Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a poly-isolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. (C) 2007 Elsevier B.V. All rights reserved.

Cardiovascular changes under normoxic and hypoxic conditions in the air-breathing teleost Synbranchus marmoratus: importance of the venous system

Synbranchus marmoratus is a facultative air-breathing fish, which uses its buccal cavity as well as its gills for air-breathing. S. marmoratus shows a very pronounced tachycardia when it surfaces to air-breathe. An elevation of heart rate decreases cardiac filling time and therefore may cause a decline in stroke volume (VS), but this can be compensated for by an increase in venous tone to maintain stroke volume. Thus, the study on S. marmoratus was undertaken to investigate how stroke volume and venous function are affected during air-breathing. To this end we measured cardiac output (Q), heart rate (fH), central venous blood pressure (PCV), mean circulatory filling pressure (MCFP), and dorsal aortic blood pressures (PDA) in S. marmoratus. Measurements were performed in aerated water (P-O2 > 130 mmHg), when the fish alternated between gill ventilation and prolonged periods of apnoeas, as well as during hypoxia (P-O2 <= 50 mmHg), when the fish changed from gill ventilation to air-breathing. Q increased significantly during gill ventilation compared to apnoea in aerated water through a significant increase in both fH and VS. PCV and MCFP also increased significantly. During hypoxia, when the animals surface to ventilate air, we found a marked rise in fH, PCV, MCFP, Q and VS, whereas PDA decreased significantly. Simultaneous increases in PCV and MCFP in aerated, as well as in hypoxic water, suggests that the venous system plays an important regulatory role for cardiac filling and VS in this species. In addition, we investigated adrenergic regulation of the venous system through bolus infusions of adrenergic agonists (adrenaline, phenylephrine and isoproterenol; 2 mu g kg(-1)). Adrenaline and phenylephrine caused a marked rise in PCV and MCFP, whereas isoproterenol led to a marked decrease in PCV, and tended to decrease MCFP. Thus, it is evident that stimulation of both alpha- and beta-adrenoreceptors affects venous tone in S. marmoratus.

The autonomic control and functional significance of the changes in heart rate associated with air breathing in the jeju, Hoplerythrinus unitaeniatus

The jeju is a teleost fish with bimodal respiration that utilizes a modified swim bladder as an air-breathing organ (ABO). Like all air-breathing fish studied to date, jeju exhibit pronounced changes in heart rate (f(H)) during air-breathing events, and it is believed that these may facilitate oxygen uptake (M-O2) from the ABO. The current study employed power spectral analysis (PSA) of f(H) patterns, coupled with instantaneous respirometry, to investigate the autonomic control of these phenomena and their functional significance for the efficacy of air breathing. The jeju obtained less than 5% of total M-O2 (M-tO2) from air breathing in normoxia at 26 degrees C, and PSA of beat-to-beat variability in fH revealed a pattern similar to that of unimodal water-breathing fish. In deep aquatic hypoxia (water P-O2=1 kPa) the jeju increased the frequency of air breathing (f(AB)) tenfold and maintained M-tO2 unchanged from normoxia. This was associated with a significant increase in heart rate variability (HRV), each air breath (AB) being preceded by a brief bradycardia and then followed by a brief tachycardia. These f(H) changes are qualitatively similar to those associated with breathing in unimodal air-breathing vertebrates. Within 20 heartbeats after the AB, however, a beat-to-beat variability in f(H) typical of water-breathing fish was re-established. Pharmacological blockade revealed that both adrenergic and cholinergic tone increased simultaneously prior to each AB, and then decreased after it. However, modulation of inhibitory cholinergic tone was responsible for the major proportion of HRV, including the precise beat-to-beat modulation of f(H) around each AB. Pharmacological blockade of all variations in f(H) associated with air breathing in deep hypoxia did not, however, have a significant effect upon f(AB) or the regulation of M-tO2. Thus, the functional significance of the profound HRV during air breathing remains a mystery.

Lactate sequestration by osteoderms of the broad-nose caiman, Caiman latirostris, following capture and forced submergence

Lactate accumulation in osteoderms; of the broad-nose caiman, Caiman latirostris, was determined following capture and surgery and after a period of forced submergence and related to concurrent values in blood. Control samples of bone and blood were taken after recovery from surgery and before submergence. In addition, samples of osteoderm were incubated in a lactate solution to determine equilibrium concentration, and additional samples were analyzed for elemental and CO2 concentrations. The composition of the osteoderms closely resembles that of typical vertebrate bone, with a high concentration of calcium and phosphate. Plasma and osteoderm lactate concentrations were both elevated following surgery and decreased significantly after 1 day of recovery. Submergence produced a typical lactate pattern in the plasma, with only a modest increase during the dive and then a sharp increase during recovery to a peak of 31.2 +/- 1.9 mumol ml(-1) after 1 h. When caimans were anesthetized 2 h after submergence, osteoderm lactate in the same animals was significantly increased to 14.8 mumol g(-1) wet mass. The ratio of the osteoderm: plasma lactate concentration after submergence was similar to the ratio observed in the incubated samples, suggesting that osteoderm lactate concentrations in vivo were equilibrated with circulating plasma levels. We conclude that caiman osteoderms sequester lactate during lactic acidosis and that the time course is fast enough to have benefit to these animals following normal anaerobic burst activity.

Morphological and physiological specialization for digging in amphisbaenians, an ancient lineage of fossorial vertebrates

Amphisbaenians are legless reptiles that differ significantly from other vertebrate lineages. Most species dig underground galleries of similar diameter to that of the animal. We studied the muscle physiology and morphological attributes of digging effort in the Brazilian amphisbaenid Leposternon microcephalum (Squamata; Amphisbaenia), which burrows by compressing soil against the upper wall of the tunnel by means of upward strokes of the head. The individuals tested (<72 g) exerted forces on the soil of up to 24 N. These forces were possible because the fibres of the longissimus dorsi, the main muscle associated with burrowing, are highly pennated, thus increasing effective muscle cross-sectional area. The muscle is characterized by a metabolic transition along its length: proximal, medial and distal fibres are fast contracting and moderately oxidative, but fibres closer to the head are richer in citrate synthase and more aerobic in nature. Distal fibres, then, might be active mainly at the final step of the compression stroke, which requires more power. For animals greater than a given diameter, the work required to compress soil increases exponentially with body diameter. Leposternon microcephalum, and probably some other highly specialized amphisbaenids, are most likely constrained to small diameters and can increase muscle mass and effective muscle cross-sectional area by increasing body length, not body diameter.

Locomotor performance of closely related Tropidurus species: relationships with physiological parameters and ecological divergence

Tropidurid lizards have colonized a variety of Brazilian open environments without remarkable morphological variation, despite ecological and structural differences among habitats used. This study focuses on two Tropidurus sister-species that, despite systematic proximity and similar morphology, exhibit great ecological divergence and a third ecologically generalist congeneric species providing an outgroup comparison. We quantified jumping capacity and sprint speed of each species on sand and rock to test whether ecological divergence was also accompanied by differences in locomotor performance. Relevant physiological traits possibly associated with locomotor performance metabolic scopes and fiber type composition, power output and activity of the enzymes citrate synthase, pyruvate kinase and lactate dehydrogenase of the iliofibularis muscle - were also compared among the three Tropidurus species. We found that the two sister-species exhibited remarkable differences in jumping performance, while Tropidurus oreadicus, the more distantly related species, exhibited intermediate values. Tropidurus psamonastes, a species endemic to sand dunes, exhibited high absolute sprint speeds on sand, jumped rarely and possessed a high proportion of glycolytic fibers and low activity of citrate synthase. The sister-species Tropidurus itambere, endemic to rocky outcrops, performed a large number of jumps and achieved lower absolute sprint speed than T. psamonastes. This study provides evidence of rapid divergence of locomotor parameters between sister-species that use different substrates, which is only partially explained by variation in physiological parameters of the iliofibularis muscle.

Autonomic control of heart rate during forced activity and digestion in the snake Boa constrictor

Reptiles, particularly snakes, exhibit large and quantitatively similar increments in metabolic rate during muscular exercise and following a meal, when they are apparently inactive. The cardiovascular responses are similar during these two states, but the underlying autonomic control of the heart remains unknown. We describe both adrenergic and cholinergic tonus on the heart during rest, during enforced activity and during digestion (24-36h after ingestion of 30% of their body mass) in the snake Boa constrictor. The snakes were equipped with an arterial catheter for measurements of blood pressure and heart rate, and autonomic tonus was determined following infusion of the beta -adrenergic antagonist propranolol (3mg kg(-1)) and the muscarinic cholinoceptor antagonist atropine (3 mg kg-1).The mean heart rate of fasting animals at rest was 26.4 +/- 1.4 min(-1), and this increased to 36.1 +/- 1.4 min(-1) (means +/- S.E.M.; N=8) following double autonomic block (atropine and propranolol). The calculated cholinergic and adrenergic tones were 60.1 +/- 0.3% and 19.8 +/- 2.2%, respectively. Heart rate increased to 61.4 +/- 1.5 min(-1) during enforced activity, and this response was significantly reduced by propranolol (maximum values of 35.8 +/-1.6 min(-1)), but unaffected by atropine. The cholinergic and adrenergic tones were 2.6 +/- 2.2 and 41.3 +/- 1.9 % during activity, respectively. Double autonomic block virtually abolished tachycardia associated with enforced activity (heart rate increased significantly from 36.1 +/- 1.4 to 37.6 +/- 1.3 min(-1)), indicating that non-adrenergic, non-cholinergic effectors are not involved in regulating heart rate during activity. Blood pressure also increased during activity.Digestion was accompanied by an increase in heart rate from 25.6 +/- 1.3 to 47.7 +/- 2.2 min(-1) (N=8). In these animals, heart rate decreased to 44.2 +/- 2.7 min-1 following propranolol infusion and increased to 53.9 +/- 1.8 min-1 after infusion of atropine, resulting in small cholinergic and adrenergic tones (6.0 +/- 3.5 and 11.1 +/- 1.1 %, respectively). The heart rate of digesting snakes was 47.0 +/- 1.0 min(-1) after double autonomic blockade, which is significantly higher than the value of 36.1 1.4 min-1 in double-blocked fasting animals at rest. Therefore, it appears that some other factor exerts a positive chronotropic effect during digestion, and we propose that this factor may be a circulating regulatory peptide, possibly liberated from the gastrointestinal system in response to the presence of food.

Ventilatory compensation of the alkaline tide during digestion in the snake Boa constrictor

The increased metabolic rate during digestion is associated with changes in arterial acid-base parameters that are caused by gastric acid secretion (the 'alkaline tide'). Net transfer of HCl to the stomach lumen causes an increase in plasma HCO3- levels, but arterial pH does not change because of a ventilatory compensation that counters the metabolic alkalosis. It seems, therefore, that ventilation is controlled to preserve pH and not P-CO2, during the postprandial period. To investigate this possibility, we determined arterial acid-base parameters and the metabolic response to digestion in the snake Boa constrictor, where gastric acid secretion was inhibited pharmacologically by oral administration of omeprazole. The increase in oxygen consumption of omeprazole-treated snakes after ingestion of 30% of their own body mass was quantitatively similar to the response in untreated snakes, although the peak of the metabolic response occurred later (36 h versus 24 h). Untreated control animals exhibited a large increase in arterial plasma HCO3- concentration of approximately 12 mmol 1(-1), but arterial pH only increased by 0.12 pH units because of a simultaneous increase in arterial P-CO2 by about 10 mmHg. Omeprazole virtually abolished the changes in arterial pH and plasma HCO3- concentration during digestion and there was no increase in arterial P-CO2. The increased arterial P-CO2 during digestion is not caused, therefore, by the increased metabolism during digestion or a lower ventilatory responsiveness to ventilatory stimuli during a presumably relaxed state in digestion. Furthermore, the constant arterial P-CO2, in the absence of an alkaline tide, of omeprazole-treated snakes strongly suggests that pH rather than P-CO2 normally affects chemoreceptor activity and ventilatory drive.

Seasonal metabolic depression, substrate utilisation and changes in scaling patterns during the first year cycle of tegu lizards (Tupinambis merianae)

The tegus increase in body mass after hatching until early autumn, when the energy intake becomes gradually reduced. Resting rates of oxygen consumption in winter drop to 20% of the values in the active season (Vo(2)=0.0636 ml g(-1) h(-1)) and are nearly temperature insensitive over the range of 17-25degreesC (Q(10)=1.55). During dormancy, plasma glucose levels are 60% lower than those in active animals, while total protein, total lipids and beta-hydroxybutyrate are elevated by 24%, 43% and 113%, respectively. In addition, a significant depletion of liver carbohydrate (50%) and of fat deposited in the visceral fat bodies (24%) and in the tail (25%) and a slight loss of skeletal muscle protein (14%) were measured halfway through the inactive period. Otherwise, glycogen content is increased 4-fold in the brain and 2.3-fold in the heart of dormant lizards, declining by the onset of arousal. During early arousal, the young tegus are still anorexic, although Vo(2) is significantly greater than winter rates. The fat deposits analysed are further reduced (62% and 45%, respectively) and there is a large decrease in tail muscle protein (50%) together with a significant increase in glycogen (2-3-fold) and an increase in plasma glucose (40%), which suggests a role for gluconeogenesis as a supplementary energy source in arousing animals. No change is detectable in citrate synthase activity, but beta-hydroxyacyl CoA dehydrogenase activities are strongly affected by season, reaching a Mold and 5-fold increase in the liver tissue of winter and arousing animals, respectively, and becoming reduced by half in skeletal muscle and heart of winter animals compared with late fall or spring active individuals. From hatching to late autumn, the increase of the fat body mass relatively to body mass is disproportionate (b=1.44), and the mass exponent changes significantly to close to 1.0 during the fasting period. The concomitant shift in the Vo(2) mass exponent in early autumn (b=0.75) to values significantly greater than 1.0 in late autumn and during winter dormancy indicates an allometric effect on the degree of metabolic depression related to the size of the fat stores and suggests greater energy conservation in the smaller young.

Role of the post-hepatic septum on breathing during locomotion in Tupinambis merianae (Reptilia : Teiidae)

Tupinambis merianae increased minute ventilation by increasing both tidal volume and breathing frequency during sustained locomotion at 0.17 m s(-1). Animals in which the post-hepatic septum (PHS) had been surgically removed were not able to increase tidal volume during locomotion. Tegus without PHS compensated, in part, by increasing breathing frequency above the levels observed for tegus with intact PHS, but minute ventilation remained less than in the control animals. The rate of oxygen consumption and the air convection requirement, however, were not significantly different between animals with and without PHS, nor at the tested speeds was endurance affected by the removal of the PHS. These data suggest that the PHS facilitates ventilation by acting as a mechanical barrier, preventing the viscera from moving cranially during physical exertion.

The contribution of air breathing to aerobic scope and exercise performance in the banded knifefish Gymnotus carapo L.

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The unequal influences of the left and right vagi on the control of the heart and pulmonary artery in the rattlesnake, Crotalus durissus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Physiological importance of the coronary arterial blood supply to the rattlesnake heart

The reptilian heart consists of a thick inner spongy myocardium that derives its oxygen and nutrient supply directly from the blood within the ventricular cavity, which is surrounded by a thin outer compact layer supplied by coronary arteries. The functional importance of these coronary arteries remains unknown. In the present study we investigate the effects of permanent coronary artery occlusion in the South American rattlesnake (Crotalus durissus) on the ability to maintain heart rate and blood pressure at rest and during short term activity. We used colored silicone rubber (Microfil) to identify the coronary artery distribution and interarterial anastomoses. The coronary circulation was occluded and the snakes were then kept for 4 days at 30 degrees C. Microfil injections verified that virtually all coronary arteries had successfully been occluded, but also made visible an extensive coronary supply to the outer compact layer in untreated snakes. Electrocardiogram (ECG), blood pressure (P(sys)) and heart rate (f(H)) were measured at rest and during enforced activity at day 1 and 4. Four days after occlusion of the coronary circulation, the snakes could still maintain a P(sys) and f(H) of 5.2 +/- 0.2 kPa and 58.2 +/- 2.2 beats min(-1), respectively, during activity and the ECG was not affected. This was not different from sham-operated snakes. Thus, while the outer compact layer of the rattlesnake heart clearly has an extensive coronary supply, rattlesnakes sustain a high blood pressure and heart rate during activity without coronary artery blood supply.

Use of genetic algorithms and solvation potential to study peptides structure

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains and implicit solvation potential are used to optimize the tertiary structure of peptides. We starting from the known PDB structure of its backbone which is kept fixed while the side chains allowed adopting the conformations present in the rotamer library. It was used rotamer library independent of backbone and a implicit solvation potential. The structure of Mastoporan-X was predicted using several force fields with a growing complexity; we started it with a field where the only present interaction was Lennard-Jones. We added the Coulombian term and we considered the solvation effects through a term proportional to the solvent accessible area. This paper present good and interesting results obtained using the potential with solvation term and rotamer library. Hence, the algorithm (called YODA) presented here can be a good tool to the prediction problem. (c) 2007 Elsevier B.V. All rights reserved.