Functional non-synonymous polymorphisms prediction methods: current approaches and future developments.

Non-synonymous single nucleotide polymorphisms (nsSNPs) are genetic variations that affect the encoded protein by an amino acid change. In humans, many naturally-occurring nsSNPs cause protein dysfunction and increase vulnerability to disease. Identification of such nsSNPs provides an important opportunity to develop drugs/nutrients with precise therapeutic targets. Therefore, current biomedical research and medicinal chemistry look for targets and functional nsSNPs, to establish correlation with disease susceptibility and foster rational drug design. We review the molecular bases of missense mutation effects at the protein level, namely on sequence conservation, including stability, conformation, biophysical parameters, and protein-protein interaction. Further, we summarize some computational methods, available information resources, and the current approaches used to predict nsSNPs functionality in human genome, most of which based on protein structures and/or evolutionary conservation. Finally, using an approach paradigmatic of the nsSNPs-gene interactions, we evaluate the functional consequences and phenotypic effects of nsSNPs on two genes associated with cholesterol response. Biophysical changes produced by exchanged amino acids I638V (rs5908) from the 3-hydroxy-3-methylglutaryl- coenzyme A reductase gene, and A370T (rs11669576) from the low density lipoprotein receptor gene have been analyzed with an emphasis on stability, activity, and structure of their related proteins. Based on available data and the results of our study, we propose that, even though the extent and precise nature of nsSNPs' role in health and disease is yet to be fully elucidated, targeted investigations are warranted and will--in the future--provide useful tools to develop targeted drugs.

FTIR microspectroscopic analysis of the effects of certain drugs on oxidative stress and brain protein structure.

This study reports the changes in lipids and proteins of different brain areas of nicotine, D+-amphetamine, and nicotine and D+-amphetamine treated rats by monitoring lipid peroxidation and protein beta-sheet formation using infrared microspectroscopy. Compared with the untreated brain samples, the peroxide level is relatively higher in the amphetamine-treated brain sections, both in the cortex and hippocampus area. However, this peroxide increase is attenuated when administering amphetamine plus nicotine. Analogous drug-dependent trends for protein beta-sheet content are observed, which suggests a connection between lipid oxidation involved in oxidative stress and beta-sheet protein structure generally present in neurodegenerative diseases. The above property of nicotine is of interest, in the sense that it might reduce the production of beta-amyloid proteins in Alzheimer's disease.

Amphetamine effects on brain protein structure and oxidative stress as revealed by FTIR microspectroscopy.

Amphetamines are psychostimulants abused by man, that eventually leads to drug dependence. Amphetamine administration to rodents has been shown to provoke significant neurotoxicity involving dopaminergic nerve terminal degeneration. However, little information related to the effect of amphetamines on reactive oxygen species (ROS) production and neurotoxicity in brain is currently available. Herein we report the biochemical alterations of lipids and proteins in brain sections from amphetamine-treated rodents using infrared microspectroscopy, immunohistochemistry, and immunoblotting. The spectroscopic changes reveal for the first time the formation of beta-sheet-rich proteins in the cortex, but no significant protein alterations are visible in hippocampus region where hydroperoxide concentration is found to be lower relative to cortex. These result suggest that ROS generated by amphetamine-mediated oxidative stress induce formation beta-sheet-rich proteins which can be of amyloid beta-like character.

Conformational features of truncated hepatitis C virus core protein in virus-like particles.

HCVc 120 is a truncated protein from the hepatitis C virus (HCV) core protein that interacts with itself to form nucleocapsid-like particles. We present here the infrared and Raman spectra of oligomeric HCVc 120 protein in order to obtain insights into its secondary structure as well as the environment surrounding some protein side chains. When compared with its monomer form, oligomeric HCVc 120 protein shows an increase in beta-sheet structure. Tryptophan residues have been found to be solvent exposed in the oligomeric form, and they likely do not significantly participate in the protein assembly. However, the beta-sheet content in oligomeric HCVc 120 protein suggests that this structural motif cannot be excluded in nucleocapsid formation, as shown recently in other viruses.

Structure of bacteriophage P22 portal protein in relation to assembly: investigation by Raman spectroscopy.

Salmonella phage P22, which serves as an assembly paradigm for icosahedral double-stranded DNA viruses, packages its viral genome through a capsid channel (portal) comprising 12 copies of a 725-residue subunit. Secondary and tertiary structures of the portal subunit in monomeric and dodecameric states have been investigated by Raman spectroscopy using a His6-tagged recombinant protein that self-assembles in vitro [Moore, S. D., and Prevelige, P. E., Jr. (2001) J. Biol. Chem. 276, 6779-6788]. The portal protein exhibits Raman secondary structure markers typical of a highly alpha-helical subunit fold that is little perturbed by assembly. On the other hand, Raman markers of subunit side chains change dramatically with assembly, an indication of extensive changes in side chain environments. The cysteinyl Raman signature of the portal consists of a complex pattern of sulfhydryl stretching bands, revealing diverse hydrogen-bonding states for the four S-H groups per subunit (Cys 153, Cys 173, Cys 283, and Cys 516). Upon assembly, the population of strongly hydrogen-bonded S-H groups decreases, while the population of weakly hydrogen-bonded S-H groups increases, implying that specific intrasubunit S-H.X hydrogen bonds must be weakened to effect dodecamer assembly and that the molecular mechanism involves reorganization of subunit domains without appreciable changes in domain conformations. Comparison with other viral protein assemblies suggests an assembly process not requiring metastable intermediates. The recently published X-ray structure of the phi29 portal [Simpson, A. A., et al. (2000) Nature 408, 745-750] shows that residues 125-225 lining the channel surface form alpha-helical modules spaced by short beta-strands and turns; a surprisingly close secondary structure homology is predicted for residues 240-350 of the P22 portal, despite no apparent sequence homology. This motif is proposed as an evolutionarily conserved domain involved in DNA translocation.

Leiomioma vesical / Leiomyoma of the bladder

Presentamos un nuevo caso de leiomioma vesical en una paciente con clínica inespecífica, y en la que las pruebas de imagen preoperatorias no lo orientaron. El diagnóstico definitivo lo dio el estudio anatomopatológico de la pieza quirúrgica (AU)

[Selective embolization of post-traumatic renal pseudoaneurysm in monorenal patient]. / Embolización selectiva de pseudoaneurisma renal post-traumático en paciente monorreno.

Presentation of one case of a patient who presented two non-penetrating abdominal traumatism along a year period. In the first incident it was necessary to practice a left nefrectomy and in the second one the therapeutic opcion was a superselective embolization of a pseudoameurism communicated with urinary tract.

Embolización selectiva de pseudoaneurisma renal post-traumático en paciente monorreno / Superselective embolization of post-traumatic pseudoaneurysm renal un a monorrenal pacient

Presentamos el caso de un paciente que en el intervalo de un año había sufrido dos traumatismos abdominales no penetrantes. En el primer episodio fue necesario practicar nefrectomía izquierda y en el segundo la opción terapéutica llevada a cabo fue la embolización selectiva de un pseudoaneurisma comunicado a la vía urinaria (AU)

[Bladder leiomyoma]. / Leiomioma vesical.

A new case of leiomyoma of the bladder is presented in a patient with unspecific symptoms and the preoperatives patterns don't give to a certainty diagnosis. The conclusive diagnosis was obtained with pathoanatomical study of the quirurgic piece.

Structural changes of hake (Merluccius merluccius L.) fillets: effects of freezing and frozen storage.

Structural changes in hake (Merluccius merluccius L.) fillets as affected by freezing method and frozen storage temperature have been studied through Raman spectroscopy and related to changes in texture and functionality. Changes in protein secondary structure were observed due to storage temperature, accompanied by changes in apparent viscosity and shear resistance. Samples at -10 degrees C showed greater structural alteration than at -30 degrees C in terms of increase of beta-sheets at the expense of alpha-helices. An increase of unordered protein structure was found only in samples stored at -10 degrees C. Exposure of buried tryptophan residues was observed at both storage temperatures. The decrease of the deltaCH(2) band upon storage suggested an increase of hydrophobic interactions of aliphatic residues. Except for liquid air frozen fillets, all samples showed a decrease of the nuO-H/nuC-H band ratio compared to the fresh ones, this decrease being higher the harsher the conditions.

Conformational structure and binding mode of glyceraldehyde-3-phosphate dehydrogenase to tRNA studied by Raman and CD spectroscopy.

Recently it has been suggested that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) play a role in nuclear tRNA export. As the structural basis of binding of GAPDH to tRNA is as yet unknown, we have employed Raman and CD spectroscopy as probes of the solution structures of GAPDH from rabbit and tRNA(Phe) from brewers yeast. Additionally, we have obtained the Raman and CD spectra of GAPDH when bound to tRNA(Phe). In the complex we find the following results: (a) The most part of the tRNA(Phe) structure is conserved, but with a slight perturbation toward a B-like form. (b) No significant changes in the secondary structure of the protein upon binding are observed. (c) The surface enhanced Raman spectra are consistent with a GAPDH-tRNA(Phe) complex molecular model that involves the insertion of TRNA(Phe) into the GAPDH tetramer groove containing the R and P axes. (d) The specific interactions that occur between GAPDH and the tRNA(Phe) involve, mainly, stacking between nucleobases and aromatic amino-acid residues, and ionic interactions of basic amino-acid residues with phosphate groups of the ribose-phosphate backbone. The above stacking interactions are also supported by the significant relatedness that we have found between an amino-acid sequence (residues 303-308) of GAPDH and RNP2 binding motifs of some RNA binding proteins.

Raman spectroscopic determination of inosine nucleoside in nucleotides.

Raman spectroscopy has been applied to the analytical determination of inosine nucleoside in nucleotides. Spectral characteristics of aqueous solutions of lithium, potassium and magnesium salts of inosine 5'-monophosphoric acid are described. Two characteristic bands located at 1553 and 1593 cm(-1) whose frequencies are not sensitive either to the nucleotide concentration or to alkaline cations present in the medium, have been used for this purpose. The concentration ranges over which the method was applicable were 2.5-80 and 11.5-80 mg ml(-1) of inosine using the 1553 and 1593 cm(-1) bands, respectively, with relative standard deviations of 2.5 and 4.0% and detection limits of 0.25 and 1.16% (w/w). As the above bands are not generated by the standard nucleobases, this method can be applied to the quantitative determination of inosine in transfer ribonucleic acids.