Three-dimensional structure of NADPH–cytochrome P450 reductase: Prototype for FMN- and FAD-containing enzymes

Microsomal NADPH–cytochrome P450 reductase (CPR) is one of only two mammalian enzymes known to contain both FAD and FMN, the other being nitric-oxide synthase. CPR is a membrane-bound protein and catalyzes electron transfer from NADPH to all known microsomal cytochromes P450. The structure of rat liver CPR, expressed in Escherichia coli and solubilized by limited trypsinolysis, has been determined by x-ray crystallography at 2.6 Å resolution. The molecule is composed of four structural domains: (from the N- to C- termini) the FMN-binding domain, the connecting domain, and the FAD- and NADPH-binding domains. The FMN-binding domain is similar to the structure of flavodoxin, whereas the two C-terminal dinucleotide-binding domains are similar to those of ferredoxin–NADP+ reductase (FNR). The connecting domain, situated between the FMN-binding and FNR-like domains, is responsible for the relative orientation of the other domains, ensuring the proper alignment of the two flavins necessary for efficient electron transfer. The two flavin isoalloxazine rings are juxtaposed, with the closest distance between them being about 4 Å. The bowl-shaped surface near the FMN-binding site is likely the docking site of cytochrome c and the physiological redox partners, including cytochromes P450 and b5 and heme oxygenase.

The exaptive excellence of spandrels as a term and prototype

In 1979, Lewontin and I borrowed the architectural term “spandrel” (using the pendentives of San Marco in Venice as an example) to designate the class of forms and spaces that arise as necessary byproducts of another decision in design, and not as adaptations for direct utility in themselves. This proposal has generated a large literature featuring two critiques: (i) the terminological claim that the spandrels of San Marco are not true spandrels at all and (ii) the conceptual claim that they are adaptations and not byproducts. The features of the San Marco pendentives that we explicitly defined as spandrel-properties—their necessary number (four) and shape (roughly triangular)—are inevitable architectural byproducts, whatever the structural attributes of the pendentives themselves. The term spandrel may be extended from its particular architectural use for two-dimensional byproducts to the generality of “spaces left over,” a definition that properly includes the San Marco pendentives. Evolutionary biology needs such an explicit term for features arising as byproducts, rather than adaptations, whatever their subsequent exaptive utility. The concept of biological spandrels—including the examples here given of masculinized genitalia in female hyenas, exaptive use of an umbilicus as a brooding chamber by snails, the shoulder hump of the giant Irish deer, and several key features of human mentality—anchors the critique of overreliance upon adaptive scenarios in evolutionary explanation. Causes of historical origin must always be separated from current utilities; their conflation has seriously hampered the evolutionary analysis of form in the history of life.

Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily

PAS domains are found in diverse proteins throughout all three kingdoms of life, where they apparently function in sensing and signal transduction. Although a wealth of useful sequence and functional information has become recently available, these data have not been integrated into a three-dimensional (3D) framework. The very early evolutionary development and diverse functions of PAS domains have made sequence analysis and modeling of this protein superfamily challenging. Limited sequence similarities between the ∼50-residue PAS repeats and one region of the bacterial blue-light photosensor photoactive yellow protein (PYP), for which ground-state and light-activated crystallographic structures have been determined to high resolution, originally were identified in sequence searches using consensus sequence probes from PAS-containing proteins. Here, we found that by changing a few residues particular to PYP function, the modified PYP sequence probe also could select PAS protein sequences. By mapping a typical ∼150-residue PAS domain sequence onto the entire crystallographic structure of PYP, we show that the PAS sequence similarities and differences are consistent with a shared 3D fold (the PAS/PYP module) with obvious potential for a ligand-binding cavity. Thus, PYP appears to prototypically exhibit all the major structural and functional features characteristic of the PAS domain superfamily: the shared PAS/PYP modular domain fold of ∼125–150 residues, a sensor function often linked to ligand or cofactor (chromophore) binding, and signal transduction capability governed by heterodimeric assembly (to the downstream partner of PYP). This 3D PAS/PYP module provides a structural model to guide experimental testing of hypotheses regarding ligand-binding, dimerization, and signal transduction.

Three-dimensional functional magnetic resonance imaging of human brain on a clinical 1.5-T scanner.

Functional magnetic resonance imaging (fMRI) is a tool for mapping brain function that utilizes neuronal activity-induced changes in blood oxygenation. An efficient three-dimensional fMRI method is presented for imaging brain activity on conventional, widely available, 1.5-T scanners, without additional hardware. This approach uses large magnetic susceptibility weighting based on the echo-shifting principle combined with multiple gradient echoes per excitation. Motor stimulation, induced by self-paced finger tapping, reliably produced significant signal increase in the hand region of the contralateral primary motor cortex in every subject tested.

A multimodal genre recognition prototype

In this paper, a multimodal and interactive prototype to perform music genre classification is presented. The system is oriented to multi-part files in symbolic format but it can be adapted using a transcription system to transform audio content in music scores. This prototype uses different sources of information to give a possible answer to the user. It has been developed to allow a human expert to interact with the system to improve its results. In its current implementation, it offers a limited range of interaction and multimodality. Further development aimed at full interactivity and multimodal interactions is discussed.

Improving kNN multi-label classification in Prototype Selection scenarios using class proposals

Prototype Selection (PS) algorithms allow a faster Nearest Neighbor classification by keeping only the most profitable prototypes of the training set. In turn, these schemes typically lower the performance accuracy. In this work a new strategy for multi-label classifications tasks is proposed to solve this accuracy drop without the need of using all the training set. For that, given a new instance, the PS algorithm is used as a fast recommender system which retrieves the most likely classes. Then, the actual classification is performed only considering the prototypes from the initial training set belonging to the suggested classes. Results show that this strategy provides a large set of trade-off solutions which fills the gap between PS-based classification efficiency and conventional kNN accuracy. Furthermore, this scheme is not only able to, at best, reach the performance of conventional kNN with barely a third of distances computed, but it does also outperform the latter in noisy scenarios, proving to be a much more robust approach.

On the suitability of Prototype Selection methods for kNN classification with distributed data

In the current Information Age, data production and processing demands are ever increasing. This has motivated the appearance of large-scale distributed information. This phenomenon also applies to Pattern Recognition so that classic and common algorithms, such as the k-Nearest Neighbour, are unable to be used. To improve the efficiency of this classifier, Prototype Selection (PS) strategies can be used. Nevertheless, current PS algorithms were not designed to deal with distributed data, and their performance is therefore unknown under these conditions. This work is devoted to carrying out an experimental study on a simulated framework in which PS strategies can be compared under classical conditions as well as those expected in distributed scenarios. Our results report a general behaviour that is degraded as conditions approach to more realistic scenarios. However, our experiments also show that some methods are able to achieve a fairly similar performance to that of the non-distributed scenario. Thus, although there is a clear need for developing specific PS methodologies and algorithms for tackling these situations, those that reported a higher robustness against such conditions may be good candidates from which to start.

Análise da precisão e reprodutibilidade de um scanner intraoral: estudo clínico

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas Moniz