemotherapy against HIV-1. Beginning from the viral-binding to reverse transcription, integration, and gene expression, to the virion maturation, the life cycle of HIV presents drug-targets at all the stages. As a result, many drugs have been developed and have entered clinical trials. Some of the most important of these are reverse transcriptase and protease inhibitors, which have been used mostly in clinical studies in the form of combined therapy. But, this combined therapy has presented the problem of resistance, due to mutations in the virus. However, targeting NF-kappaB for the suppression of virus does not present the problem of resistance, as NF-kappaB is a normal part of the human T-4 cell, and is not subject to mutations, as is the virus. An overview of the NF-kappaB system and its role in HIV-1 is presented, followed by a critical review of its current and potential synthetic inhibitors. The drugs studied against NF-kappaB fall mainly into three categories: (1) Antioxidants, against oxidative stress conditions, which aid in NF-kappaB activation, (2) IkappaB phosphorylation and degradation inhibitors (the phosphorylation and degradation of IkappaB is necessary to make NF-kappaB free and move to the nucleus), and (3) NF-kappaB DNA binding inhibitors. The antioxidants include N-Acetyl-L-cysteine (NAC), alpha-Lipoic acid, glutathione monoester, pyrrolidine dithiocarbamate, and tepoxalin, of which NAC is the best studied. The IkappaB phosphorylation and degradation inhibitors, which have been studied in the context of HIV-1 include the salicylates (sodium salicylate, and acetylsalicylic acid (aspirin)). Finally, the NF-kappaB DNA binding inhibitors, which have received attention only recently, are reviewed. These include the most potential, aurine tricarboxylic acid (ATA), a chelating agent, which has been found to inhibit NF-kappaB DNA binding at a low concentration of 30 micro M. The probable mechanism of action of these drugs is discussed alongwith relevant suggestions and conclusions.

Anti-HIV Agents↗
PubMed2001

Clinical significance of donor-unrecognized bacteremia in the outcome of solid-organ transplant recipients.

We evaluated the clinical significance of unrecognized bacteremia in the organ donor (i.e., blood culture results that were reported to be positive after transplantation) on the outcome of transplant recipients. Twenty-nine of 569 liver and heart donors (5%) had bacteremia at the time of organ procurement, but there were no documented instances of transmission of the isolated bacteria from the donor to the recipient. Unrecognized bacteremia in the donor does not have a negative clinical impact on the outcome of organ transplant recipients.

Adolescent↗
PubMed2001

The search for a new model structure of beta-factor XIIa.

We present the search for a new model of beta-factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modelers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and beta-factor XIIa, in particular.

Amino Acid Sequence↗
PubMed2000

Prevalence and risk factors of tinea unguium and tinea pedis in the general population in Spain.

This study prospectively evaluated the prevalence and risk factors of tinea unguium and tinea pedis in the general adult population in Madrid, Spain. One thousand subjects were clinically examined, and samples of nails and scales from the interdigital spaces of the feet were taken from those patients presenting with signs or symptoms of onychomycosis and/or tinea pedis, respectively. In addition, a sample from the fourth interdigital space of both feet was collected from all individuals with a piece of sterilized wool carpet. Tinea unguium was defined as a positive direct examination with potassium hydroxide and culture of the etiological agent from subjects with clinically abnormal nails. Patients with positive dermatophyte cultures of foot specimens were considered to have tinea pedis. The prevalence of tinea unguium was 2.8% (4.0% for men and 1.7% for women), and the prevalence of tinea pedis was 2.9% (4.2% for men and 1.7% for women). The etiological agents of tinea unguium were identified as Trichopyton rubrum (82.1%), followed by Trichopyton mentagrophytes var. interdigitale (14.3%) and Trichopyton tonsurans (3.5%). Trichophyton rubrum (44.8%) and Trichophyton mentagrophytes (44.8%), followed by Epidermophyton floccosum (7%) and T. tonsurans (3.4%), were the organisms isolated from patients with tinea pedis. The percentage of subjects who suffered simultaneously from both diseases was 1.1% (1.7% for men and 0.6% for women). In a multivariate logistic regression analysis, age (relative risk [RR], 1.03) and gender (RR, 2.50) were independent risk factors for tinea unguium, while only gender (RR, 2.65) was predictive for the occurrence of tinea pedis. In both analyses, the presence of one of the two conditions was associated with a higher risk for the appearance of the other disease (RR, >25).

Adult↗
PubMed1999

Incidence and clinical impact of fluoroquinolone-resistant Escherichia coli in the faecal flora of cancer patients treated with high dose chemotherapy and ciprofloxacin prophylaxis.

This study evaluated the susceptibility of Escherichia coli to quinolones in 72 stool samples collected from 31 patients with solid tumours who had undergone high dose chemotherapy (HDC) and peripheral blood stem-cell (PBSC) rescue with ciprofloxacin prophylaxis. Samples were obtained at admission, after completing prophylaxis and three months later. All E. coli strains isolated from baseline samples were susceptible to quinolones. Fluoroquinolone-resistant E. coli strains were isolated in 10 (32%) patients in the second sample. In eight of these patients isolates were susceptible 3 months later. No patient developed infection due to fluorquinolone-resistant E. coli. No differences were observed in outcome between patients with susceptible and resistant flora.

Adult↗
PubMed1997

Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein.

A new approach to the molecular modelling of homologous serine proteases is adopted, by including a set of 21 buried waters known to be preserved in enzymes sharing the primary specificity of trypsin, in the homology modelling of rat submaxillary gland kallikrein. Buried waters--water molecules sequestered from bulk solvent within a protein matrix--appear to be integral conserved components of all serine proteases of known structure and should be incorporated into serine protease models built on the basis of sequence/structural homology to this family. The absence of such waters might induce errors in a force field simulation, favouring the formation of nonexistent hydrogen bonds and locally inaccurate structure. The kallikrein model refinement has led to the conclusion that an additional buried water should be added to the original rigid matrix of 21 conserved water molecules. The structurally preserved protein cavities of such waters validate the modelled structure.

Amino Acid Sequence↗
PubMed1997

The nature of trypsin-pancreatic trypsin inhibitor binding: free energy calculation of Tyr39-->Phe39 mutation in trypsin.

The main goal of this work is the detailed study of the binding interactions in the trypsin-pancreatic trypsin inhibitor (PTI) complex and, here, we present how meaningful the Tyr39-Ile19 interaction is to the stability of that particular complex using free energy methods. This knowledge should be very important in the design of new inhibitors for trypsin and enzymes homologous to it. In particular, it could help to decide whether it is possible to produce selective inhibitors for these enzymes by appropriate mutations of residues in the contact region of PTI.

Amino Acid Substitution↗
PubMed1996

Autonomic profile of subjects prone to fainting.

Syncope is the most common form of fainting that may occur at least once during a life-time in up to one-third of the general population. In 50% of patients the cause remains unknown. In an attempt to identify subtle disturbances of the autonomic nervous system, we examined 70 subjects, aged from 14 to 39 years, who suffered from recurrent neurally mediated syncope. We performed a battery of non-invasive tests assessing cardiovagal, sympathetic cholinergic and sympathetic adrenergic function. We compared the results with a group of 30 healthy, non-fainting subjects matched for age and sex. Basal records were similar in both groups. Patients had preserved cardiovagal function. The multivariate cluster analysis allowed us to find a homogeneous group of cases (46%) that simultaneously presented: greater fall in systolic and diastolic blood pressure after standing, increased 15:30 ratio, exaggerated absolute heart rate rise in response to standing and subclinical reduced sudomotor function in the foot. The results suggest the existence of a subclinical autonomic profile, with subtle sympathetic postganglionic impairment, evident in lower limbs. These findings may contribute to proving the existence of different types of neurally mediated syncope, all different in their onset and mechanism but with a common final manifestation: syncopal loss of consciousness.

Adolescent↗
PubMed1996

Evaluation of congenital dysautonomia other than Riley-Day syndrome.

We report on four children, from different families, who suffer from a congenital autonomic disorder, presumably inherited. Three of them have a sensory neuropathy but do not fit any described hereditary sensory and autonomic neuropathy. All four were examined along with some of their immediate family members. We assessed the cardiovagal, sympathetic adrenergic and sympathetic cholinergic functions with a battery of non-invasive tests. Results demonstrated that sudomotor and cardiovascular orthostatic regulation exhibited the greatest abnormalities, pointing to a predominant impairment of sympathetic components, both cholinergic and adrenergic. The overall examination showed a heterogeneous group of congenital dysautonomia, exclusive of Riley-Day or other recognized hereditary sensory and autonomic neuropathies. We emphasize the importance of studying whole family groups to diagnose subclinical impairment and to provide correct genetic counselling.

Adolescent↗
PubMed1995

Evaluation of recombinant Ro/SSA, La/SSB, Sm, and U1 RNP autoantigens in clinical diagnosis.

This study comprises an analysis of the diagnostic usefulness of Ro/SSA, La/SSB, Sm and U1 RNP autoantigens obtained by DNA recombinant technology. We studied the presence of these autoantibodies in 33 patients with systemic lupus erythematosus (SLE) and 30 normal individuals by enzyme-linked immunosorbent assay (ELISA) using recombinant autoantigens and by Western immunoblot with these same antigens obtained from natural sources (rabbit thymus and human spleen). The strength of agreement between results found with these two techniques was moderate in the case of anti-Ro/SSA (kappa = 0.474, P < 0.001) and anti-U1 RNP (kappa = 0.566. P < 0.001) antibodies and almost perfect in the case of anti-La/SSB (kappa = 0871, P < 0.001) and anti-Sm (kappa = 0.833, P < 0.001). Furthermore, analysis of the disagreement between the two techniques evidenced a measurement bias for anti-Ro/SSA and anti-U1 RNP antibodies (Mc NEMAR'S statistic 13 and 11, respectively) whose direction, though difficult to define in the absence of a gold standard for such determinations, could be accounted for by the ELISA technique's greater tendency to produce positive results. Our conclusion is that the diagnostic usefulness of recombinant La/SSB and Sm autoantigens has been satisfactorily proven, whereas the case of the Ro/SSA and U1 RNP systems should be subject to further in-depth study of the autoepitopes recognised and the possible modifications which the latter might undergo as a result of their obtension from procariotic sources.

Autoantigens↗
PubMed1995

Sympathetic sudomotor function and aging.

Many studies have reported the influence of aging on different portions of the autonomic nervous system components but only partially for the sympathetic cholinergic system. We evaluated postganglionic sudomotor function in 196 healthy subjects, 104 women and 92 men, by determining sweat gland density (SGD) per square centimeter of skin, on the dorsum of the hand and foot, with the impression mold technique. The age range was from 5 to 84 years. A significant decrease of SGD was observed in both hand and foot in relation to age (P < 0.001). The ANOVA analysis of foot data shows that age is the only significant factor for SGD reduction. In the hand, both sex and body surface area are significant covariates with age. The dorsum of the foot is the most appropriate place to examine sweating in studies of aging. The lower normal limits for SGD in the foot are 213/cm2 for subjects younger than 30 years, 199/cm2 for those from 30 to 59 years, and 123/cm2 for subjects over 59 years old.

Adolescent↗
PubMed1991

Model structure for the human blood coagulation agent beta-factor XIIa.

An improvement to the human blood coagulation agent beta-factor XIIa three-dimensional model is proposed. The sequence alignment as well as the modeling procedures are presented and the minimized energy of the new model is reported before and after solvation of the active center.

Amino Acid Sequence↗