Biasing a Monte Carlo chain growth method with Ramachandran's plot: Application to twenty-L-alanine

In this paper, we explore the possibility of using experimental observations in the Monte Carlo chain growth method that we have previously developed. In this method, the macromolecule (peptide, protein, nucleic acid, etc.) is grown atom-by-atom (or residue-by-residue, etc.) and partial chains are replicated according to their Boltzmann weights. Once the molecule completed, we are left with a Boltzmann-distributed ensemble of configurations. For long molecules, an efficient sampling of the (extremely large) phase space is difficult for obvious reasons (existence of many local minima, limited computer memory, etc.). In the case in which one is mainly interested in the low energy conformations, we have incorporated in the growth scheme experimental observations taken from the Protein Data Banks. More precisely, we have considered the case of twenty-L -alanine and we have used the (experimental) Ramachandran's plot for this residue. The biased growth procedure goes as follows: (a) each time one adds along the main backbone chain, either a carbon atom belonging to a carbonyl group, or a nitrogen atom, its dihedral angle (?) or (ψ) is drawn with a probability law that reflects the experimental Ramachandran (?,ψ) plot; (b) the bias introduced in this way is canceled through an extra term in the energy (replication energy = true energy + bias energy); (c) the configurations, generated at T = 1000 K, are then energy minimized. We have worked with an all-atom CHARMM force field, and Ramachandran's plot for the alanine was modeled through three angular zones (α-helix, β-sheet, coil). In our calculations, the probabilities of the α (p_α) and β (p_β) regions have been varied in large proportions (p_α between 0.64 and 0.19, the “experimental” value being 0.59). The results, based on 35 “unbiased” and 25 “biased” (or “guided”) distinct minimized configurations clearly demonstrate the efficiency of the method. The low energy configurations, for all tested values of p_α, have a total (or almost total) a helix content. The unbiased configurations have much higher energies (in general, even higher than the left-handed helix). Note that the method is not “α helix in-α helix out,” since working at T = 300 K with the experimental (p_α = 0.59) value yields configurations partially frozen in a C alanine dipeptide type of local minima. © 1993 John Wiley & Sons, Inc.     

Test of the extended two-state model for the kinetic intermediates observed in the folding transition of ribonuclease A

A test has been made of the proposal that: (a) the extended two-state model describes the kinetic intermediates seen in the folding transition of RNAase A, i.e. that the only species present in folding experiments are the native protein and multiple forms of the completely unfolded protein; and (b) that the interconversion between the two known unfolded forms of RNAase A (the U₁

U₂ reaction) is described solely by the cis-trans isomerization of the proline residues. The test is to measure the rate of the U₁

U₂ reaction in a wide range of refolding conditions and to compare these data with the kinetic properties of proline isomerization.The main results are as follows. (1) The activation enthalpy of the U₁

U₂ reaction in refolding conditions (pH 6, 20 ° to 40 °C) is less than 5 kcal/mol. This is much too small to be explained as proline isomerization. (2) Both the rate and the activation enthalpy change sharply at guanidine hydrochloride concentrations below 2 m. There appear to be two pathways for the U₁

U₂ reaction in refolding conditions, and the slower pathway is favored by adding guanidine hydrochloride. (3) The rate and activation enthalpy for proline isomerization in l-alanyl-l-proline are unaffected by 2 m-guanidine hydrochloride.The results show that the proline isomerization hypothesis and the extended two-state model cannot both be correct for RNAase A. They suggest that partial folding occurs rapidly in refolding conditions and that the extended two-state model is invalid. They leave open the question of whether or not proline isomerization is the rate-limiting step in the U₁

U₂ reaction.Another possible source of slow configurational reactions in the unfolded state is mentioned. The three major, overlapping, disulfide-bonded loops of RNAase A can exist in two isomeric configurations. Interconversion of these isomers requires pulling one loop, or one end of the polypeptide chain, through a second loop and this is likely to be a slow process.In some conditions, heat-unfolded but not guanidine-unfolded RNAase A shows a second slow-refolding process. It may result from aggregates of the heatunfolded protein which are formed and broken up slowly. Conditions are given for eliminating this reaction.     

Vitamin D-dependent calcium-binding protein. Changes during gestation, prenatal and postnatal development in rats

During the perinatal period, calcium metabolism is stressed. As intestinal Ca-binding protein is considered as a molecular expression of the hormonal effect of 1,25-dihydroxycholecalciferol (1,25(OH)2D3), Ca-binding protin measurements may document the vitamin D roles during this period. We describe the variations of Ca-binding protein concentrations in the rat during the last 5 days of gestation, in the maternal duodenum, placentas, fetal membranes and fetal intestines. We also report intestinal Ca-binding protein changes from birth until weaning. The evolution of the maternal intestinal Ca-binding protein, which increases on day 19.5 of gestation, is consistent with that of calcium intestinal absorption and may be explained by increased 1,25(OH)2D3 production. Placental Ca-binding protein rises from day 17.5 until the end of gestation, and may be related to the profile of calcium transfer from mother to fetuses. It is noteworthy that the placental Ca-binding protein is predominantly found in the fetal part of the organ where materno-fetal exchanges occur. The yolk sac synthesizes substantial amounts of Ca-binding protein. In the fetal membranes, Ca-binding protein plateaus from day 17.5 until day 20.5 and decreases on day 21.5. The Ca-binding protein presence in the fetal placenta and in the yolk sac may suggest that these tissues are also targets for vitamin D. In the fetus the intestinal Ca-binding protein s is detected as early as day 17.5 of gestation and increases markedly during the last day of gestation. From birth and during the first 3 weeks of postnatal life, the intestinal Ca-binding protein concentration does not change. It undergoes a sharp rise just at the time of weaning. We have also shown that the specific distribution of Ca-binding protein along the intestine is acquired during intrauterine life and does not change with sucking or weaning. The two main changes of intestinal Ca-binding protein, observed just before birth and at weaning, may reflect the intestinal maturation and/or variations in vitamin D metabolism.     

Changes of polymerization and conformation of hemoglobin S induced by thiol reagents

Thiol reagents, covalently bound to cysteine beta 93, either inhibit or facilitate the polymerization process of hemoglobin S. The progelling effect of parahydroxymercurybenzoate or 2,2'-dithiodipyridine contrasted with the increased oxygen affinity and the destabilization of the T state of Hb shown by functional and NMR studies. Thiol reagents increased the oxygen affinity of Hb from 30 to 1000%. Such variability was also observed in the reduction (up to 50%) of the alkaline Bohr effect. We show that the antigelling or progelling activity of thiol reagents does not depend solely on the concentration of molecules present in the deoxy T state but that specific effects of the reagent affects molecular interactions of the hemoglobin S polymerization process.     

Ageing of ungulate pellets in semi-arid landscapes: how the shade of colour can refine pellet-group counts

Pellet-group counts can be useful in monitoring ungulate population trends, particularly in elusive species. In semi-arid areas, ambient conditions conserve the pellets during the dry season. Thus, dating of accumulated pellet groups should be helpful in approximating the numbers of ungulates present during any chosen part of the dry season. The aims of this study were to confirm that the decay rate of pellet groups was low during the dry season, to identify the major causes of decay and to test the usefulness of criteria, easily measurable in the field, in dating pellets. Every month during the dry season pellet groups of five African savanna ungulates were collected fresh and deposited on bare ground at an experimental site. The levels of hardness, cracking, scattering, attack by insects and shade of colour of the pellets were monitored until the rainy season started. As expected, only a few pellet groups decayed completely during the dry season. The pellets’ shade of colour was the best criterion to date them. We discuss pellet colour as an original tool for monitoring the trends in ungulate use of target areas in semi-arid environments.     

The social environment influences the behavioural responses of beef cattle to handling

In cattle, a gregarious species, the social group influences individual stress responses to fear-eliciting situations. As handling can be stressful for farm animals, it can be hypothesised that social partners modify individual responses to handling. The present experiment investigated the effect of the presence or absence of social partners on behavioural reactions of beef calves in a handling test. At the age of 10 months, 38 calves from two breeds (Salers and Limousine) were individually subjected to the docility test, once while in visual contact with four familiar peers, and once in the absence of peers, following a crossover design. The docility test procedure included physical separation from peers (30 s; period 1), exposition to a stationary human (30 s; period 2), and handling by human (30 s-2.5 min, according to the success in handling; period 3). In absence of human (period 1), calves in visual contact with their peers spent more time motionless than when peers were totally absent (P<0.001). The social environment also influenced the duration of handling (period 3); the human required more time to successfully handle calves when peers were present (P<0.05). In conclusion, the presence of peers affects individual calves' reactions to the docility test.