FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which can be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been derived from structural alignments in the HOMSTRAD database (http://www-cryst.bioc. cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other cases. The gap penalty at each position of the structure is determined according to its solvent accessibility, its position relative to the secondary structure elements (SSEs) and the conservation of the SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy.     

Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure

The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher.     

SPINFAST: using structure alignment profiles to enhance the accuracy and assess the reliability of protein side-chain modeling

We present a novel, knowledge-based method for the side-chain addition step in protein structure modeling. The foundation of the method is a conditional probability equation, which specifies the probability that a side-chain will occupy a specific rotamer state, given a set of evidence about the rotamer states adopted by the side-chains at aligned positions in structurally homologous crystal structures. We demonstrate that our method increases the accuracy of homology model side-chain addition when compared with the widely employed practice of preserving the side-chain conformation from the homology template to the target at conserved residue positions. Furthermore, we demonstrate that our method accurately estimates the probability that the correct rotamer state has been selected. This interesting result implies that our method can be used to understand the reliability of each and every side-chain in a protein homology model.     

Coextraction during reactive extraction of phenylalanine using Aliquat 336: modeling extraction equilibrium

Reactive liquid-liquid extraction can be used to recover hydrophilic fermentation products that would not otherwise partition into nonpolar solvents through an ion-exchange reaction at the two-phase interface. However, the ion-exchange reagent may not be specific to the solute of interest and other compounds present may also be extracted. In this study, the effect on solute extraction of other compounds present in the extraction medium was investigated for phenylalanine extraction using Aliquat 336. The extent of extraction at equilibrium was modeled using the equilibrium constants for the reactions present in the process. The interaction of different species within a multicomponent medium was examined using the model and experimental results. It was found that the extent of extraction and coextraction is controlled by the thermodynamics of each extraction reaction and, due to the formation of a common product, the interaction between each of the reactions. The main competition to reactive extraction will come from hydrophobic anionic compounds that will be present in fermentation broth.     

A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution

Semi-squaraines (SMSQ) are known as donor-acceptor (D-A) type molecules whereas squaraines (SQ), which differs from SMSQ by an extra donor group, are more or less biradicaloids in nature. The effect of the additional donor group in SQ, which changes the nature of the molecule, on geometrical and electronic structure are studied here and compared with the corresponding SMSQ. It is noticed from the geometrical parameters that, a strong resonance exists in SQ whereas disparity in carbon-carbon bond lengths of central C₄ ring is seen in SMSQ dyes. The increasing and decreasing of antibonding interactions between central C₄ ring and side donor groups cause destabilization of HOMO and stabilization of LUMO respectively in case of SQ compared to SMSQ molecules. This leads to decreasing the HOMO-LUMO gap and promotes biradicaloid character of SQ. The absorption maxima obtained by using TD-DFT method with BLYP, B3LYP, BHandHLYP, CAM-B3LYP and M06-2X functionals are not in good agreement with experimental results. On the other hand SAC-CI method gives better results for all the molecules. From this work we can evolve a design principle of these molecules which play a role as sensitizers in dye sensitized solar cells.     

Developmental constraints in a comparative framework: a test case using variations in phalanx number during amniote evolution

Constraints are factors that limit evolutionary change. A subset of constraints is developmental, and acts during embryonic development. There is some uncertainty about how to define developmental constraints, and how to formulate them as testable hypotheses. Furthermore, concepts such as constraint-breaking, universal constraints, and forbidden morphologies present some conceptual difficulties. One of our aims is to clarify these issues. After briefly reviewing current classifications of constraint, we define developmental constraints as those affecting morphogenetic processes in ontogeny. They may be generative or selective, although a clear distinction cannot always be drawn. We support the idea that statements about constraints are in fact statements about the relative frequency of particular transformations (where 'transformation' indicates a change from the ancestral condition). An important consequence of this is that the same transformation may be constrained in one developmental or phylogenetic context, but evolutionarily plastic in another. In this paper, we analyse developmental constraints within a phylogenetic framework, building on similar work by previous authors. Our approach is based on the following assumptions from the literature: (1) constraints are identified when there is a discrepancy between the observed frequency of a transformation, and its expected frequency; (2) the 'expected' distribution is derived by examining the phylogenetic distribution of the transformation and its associated selection pressures. Thus, by looking for congruence between these various phylogenetic distribution patterns, we can test hypotheses about constraint. We critically examine this approach using a test case: variation in phalanx-number in the amniote limb.     

A computational model of visual marking using an inter-connected network of spiking neurons: the spiking search over time & space model (sSoTS).

In the real world, visual information is selected over time as well as space, when we prioritise new stimuli for attention. Watson and Humphreys [Watson, D., Humphreys, G.W., 1997. Visual marking: prioritizing selection for new objects by top-down attentional inhibition of old objects. Psychological Review 104, 90-122] presented evidence that new information in search tasks is prioritised by (amongst other processes) active ignoring of old items - a process they termed visual marking. In this paper we present, for the first time, an explicit computational model of visual marking using biologically plausible activation functions. The "spiking search over time and space" model (sSoTS) incorporates different synaptic components (NMDA, AMPA, GABA) and a frequency adaptation mechanism based on [Ca(2+)] sensitive K(+) current. This frequency adaptation current can act as a mechanism that suppresses the previously attended items. We show that, when coupled with a process of active inhibition applied to old items, frequency adaptation leads to old items being de-prioritised (and new items prioritised) across time in search. Furthermore, the time course of these processes mimics the time course of the preview effect in human search. The results indicate that the sSoTS model can provide a biologically plausible account of human search over time as well as space.     

Differential activation of phospholipases during necrosis or apoptosis: A comparative study using tumor necrosis factor and anti-Fas antibodies

Phospholipases generate important secondary messengers in several cellular processes, including cell death. Tumor necrosis factor (TNF) can induce two distinct modes of cell death, viz. necrosis and apoptosis. Here we demonstrate that phospholipase D (PLD) and cytosolic phospholipase A₂ (cPLA₂) are differentially activated during TNF-induced necrosis or apoptosis. Moreover, a comparative study using TNF and anti-Fas antibodies as cell death stimuli showed that PLD and cPLA₂ are specifically activated by TNF. These results indicate that both the mode of cell death and the type of death stimulus determine the potential role of phospholipases as generators of secondary messengers. J. Cell. Biochem. 71:392–399, 1998. © 1998 Wiley-Liss, Inc.     

Abdominal aortic hemodynamics in young healthy adults at rest and during lower limb exercise: quantification using image-based computer modeling

Localization of atherosclerotic lesions in the abdominal aorta has been previously correlated to areas of adverse hemodynamic conditions, such as flow recirculation, low mean wall shear stress, and high temporal oscillations in shear. Along with its many systemic benefits, exercise is also proposed to have local benefits in the vasculature via the alteration of these regional flow patterns. In this work, subject-specific models of the human abdominal aorta were constructed from magnetic resonance angiograms of five young, healthy subjects, and computer simulations were performed under resting and exercise (50% increase in resting heart rate) pulsatile flow conditions. Velocity fields and spatial variations in mean wall shear stress (WSS) and oscillatory shear index (OSI) are presented. When averaged over all subjects, WSS increased from 4.8 +/- 0.6 to 31.6 +/- 5.7 dyn/cm2 and OSI decreased from 0.22 +/- 0.03 to 0.03 +/- 0.02 in the infrarenal aorta between rest and exercise. WSS significantly increased, whereas OSI decreased between rest and exercise at the supraceliac, infrarenal, and suprabifurcation levels, and significant differences in WSS were found between anterior and posterior sections. These results support the hypothesis that exercise provides localized benefits to the cardiovascular system through acute mechanical stimuli that trigger longer-term biological processes leading to protection against the development or progression of atherosclerosis.     

Protein flexibility and conformational states of Leishmania antigen eIF-4A: identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling

Recent homology modeling studies have identified specific residues (epitope) of the Leishmania RNA helicase protein (LmeIF) that stimulates production of IL-12 cytokine. However, question remains concerning how LmeIF’s N-terminal moiety initiates adjuvant effects. Extensive molecular modeling combining the normal mode analysis (NMA) and molecular dynamics simulations, in the present study, has demonstrated that the LmeIF structure may exist in two different forms corresponding to the extended and collapsed (closed) states of the entire structure. The computational results showed that the two domains of the LmeIF structure tend to undergo large fluctuations in a concerted fashion and have strong effect on the solvent accessible surface of the epitope situated on the N-terminal structure. The conformational freedom of the C-terminal domains may explain why the entire LmeIF protein is not as active as the N-terminal moiety. Thereafter, a comparative genome analysis with subsequent homology modeling and molecular electrostatic potential (MEP) techniques allowed us to predict a novel and plausible RNA helicase (LI-helicase) from the Listeria source with adjuvant property as observed for the Leishmania eIF-4A protein. The structural folding and MEP maps revealed similar topologies of the epitope of both LmeIF and LI-helicase proteins and striking identity in the local disposition of the charged groups.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:7     

Energetics of free existence in swallows and martins (hirundinidae) during breeding: a comparative study using doubly labeled water

Energy metabolism of three sympatric swallows (Hirundinidae) was investigated during the breeding season using doubly labeled water (²H₂ ¹⁸O). Interspecific and intraspecific differences in energy metabolism were examined in relation to the habits, size and environment of the birds. To facilitate comparisons we expressed energy metabolism (M) as the ratio of average daily metabolic rate (ADMR, cm³CO_2g ^-1h^-1) to basal metabolic rate (BMR). We observed adults during incubation and when feeding nestlings. Then, both sexes of Sand Martins Riparia riparia and House Martins Delinchon urbica were either at the nest or on the wing. Incubation reduced activity levels during the day resulting in M (incubation) being 17–26% lower than during rearing. Differences in energy costs for rearing chicks depended mainly on flight behaviour, the smaller Sand Martin doing nearly twice as much flapping during flight as the House Martin, giving higher values for M. In Swallows Hirundo rustica the female incubates alone, alternating between short feeding trips and incubating in daytime. This pattern was linked with a relatively high value for M in the only individual behaving like our controls. Both sexes of Swallows feed the chicks, and they showed similar values of M. They also closely resembled House Martins, despite contrasts in the time spent flying and their behaviour during flight. Feeding conditions affected activity, and thereby M, in a species specific way. The House Martin did more gliding in poor weather, taking less mobile prey, reducing M. Swallows reduced foraging costs further by using body reserves, as in the House Martin. The smaller Sand Martin, in contrast, showed a high expenditure in poor weather. Over two breeding seasons ADMR reached values around 5 BMR for all three species.     

Behavior and reproduction of invertebrate animals during and after a long-term microgravity: space experiments using an Autonomous Biological System (ABS).

Aquatic invertebrate animals such as Amphipods, Gastropods (pond snails), Ostracods and Daphnia (water flea) were placed in water-filled cylindrical vessels together with water plant (hornwort). The vessels were sealed completely and illuminated with a fluorescent lamp to activate the photosynthesis of the plant for providing oxygen within the vessels. Such ecosystem vessels, specially termed as Autonomous Biological System or ABS units, were exposed to microgravity conditions, and the behavior of the animals and their reproduction capacity were studied. Three space experiments were carried out. The first experiment used a Space shuttle only and it was a 10-day flight. The other two space experiments were carried out in the Space station Mir (Shuttle/Mir mission), and the flight units had been kept in microgravity for 4 months. Daphnia produced their offspring during a 10-day Shuttle flight. In the first Mir experiment, no Daphnia were detected when recovered to the ground. However, they were alive in the second Mir experiment. Daphnia were the most fragile species among the invertebrate animals employed in the present experiments. All the animals, i.e., Amphipods, pond snails, Ostracods and Daphnia had survived for 4 months in space, i.e., they had produced their offspring or repeated their life-cycles under microgravity. For the two Mir experiments, in both the flight and ground control ecosystem units, an inverse relationship was noted between the number of Amphipods and pond snails in each unit. Amphipods at 10 hours after the recovery to the ground frequently exhibited a movement of dropping straight-downward to the bottom of the units. Several Amphipods had their legs bent abnormally, which probably resulted from some physiological alterations during their embryonic development under microgravity. From the analysis of the video tape recorded in space, for Ostracods and Daphnia, a half of their population were looping under microgravity. Such looping animals could be observed still at the end of the 4 month stay in space. No looping behavior was noted for Amphipods and pond snails.     

NHE inhibition does not improve Na(+) or Ca(2+) overload during reperfusion: using modeling to illuminate the mechanisms underlying a therapeutic failure

Reperfusion injury results from pathologies of cardiac myocyte physiology that develop when previously ischemic myocardium experiences a restoration of normal perfusion. Events in the development of reperfusion injury begin with the restoration of a proton gradient upon reperfusion, which then allows the sodium-proton exchanger (NHE) to increase flux, removing protons from the intracellular space while importing sodium. The resulting sodium overload drives increased reverse-mode sodium-calcium exchanger (NCX) activity, creating a secondary calcium overload that has pathologic consequences. One of the attempts to reduce reperfusion-related damage, NHE inhibition, has shown little clinical benefit, and only when NHE inhibitors are given prior to reperfusion. In an effort to further understand why NHE inhibitors have been largely unsuccessful, we employed a new mathematical cardiomyocyte model that we developed for the study of ischemia and reperfusion. Using this model, we simulated 20 minutes of ischemia and 10 minutes of reperfusion, while also simulating NHE inhibition by reducing NHE flux in our model by varying amounts and at different time points. In our simulations, when NHE inhibition is applied at the onset of reperfusion, increasing the degree of inhibition increases the peak sodium and calcium concentrations, as well as reducing intracellular pH recovery. When inhibition was instituted at earlier time points, some modest improvements were seen, largely due to reduced sodium concentrations prior to reperfusion. Analysis of all sodium flux pathways suggests that the sodium-potassium pump (NaK) plays the largest role in exacerbated sodium overload during reperfusion, and that reduced NaK flux is largely the result of impaired pH recovery. While NHE inhibition does indeed reduce sodium influx through that exchanger, the resulting prolongation of intracellular acidosis paradoxically increases sodium overload, largely mediated by impaired NaK function.