Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

SPEECH ENHANCEMENT USING DISCRIMINATIVE RANDOM FIELDS

Speech enhancement in stationary noise is addressed using the ideal channel selection framework. In order to estimate the binary mask, we propose to classify each time-frequency (T-F) bin of the noisy signal as speech or noise using Discriminative Random Fields (DRF). The DRF function contains two terms - an enhancement function and a smoothing term. On each T-F bin, we propose to use an enhancement function based on likelihood ratio test for speech presence, while Ising model is used as smoothing function for spectro-temporal continuity in the estimated binary mask. The effect of the smoothing function over successive iterations is found to reduce musical noise as opposed to using only enhancement function. The binary mask is inferred from the noisy signal using Iterated Conditional Modes (ICM) algorithm. Sentences from NOIZEUS corpus are evaluated from 0 dB to 15 dB Signal to Noise Ratio (SNR) in 4 kinds of additive noise settings: additive white Gaussian noise, car noise, street noise and pink noise. The reconstructed speech using the proposed technique is evaluated in terms of average segmental SNR, Perceptual Evaluation of Speech Quality (PESQ) and Mean opinion Score (MOS).

汽车模具棱边的三维自适应测量及六维加工轨迹划分

针对大型汽车冲压模具棱边数字化的问题提出了三维自适应测量算法。为满足激光表面强化加工的特殊要求，在后续测量数据处理过程中建立了复杂棱边的简单模型，提出了六维加工轨迹划分算法，并对算法进行了加工实验验证。所提出的算法已应用到集成化柔性激光加工系统中。

Corporeidad, herencia y educación : la representación de la infancia en tres poemas castellanos del siglo XIII

Resumen: Tomando como punto de partida el gesto inaugural de Philippe Ariès en lo concerniente a los estudios sobre la niñez, el presente artículo se propone abordar las formas de representación de la infancia presentes en los tres poemas que componen el Ms. K-III-4 de la Biblioteca de San Lorenzo de El Escorial (Libro de Apolonio, Vida de Santa María Egipciaca, Libre dels tres reys d’Orient), buscando así, delinearle un espacio de comprensión a los modos de ser niño que se dejan leer en este códice. Modos de ser que, no sólo permiten rectifi car las afi rmaciones fundantes del historiador francés, sino que a su vez, devienen signo del imaginario y los saberes de un siglo XIII propenso a la condición terrena del hombre.

El códice como entidad unitaria : apuntes para la edición crítica del manuscrito 431 de la Biblioteca Nacional de Madrid

Resumen: El manuscrito 431 de la Biblioteca Nacional de Madrid fue compuesto hacia 1360, al calor de la Guerra Civil que enfrentó a Pedro I y Enrique II. Este códice constituye uno de los mayores testimonios de un intento de formalización escrita, a mediados del siglo XIV, del derecho señorial nunca fi jado ofi cialmente en Castilla. Los textos allí contenidos nunca fueron considerados como una unidad y por lo tanto fueron siempre editados y estudiados separadamente. El artículo se propone identifi car pautas formales que permitan establecer la entidad unitaria basándose no sólo en sus aspectos físicos (tipo de letra, materiales utilizados, lengua, etc.) sino también en líneas internas de signifi cación tanto en el plano sintagmático (relaciones de contigüidad in praesentia) como en el paradigmático (asociaciones que organizan patrones de lectura).

Développement des méthodes de stabilisation pour la conception des circuits hyperfréquences : application à l'optimisation d'un amplificateur de puissance spatial

209 p. : graf.

Kohesioa ikasleek idatzitako iritzi gutunetan. Zenbait testu aztergai

[EUS]Argudiatzeko orduan izen kohesiorako mekanismoak nola erabiltzen diren aztertzen du lan honek. Horretarako 12 eta 14 urteko ikasleek iritzia emateko idazten dituzten gutunak hartzen dira kontuan, bi alderdi hauei erreparatuz: aurrekaria aurkeztu eta mantentzeko erabiltzen diren adierazpide anaforikoen ezaugarriei, eta adinaren arabera adierazpide horien erabileran egon daitezkeen ezberdintasunei. Adibide batzuen bitartez ikusiko dugunaren arabera, 14 urteko ikasleek estrategia diskurtsibo hobeak erabiltzen dituzte gutunari izen kohesioa emateko, besteak beste testuaren gestio globala eta planifikazioa ere hobeak direlako.

A comparative study of Young's modulus of single-walled carbon nanotube by CPMD, MD, and first principle simulations

Carbon nanotubes (CNTs), due to their exceptional magnetic, electrical and mechanical properties, are promising candidates for several technical applications ranging from nanoelectronic devices to composites. Young's modulus holds the special status in material properties and micro/nano-electromechanical systems (MEMS/NEMS) design. The excellently regular structures of CNTs facilitate accurate simulation of CNTs' behavior by applying a variety of theoretical methods. Here, three representative numerical methods, i.e., Car-Parrinello molecular dynamics (CPMD), density functional theory (DFT) and molecular dynamics (MD), were applied to calculate Young's modulus of single-walled carbon nanotube (SWCNT) with chirality (3,3). The comparative studies showed that the most accurate result is offered by time consuming DFT simulation. MID simulation produced a less accurate result due to neglecting electronic motions. Compared to the two preceding methods the best performance, with a balance between efficiency and precision, was deduced by CPMD.

Fiabilidad de los predictores clínicos y de la biopsia de arteria temporal en el diagnóstico de la arteritis de células gigantes

182 p. : il.

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Sequence specific complexation of b DNA at sites containing g,c base pairs

A series of eight related analogs of distamycin A has been synthesized. Footprinting and affinity cleaving reveal that only two of the analogs, pyridine-2- car box amide-netropsin (2-Py N) and 1-methylimidazole-2-carboxamide-netrops in (2-ImN), bind to DNA with a specificity different from that of the parent compound. A new class of sites, represented by a TGACT sequence, is a strong site for 2-PyN binding, and the major recognition site for 2-ImN on DNA. Both compounds recognize the G•C bp specifically, although A's and T's in the site may be interchanged without penalty. Additional A•T bp outside the binding site increase the binding affinity. The compounds bind in the minor groove of the DNA sequence, but protect both grooves from dimethylsulfate. The binding evidence suggests that 2-PyN or 2-ImN binding induces a DNA conformational change.

In order to understand this sequence specific complexation better, the Ackers quantitative footprinting method for measuring individual site affinity constants has been extended to small molecules. MPE•Fe(II) cleavage reactions over a 10^5 range of free ligand concentrations are analyzed by gel electrophoresis. The decrease in cleavage is calculated by densitometry of a gel autoradiogram. The apparent fraction of DNA bound is then calculated from the amount of cleavage protection. The data is fitted to a theoretical curve using non-linear least squares techniques. Affinity constants at four individual sites are determined simultaneously. The distamycin A analog binds solely at A•T rich sites. Affinities range from 10^(6)- 10^(7)M^(-1) The data for parent compound D fit closely to a monomeric binding curve. 2-PyN binds both A•T sites and the TGTCA site with an apparent affinity constant of 10^(5) M^(-1). 2-ImN binds A•T sites with affinities less than 5 x 10^(4) M^(-1). The affinity of 2-ImN for the TGTCA site does not change significantly from the 2-PyN value. At the TGTCA site, the experimental data fit a dimeric binding curve better than a monomeric curve. Both 2-PyN and 2-ImN have substantially lower DNA affinities than closely related compounds.

In order to probe the requirements of this new binding site, fourteen other derivatives have been synthesized and tested. All compounds that recognize the TGTCA site have a heterocyclic aromatic nitrogen ortho to the N or C-terminal amide of the netropsin subunit. Specificity is strongly affected by the overall length of the small molecule. Only compounds that consist of at least three aromatic rings linked by amides exhibit TGTCA site binding. Specificity is only weakly altered by substitution on the pyridine ring, which correlates best with steric factors. A model is proposed for TGTCA site binding that has as its key feature hydrogen bonding to both G's by the small molecule. The specificity is determined by the sequence dependence of the distance between G's.

One derivative of 2-PyN exhibits pH dependent sequence specificity. At low pH, 4-dimethylaminopyridine-2-carboxamide-netropsin binds tightly to A•T sites. At high pH, 4-Me_(2)NPyN binds most tightly to the TGTCA site. In aqueous solution, this compound protonates at the pyridine nitrogen at pH 6. Thus presence of the protonated form correlates with A•T specificity.

The binding site of a class of eukaryotic transcriptional activators typified by yeast protein GCN4 and the mammalian oncogene Jun contains a strong 2-ImN binding site. Specificity requirements for the protein and small molecule are similar. GCN4 and 2-lmN bind simultaneously to the same binding site. GCN4 alters the cleavage pattern of 2-ImN-EDTA derivative at only one of its binding sites. The details of the interaction suggest that GCN4 alters the conformation of an AAAAAAA sequence adjacent to its binding site. The presence of a yeast counterpart to Jun partially blocks 2-lmN binding. The differences do not appear to be caused by direct interactions between 2-lmN and the proteins, but by induced conformational changes in the DNA protein complex. It is likely that the observed differences in complexation are involved in the varying sequence specificity of these proteins.

Modelagem do potencial elétrico através da membrana do neurônio ganglionar e células de neuroblastoma: efeitos das cargas superficiais.

O objetivo do presente trabalho é comparar, do ponto de vista elétrico, a membrana do neurônio ganglionar com a da célula de neuroblastoma, analisando os efeitos das cargas fixas sobre o potencial elétrico nas superfícies da bicamada lipídica e também sobre o comportamento do perfil de potencial através da membrana, considerando as condiçõesfísico-químicas do estado de repouso e do estado de potencial de ação. As condições para a ocorrência dos referidos estados foram baseadas em valores numéricos de parâmetros elétricos e químicos, característicos dessas células, obtidos na literatura. O neurônio ganglionar exemplifica um neurônio sadio, e a célula de neuroblastoma, que é uma célula tumoral, exemplifica um neurônio patológico, alterado por esta condição. O neuroblastoma é um tumor que se origina das células da crista neural (neuroblastos), que é uma estrutura embrionária que dá origem a muitas partes do sistema nervoso, podendo surgir em diversos locais do organismo, desde a região do crânio até a área mais inferior da coluna. O modelo adotado para simular a membrana de neurônio inclui: (a) as distribuições espaciais de cargas elétricas fixas no glicocálix e na rede de proteínas citoplasmáticas; (b) as distribuições de cargas na solução eletrolítica dos meios externo e interno; e (c) as cargas superficiais da bicamada lipídica. Os resultados que obtivemos mostraram que, nos estados de repouso e de ação, os potenciais superficiais da bicamada interno (ÁSbc) e externo (ÁSgb) da célula de neuroblastoma não sofrem alteração mensurável, quando a densidade de carga na superfície interna (QSbc) torna-se 50 vezes mais negativa, tanto para uma densidade de carga na superfície externa da bicamada nula (QSgb = 0), como para um valor de QSgb 6= 0. Porém, no estado de repouso, uma leve queda em ÁSbc do neur^onio ganglionar pode ser observada com este nível de variação de carga, sendo que ÁSgb do neurônio ganglionar é mais negativo quando QSgb = 1=1100 e/A2. No estado de ação, para QSgb = 0, o aumento da negatividade de QSbc não provoca alteração detectável de ÁSbc e ÁSgb para os dois neurônios. Quando consideramos QSgb = 1=1100 e/A2, ÁSgb do neurônio ganglionar se torna mais negativo, não se observando variações detectáveis nos potenciais superficiais da célula de neuroblastoma. Tanto no repouso quanto no estado de ação, ÁSgb das duas células não sofre variação sensível com o aumento da negatividade da carga fixa distribuída espacialmente no citoplasma. Já a ÁSbc sofre uma queda gradativa nos dois tipos celulares; porém, no estado de ação, esta queda é mais rápida. Descobrimos diferenças importantes nos perfis de potencial das duas células, especialmente na região do glicocálix.

Trends in Income and Price Elasticities of Transport Demand (1850-2010)

40 p.