Is apolipoprotein D a mammalian bilin-binding protein?

Human apolipoprotein D (APO-D) is a serum glycoprotein that has no sequence similarity with other apolipoproteins but rather belongs to the alpha 2-microglobulin superfamily whose other members transport small hydrophobic ligands in a wide variety of biological contexts. To investigate the ligand specificity of APO-D, we analyzed its relationship with the other members of this superfamily and constructed a detailed molecular model using the atomic coordinates of its most closely related homolog--insecticyanin from the tobacco hornworm, Manduca sexta. We studied the geometry of the binding pocket of APO-D and the topology of characteristic patches of both hydrophobic and polar side chains that also occur in crystal structures of insecticyanin and bilin-binding protein from the butterfly Pieris brassicae. From the data obtained we hypothesize that heme-related compounds may be more favorable ligands for APO-D than either cholesterol or cholesteryl ester. Preliminary experiments showed that purified human APO-D binds bilirubin in an approximately one-to-one molar ratio. These results suggest a new biological role for APO-D that is more congruent with its tissue distribution and evolutionary history.     

Is the PTPase-vanadate complex a true transition state analogue?

Vanadate can often bind to phosphoryl transfer enzymes to form a trigonal-bipyramidal structure at the active site. The enzyme-vanadate dissociation constants in these enzymes are much lower than those for phosphate. Therefore, enzyme-bound vanadate moieties are often considered as transition state analogues. To test whether the enzyme-vanadate complex is a true transition state analogue beyond the simple geometry and binding affinity arguments and whether the bond orders of the VO bonds in the complex approach those of the PO bonds in the transition state, the binding properties of vanadate in the Yersinia protein-tyrosine phosphatase (PTPase) and its T410A, D356N, W354A, R409K, and D356A mutants have been studied by steady-state kinetic measurements and by difference Raman measurements. The results of the kinetic measurements show no correlation between K(I) and kcat or kcat/K(m) in these mutants. In addition, our analysis of the Raman data shows that the bond order change of the nonbridging V--O bonds in the vanadate complexes does not correlate with the kinetic parameters in a number of PTPase variants as predicted by the transition state binding paradigm. Furthermore, the ionization state of the bound vanadate moiety is not invariant across the PTPase variants studied, and the average bond order of the nonbridging V--O bonds decreased by 0.06-0.07 valence unit in the wild type and all of the mutant PTPases, either in dianionic or in monoanionic form. Thus the complex would resemble an associative transition state, contrary to the previously determined dissociative structure of the transition state. Therefore, it is concluded that vanadate is not a true transition state analogue for the PTPase reactions.     

Is the mammalian cell plasma membrane a barrier to oxygen transport?

Oxygen transport in the Chinese hamster ovary (CHO) plasma membrane has been studied by observing the collision of molecular oxygen with nitroxide radical spin labels placed in the lipid bilayer portion of the membrane at various distances from the membrane surface using the long-pulse saturation-recovery electron spin resonance (ESR) technique. The collision rate was estimated for 5-, 12-, and 16-doxylstearic acids from spin-lattice relaxation times (T1) measured in the presence and absence of molecular oxygen. Profiles of the local oxygen transport parameters across the membrane were obtained showing that the oxygen diffusion-concentration product is lower than in water for all locations at 37 degrees C. From oxygen transport parameter profiles, the membrane oxygen permeability coefficients were estimated according to the procedure developed earlier by Subczynski et al. (Subczynski, W. K., J. S. Hyde, and A. Kusumi. 1989. Proceedings of the National Academy of Sciences, USA. 86:4474-4478). At 37 degrees C, the oxygen permeability coefficient for the plasma membrane was found to be 42 cm/s, about two times lower than for a water layer of the same thickness as the membrane. The oxygen concentration difference across the CHO plasma membrane at physiological conditions is in the nanomolar range. It is concluded that oxygen permeation across the cell plasma membrane cannot be a rate-limiting step for cellular respiration. Correlations of the form PM = cKs between membrane permeabilities PM of small nonelectrolyte solutes of mol wt less than 50, including oxygen, and their partition coefficients K into hexadecane and olive oil are reported. Hexadecane: c = 26 cm/s, s = 0.95; olive oil: c = 23 cm/s, s = 1.56. These values of c and s differ from those reported in the literature for solutes of 50 less than mol wt less than 300 (Walter, A., and J. Gutknecht. 1986. Journal of Membrane Biology. 90:207-217). It is concluded that oxygen permeability through membranes can be reliably predicted from measurement of partition coefficients.     

Is there a mucosal immune system associated with the mammalian oviduct?

The oviduct is a key component of the reproductive system where essential states such as spermatozoa capacitation, fertilization and early embryo development take place. Recently, an additional role for the entire female reproductive tract has emerged with important implications for our understanding and management of reproductive health, namely, its role in mounting local immune responses against microbial pathogens. Most of the evidence about mucosal immune responses in the female reproductive tract is related to the vagina, with less information available for the uterus. The less known segment in this regard is the oviduct, which prompted us to review and summarize the current state of knowledge on the immune system at the level of the mammalian oviduct. A comprehensive search was conducted in Medline and--for the last two years--also in Current Contents. Result demonstrate that the mammalian oviduct is endowed with many of the elements that characterize a mucosal immune system. However, there are gaps in our knowledge that, in addition to important interspecies differences, make it essential to explore further some fundamental questions regarding this system.     

Is canavanine a natural component of mammalian metabolism?

A group of non-protein amino acids of higher plants, namely l-canavanine, l-canaline, 0-ureido-l-homoserine, and l-canavaninosuccinic acid, have been implicated in mammalian intermediary metabolism. The clinical observations and biochemical basis for this hypothesis as well as conflicting experimental evidence are presented. A possible explanation for the apparent role of these non-protein amino acids in mammalian metabolism is offered.     

Is phospholipid a required cofactor for the activity of mammalian signal peptidase?

To determine whether phospholipid is required for the activity of mammalian signal peptidase, the enzyme was partially purified from porcine pancreas and then extensively freed of phospholipid by SP-Sephadex C-50 chromatography. The delipidated enzyme showed signal peptidase activity, with a low concentration of detergent. Phospholipid was found to release the enzyme from the inhibition due to excess detergent.     

The visual input stage of the mammalian circadian pacemaking system: I. Is there a clock in the mammalian eye?

Threads of evidence from recent experimentation in retinal morphology, neurochemistry, electrophysiology, and visual perception point toward rhythmic ocular processes that may be integral components of circadian entrainment in mammals. Components of retinal cell biology (rod outer-segment disk shedding, inner-segment degradation, melatonin and dopamine synthesis, electrophysiological responses) show self-sustaining circadian oscillations whose phase can be controlled by light-dark cycles. A complete phase response curve in visual sensitivity can be generated from light-pulse-induced phase shifting. Following lesions of the suprachiasmatic nuclei, circadian rhythms of visual detectability and rod outer-segment disk shedding persist, even though behavioral activity becomes arrhythmic. We discuss the converging evidence for an ocular circadian timing system in terms of interactions between rhythmic retinal processes and the central suprachiasmatic pacemaker, and propose that retinal phase shifts to light provide a critical input signal.     

Is the hemidesmosome a half desmosome? An immunological comparison of mammalian desmosomes and hemidesmosomes

Although the mammalian epidermal basal cell hemidesmosome bears some superficial resemblance to one half of a desmosome at the ultrastructural level, examination of the structure of the electron-dense submembranous plaques of the hemidesmosome and desmosome reveals that they differ with respect to their overall morphology and dimensions. Based on these findings, we wondered whether components of the desmosome are present in the hemidesmosome. In order to determine this we prepared a number of stratified squamous epithelial tissues for indirect immunofluorescence using antibody preparations directed against known desmosome components including desmoplakin and certain glycoproteins. These antibody preparations do not show reaction with hemidesmosomes by indirect immunofluorescence criteria. We have also utilized bullous pemphigoid (BP) autoantibodies that have been shown to recognize hemidesmosomes in mammalian skin cells [Mutasim et al., J. Invest. Derm., 84:47-53, 1985]. Double label indirect immunofluorescence observations of neonatal mouse skin prepared using desmoplakin antibodies and BP autoantibodies reveal that hemidesmosomes that are stained by the BP autoantibodies are not recognized by the desmoplakin antibodies. We confirmed these findings at the ultrastructural level by indirect immunogold localization of desmoplakin antibodies and BP autoantibodies. Therefore, the hemidesmosome does not appear to be one half of a desmosome and may possess a very different molecular organization relative to the desmosome. We raise the possibility that the variability between the hemidesmosome and desmosome that we detect at the morphological and immunological level may reflect the functional differences of these two types of junctions.     

Is histoaspartic protease a serine protease with a pepsin‐like fold?

The primary structure of the so-called histoaspartic protease from Plasmodium falciparum has a very high percentage of identity and homology with the pepsin-like enzyme plasmepsin II. A homology modeling approach was used to calculate the three-dimensional structure of the enzyme. Molecular dynamics (MD) simulations were applied to find those structural properties of the histoaspartic protease that had a tendency to remain stable during all runs. The results have shown that hydrogen-bonded residues Ser37-His34-Asp214 are arranged without any strain, in a manner that resembles the active site of a serine protease, while Ser38 and Asn39 take up positions appropriate to formation of an oxyanion hole. Although there are several important differences between the enzyme and plasmepsin II, all of the structural features associated with a typical pepsin-like aspartic protease are present in the final model of the histoaspartic protease. A possibility that this enzyme may function as a serine protease is discussed.     

Is the Pope a Catholic?

The whole-part relationship is generally considered transitive, but there are some apparent exceptions. Componential sortals create some apparent problems. Homo sapiens, the Pope, and his heart are all individuals. A human being, such as the Pope, is an organism-level component of Homo sapiens. The Pope’s heart is an organ-level component of both Homo sapiens and the Pope. Although the Pope is a part, and not an instance, of the Roman Catholic Church, it seems odd to say that his heart is a part of that church. This is largely because the Pope’s heart does not have a place in the ecclesiastical government. However, it does contribute to the functioning of the organization. One popular alternative to the view that Homo sapiens is an individual is the notion that it is a natural kind. This has been done by redefining ‘natural kind’ in such a manner that not just the Roman Catholic Church, but the Pope and every other human being is a natural kind as well.     

Is there a weak H‐bond → LBHB transition on tetrahedral complex formation in serine proteases?

The transformation of a weak hydrogen bond in the free enzyme into a low-barrier hydrogen bond (LBHB) in the tetrahedral intermediate has been suggested as an important factor facilitating catalysis in serine proteases. In this work, we examine the structure of the H-bond in the Asp102-His57 diad of serine proteases in the free enzyme and in a covalent tetrahedral complex (TC) with a trifluoromethylketone inhibitor. We apply ab initio quantum mechanical calculations to models consisting of a large molecular fragment of the enzyme active site, and the combined effect of the rest of the protein body and the solvation by surrounding bulk water was simulated by a self-consistent reaction field method in our novel QM/SCRF(VS) approach. Potential profiles of adiabatic proton transfer in the Asp102-His57 diad in these model systems were calculated. We conclude that the hydrogen bond in both the free enzyme and in the enzyme-inhibitor TC is a strong ionic asymmetric one-well hydrogen bond, in contrast to a previous suggestion that it is a weak H-bond in the former and a double-well LBHB in the latter.     

Is the Testis a Chemo-Privileged Site? Is There a Blood-Testis Barrier?

The incidence of testicular cancer, primarily seminoma, has been increasing in many countries, including the United States. The testis is often the site of residual cancer after adequate treatment with systemic chemotherapy. The blood-testis barrier is commonly cited as the explanation for residual tumor within the gonad after chemotherapy and as the indication for delayed orchiectomy. Conversely, complete eradication of viable tumor from the primary site is common and argues against the testis as a "tumor sanctuary." Residual tumor is also demonstrated within metastatic foci, and the disparity between the histopathologic response of the primary tumor and metastatic sites may be best explained by tumor heterogeneity and multiple tumor clones. Regardless of the scientific and academic arguments, delayed radical orchiectomy remains an important part of treatment for patients undergoing primary chemotherapy.     

Is there an acceleration of the CpG transition rate during the mammalian radiation?

MOTIVATION: In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates. RESULTS: When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.     

Is astrocyte laminin involved in axon guidance in the mammalian CNS?

This paper provides evidence for the expression of laminin on glia in correlation with axon elongation and nerve pathway formation during embryonic development of the mouse optic nerve and other parts of the central nervous system (CNS). We show that punctate deposits of laminin on immature glial cells precede the entrance of the first optic axons into the nerve, and remain in close association with growing axons. Furthermore, we show that in one particular region of the optic pathway that the retinal ganglion cell axons avoid in normal animals (i.e., the pigmented area of the distal nerve) the punctate laminin matrix is missing. As the optic nerve matures punctate laminin deposits disappear, and laminin is reduced in the astroglial cytoplasm. The close correlation of the punctate form of laminin with early axonal growth is true not only in the optic nerve but also in some other parts of the CNS. We demonstrate such punctate laminin deposits in a model of astrocyte-induced regeneration of the corpus callosum in acallosal mice (G. Smith, R. Miller, and J. Silver, 1986, J. Comp. Neurol. 251, 23-43), and in glia associated with several normal developing axon trajectories, such as the corpus callosum, fornix, and pathways in the embryonic hindbrain. In all of these regions punctate laminin deposits are found on astroglia that are associated with early growing axons. Our results indicate that the punctate form of laminin, produced by astrocytes, may be an important factor involved in axon elongation and nerve pathway formation in the mammalian CNS.     

Is the membrane attack complex of complement an enzyme?

Summary Recent studies on the functional activities of the membrane attack complex of complement, C5b-9, are reviewed. A new speculative hypothesis has been advanced to account for the ability of complement to mediate lysis of various targets. This hypothesis has three major elements: 1) that the membrane attack complex is an enzyme; 2) that the substrate for this putative enzyme is a membrane constituent; 3) that the substrate specificity of the putative enzyme is dependent on the species source of individual complement components within the C5b-9 complex.Abbreviations E = sheep red cells - A = rabbit IgM anti-Forssman antibody - Hu or hu = human - GP or gp = guinea pig     

Structure of the mammalian ribosomal pre-termination complex associated with eRF1?eRF3?GDPNP

Eukaryotic translation termination results from the complex functional interplay between two release factors, eRF1 and eRF3, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, we present a cryo-electron microscopy structure of pre-termination complexes associated with eRF1•eRF3•GDPNP at 9.7 -Å resolution, which corresponds to the initial pre-GTP hydrolysis stage of factor attachment and stop codon recognition. It reveals the ribosomal positions of eRFs and provides insights into the mechanisms of stop codon recognition and triggering of eRF3’s GTPase activity.     

Revisiting the dietary niche: When is a mammalian herbivore a specialist?

Understanding dietary specialization in herbivores has theoretical and practical implications in ecology, yet defining niche breadth consistently has been problematic. To increase clarity and communication among ecologists and among disciplines (i.e., chemists, pharmacologists), we propose a specialization key for mammalian herbivores that assigns "obligatory" and "facultative" modifiers to the terms "specialist" and "generalist". These modifiers are assigned based on (1) relative breadth of the animal's realized niche and diet (what it eats), (2) relative breadth of the fundamental niche and available diet (what it could eat), (3) the extent of chemical or physical characteristics, termed "difficulty", that make food items either low in value or unpalatable to most herbivores, and (4) relevant temporal and spatial scales at which diets and niche breadth were measured. Obligatory specialists always have a narrow realized niche consisting of difficult food items, and morphological adaptations and/or the loss of redundant behavioral flexibility that effectively limit their fundamental niches, precluding them from expanding their diet under changed environmental conditions. Facultative specialists have a consistently narrow realized niche for difficult foods during at least one spatial or temporal scale, but have a broad enough fundamental niche to allow them to expand their diet to include less difficult foods when environmental conditions allow. Facultative generalists have the broadest fundamental niche, allowing them to consume a wide variety of foods. However, they may occasionally demonstrate a narrow realized niche, focused on less difficult plants than is the case with specialists. Finally, the obligatory generalists always have a wide realized niche because of a relatively narrow fundamental niche, precluding them from eating much of any difficult plant. We summarize hypothesized characteristics of mammalian herbivores in each of the four categories of specialization. We demonstrate the need for further work on defining the realized and fundamental niches, comparing among herbivores across categories conducted under similar conditions, and understanding the nature of trade-offs required for specialization and generalization for both community and phylogenetically based analyses.     

Is the dynein motor a winch?

Dyneins are the largest and most complex of the three classes of linear motor proteins in eukaryotic cells. The mass of the dynein motor domain is about ten times that of the other microtubule motor, kinesin. Dynein's homology with the AAA+ superfamily of mechanoenzymes distinguishes it from both kinesin and myosin, which share a common fold and ancestry as members of the G-protein superfamily. In contrast to the other motor proteins, little is known about the mechanism of dynein; its three-dimensional structure is unknown even at low resolution. Recent two-dimensional images from electron microscopy have revealed new details of its structure and how this changes to produce movement. These and the recently solved crystal structure of another AAA+ protein, ClpB, offer tantalising hints about dynein's mechanism, suggesting it may act like a molecular winch.