Homology modeling by the ICM method

Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the noncon-served portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed. © 1995 Wiley-Liss, Inc.     

Division synchrony and the dynamics of microbial populations: A size-specific model

A discrete, environmentally coupled, size-specific model of microbial population dynamics in continuous culture is presented. It is mathematically simpler than other models based on similar assumptions and lends itself to numerical and analytic solutions. It displays several phenomena which have been reported in the experimental literature but which are not well understood; specifically, a loose relationship between biomass and numbers (i.e., a time lag between mass growth and cell division) and a critical damping of biomass while numbers continue to oscillate. In addition, the model provides several new predictions: The stable biomass distribution is independent of the environmental factors considered in the model and uniformly distributes the biomass among the size classes. The rate of approach to stability and the frequency of waves through the size distributions are a function of the flow rate and the variance in rate of growth and size at division. The model should provide a useful basis for studying the effects of size specificity on the dynamics of microbial populations cultured in chemostats.     

Removal of insect basal laminae using elastase

We have used the enzyme elastase to remove the basal lamina of epithelia from two insects: the upper Malpighian tubules of Rhodnius prolixus and imaginai discs of Drosophila melanogaster. Removal of the basal lamina was confirmed using scanning and transmission electron microscopy. Use of the technique on the Malphighian tubules of Rhodnius reveals for the first time the three-dimensional organization of the circumferential folds of the basal plasma membrane. Elastase is much more effective in removing the basal lamina than are the enzymes hyaluronidase, collagenase, and chymotrypsin, either alone or in combination. Following elastase treatment, cells of the Malpighian tubules dissociate with only mild mechanical agitation into single, viable cells. Treatment with elastase removes the basal laminae of imaginai discs of Drosophila and accelerates evagination as has been previously described for trypsin. To obtain single cell preparations from elastase-treated imaginai discs, mechanical stirring in Ringer low in Ca²⁺ was required. In addition to its usefulness in cell isolation, elastase treatment allows examination of the effect of removal of basal laminae on the physiology and development of insect epithelia.     

A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular1H−1H proximities in solution

DISGEO is a new implementation of a distance geometry algorithm which has been specialized for the calculation of macromolecular conformation from distance measurements obtained by two-dimensional nuclear Overhauser enhancement spectroscopy. The improvements include (1) a decomposition of the complete embedding process into two successive, more tractable calculations by the use of “substructures”, (2) a compact data structure for storing incomplete distance information on a structure, (3) a more efficient shortest-path algorithm for computing the triangle inequality limits on all distances from this information, (4) a new algorithm for selecting random metric spaces from within these limits, (5) the use of chirality constraints to obtain good covalent geometry without the use ofad hoc weights or excessive optimization. The utility of the resultant program with nuclear magnetic resonance data is demonstrated by embedding complete spatial structures for the protein basic pancreatic trypsin inhibitor vs all 508 intramolecular, interresidue proton-proton contacts shorter than 4.0 Å that were present in its crystal structure. The crystal structure could be reproduced from this data set to within 1.3 Å minimum root mean square coordinate difference between the backbone atoms. We conclude that the information potentially available from nuclear magnetic resonance experiments in solution is sufficient to define the spatial structure of small proteins.     

The response of the atrium to direct mechanical wounding in the adult heart of the newt,Notophthalmus viridescens

Summary Wound repair and proliferation were examined in the injured newt atrium with light- and electron-microscopic techniques including autoradiography. Hearts were injured by removing a piece approximately 0.5 mm² of the atrial wall. The five-day wound was an endothelial and mesothelial-lined blood clot bordered by a 150-m necrotic zone. Repair progressed from the periphery inward with areas of macrophage activity replaced by fibroblasts and connective tissue. The wound at 25 days consisted of a scar with few myocytes. There was no difference in the proliferative behavior between the right and left atria. Proliferative cells were localized to a 500-m reactive zone surrounding the wound. The maximum mesothelial cell thymidine-labeling index of 20.5% and mitotic index of 1.4% were seen 5 days after injury. The peak connective tissue cell thymidine-labeling index of 10.2% and mitotic index of 0.4% were seen 10 days after wounding. The peak thymidine-labeling index of 9.8% for myocardial cells was recorded 10 days after injury with a mitotic index of 0.2%. Proliferation returned to control levels by 25 days post-injury. Electron microscopy demonstrated that myocytes engaged in DNA synthesis were indistinguishable from control myocytes. Z-band material was not observed in mitotic myocytes, but myofilaments and junctions were present.     

Reconstitution of a proton pump from gastric mucosa.

Purified vesicular fractions from hog gastric mucosa have been incorporated into phosphatidyl serine bilayers. In the presence of MgATP on one side and symmetrical Na2SO4 solutions, a short circuit current (SCC) away from that side is observed increasing exponentially with time, while the corresponding open circuit potential (OCP) is maintained constant for greater than 30 min. In K2SO4 solutions the SCC time course is essentially unchanged, but the OCP falls to almost zero after 15-20 min. In Na -- K gradient there is a similar SCC away from the K-side whose exponential rate is increased by ATP added to both sides. The time course of these events depends only on the time from the formation on the black film. These results are interpreted as showing: (1) There is an ATP-driven proton pump generating a constant potential EH in series with a time dependent conductance gHocekt. (2) There is a shunting K-conductance gKocek't. (3) In the presence of ATP k' greater than k. (4) This time dependence is due to thickness changes in the bilayer. A model relates these results to those obtained with the intact vesicles.     

Effects of freezing on the estimated amounts of Tamm--Horsfall glycoprotein in urine, as determined by radioimmunoassay.

Freeze-drying or freezing of salt-free solutions of human Tamm--Horsfall glycoprotein appeared to lead to changes in the structure of the latter, changes that increased its ability to bind with antibody raised, in rabbits, against it. This alteration in avidity of the glycoprotein was observed irrespective of whether antiserum was raised against freeze-dried or non-frozen antigen. The implications of this finding for the radioimmunoassay of the glycoprotein in urine samples were studied. Appropriate treatment for urine samples, before assay, was devised. The amount of Tamm--Horsfall glycoprotein excreted was shown to range from 30 to 138 mg in normal males and 43 to 126 mg in normal females per 24 h.     

Dark adaptation,sensitivity, and rhodopsin level in the eye of the lobster,Homarus

Summary Dark adaptation of living lobsters was measured by recording the ERG at several temperatures in the range 5–20 °C following adapting flashes that convert about 70% of the rhodopsin to metarhodopsin. Recovery of log threshold is rapid, and at 10–20° is nearly complete in 10 min. Only at 5 °C is dark adaptation significantly slowed. Comparison of dark adaptation with data on regeneration of pigment (Bruno et al., 1977) is consistent with the hypothesis that as rhodopsin concentration rises and falls, its only effect on sensitivity is to alter the probability of quantum catch. This interpretation is further bolstered by observations on winter lobsters that have a 70% deficiency of rhodopsin without the concomitant increase in metarhodopsin that accompanies light adaptation. No effect of metarhodopsin on sensitivity was detected. These experiments support the growing body of evidence indicating that the relationship between rhodopsin concentration and log threshold is fundamentally different in the rhabdomeric photoreceptors of invertebrates and the rods and cones of vertebrates.This work was supported by USPHS research grant EY 00222 to Yale University. S.N.B. was aided by NIH Postdoctoral Fellowship EY 52378, by funds made available through the Unidel Foundation, and by a grant from the University of Delaware Research Foundation.     

Studies on the H-Y antigen in rats

The H-Y antigen has been studied under a variety of experimental conditions in BN and Lewis rats. The results indicate that 1. graft size is crucially important in determining the fate of male skin isografts on females; 2. H-Y incompatible ear skin grafts survive significantly better than those of trunk origin; 3. prior exposure of females to male lymphoid cells greatly increases their capacity to reject male skin isografts; 4. neonatal castration has no influence on the expression of H-Y; 5. multiparity can induce unresponsiveness to H-Y; and 6. although BN females respond better than do Lewis females to H-Y, the antigen is stronger in Lewis males. These findings are compared with the results of similar experiments conducted with mice.Submitted in memory of Dr. Joy Palm, member of the Wistar Institute, who pioneered the genetic analysis of histocompatibility in rats.