Dynamic attractor for the Berendsen thermostat an the slow dynamics of biomacromolecules

It was shown that the nonlinear relaxation of a model system confined to the Berendsen's thermostat is determined by an attractor regime. The latter does not correspond generally to the true thermodynamic state of the system. Therefore, the use of the Berendsen's thermostat for molecular dynamics simulations, even in the case of large protein molecules at trajectory lengths of more than 10 ns, can lead to wrong conclusions. Our results agree with the concept of slow dynamics for macroscopic systems considered within the framework of the topological approach to stochastic dynamics.     

MSX2 expression in the apical ectoderm ridge is regulated by an MSX2 and Dlx5 binding site.

The apical ectodermal ridge (AER) is a specialized ectodermal region essential for limb outgrowth. Msx2 expression patterns in limb development strongly suggest an important role for Msx2 in the AER. Our previous studies identified a 348-bp fragment of the chicken Msx2 gene with AER enhancer activity. In this study, the functions of four potential homeodomain binding TAAT sites in this enhancer were studied using transgenic mice and in vitro protein-DNA interactions. Transgenic studies indicate that the four TAAT sites are not redundant and that only the B-TAAT site is critical for AER enhancer activity. The expression patterns of Msx2 and Dlx5 genes in the AER suggest that they might be involved in the regulation of Msx2. In support of this hypothesis, we found that Msx2 and Dlx5 can bind to the B-TAAT site as well as to a fragment containing the D- and E-TAAT sites in the Msx2 AER enhancer sequences. (c)2002 Elsevier Science (USA).     

Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota

While the human gut microbiota are suspected to produce diffusible small molecules that modulate host signaling pathways, few of these molecules have been identified. Species of Bacteroides and their relatives, which often comprise >50% of the gut community, are unusual among bacteria in that their membrane is rich in sphingolipids, a class of signaling molecules that play a key role in inducing apoptosis and modulating the host immune response. Although known for more than three decades, the full repertoire of Bacteroides sphingolipids has not been defined. Here, we use a combination of genetics and chemistry to identify the sphingolipids produced by Bacteroides fragilis NCTC 9343. We constructed a deletion mutant of BF2461, a putative serine palmitoyltransferase whose yeast homolog catalyzes the committed step in sphingolipid biosynthesis. We show that the Δ2461 mutant is sphingolipid deficient, enabling us to purify and solve the structures of three alkaline-stable lipids present in the wild-type strain but absent from the mutant. The first compound was the known sphingolipid ceramide phosphorylethanolamine, and the second was its corresponding dihydroceramide base. Unexpectedly, the third compound was the glycosphingolipid α-galactosylceramide (α-GalCer_Bf), which is structurally related to a sponge-derived sphingolipid (α-GalCer, KRN7000) that is the prototypical agonist of CD1d-restricted natural killer T (iNKT) cells. We demonstrate that α-GalCer_Bf has similar immunological properties to KRN7000: it binds to CD1d and activates both mouse and human iNKT cells both in vitro and in vivo. Thus, our study reveals BF2461 as the first known member of the Bacteroides sphingolipid pathway, and it indicates that the committed steps of the Bacteroides and eukaryotic sphingolipid pathways are identical. Moreover, our data suggest that some Bacteroides sphingolipids might influence host immune homeostasis.     

Unique interplay between sugar and lipid in determining the antigenic potency of bacterial antigens for NKT cells

Invariant natural killer T (iNKT) cells are an evolutionary conserved T cell population characterized by features of both the innate and adaptive immune response. Studies have shown that iNKT cells are required for protective responses to Gram-positive pathogens such as Streptococcus pneumoniae, and that these cells recognize bacterial diacylglycerol antigens presented by CD1d, a non-classical antigen-presenting molecule. The combination of a lipid backbone containing an unusual fatty acid, vaccenic acid, as well as a glucose sugar that is weaker or not stimulatory when linked to other lipids, is required for iNKT cell stimulation by these antigens. Here we have carried out structural and biophysical studies that illuminate the reasons for the stringent requirement for this unique combination. The data indicate that vaccenic acid bound to the CD1d groove orients the protruding glucose sugar for TCR recognition, and it allows for an additional hydrogen bond of the glucose with CD1d when in complex with the TCR. Furthermore, TCR binding causes an induced fit in both the sugar and CD1d, and we have identified the CD1d amino acids important for iNKT TCR recognition and the stability of the ternary complex. The studies show also how hydrogen bonds formed by the glucose sugar can account for the distinct binding kinetics of the TCR for this CD1d-glycolipid complex. Therefore, our studies illuminate the mechanism of glycolipid recognition for antigens from important pathogens.     

Procollagen C-proteinase enhancer stimulates procollagen processing by binding to the C-propeptide region only

Bone morphogenetic protein-1 (BMP-1) and the tolloid-like metalloproteinases control several aspects of embryonic development and tissue repair. Unlike other proteinases whose activities are regulated mainly by endogenous inhibitors, regulation of BMP-1/tolloid-like proteinases relies mostly on proteins that stimulate activity. Among these, procollagen C-proteinase enhancers (PCPEs) markedly increase BMP-1/tolloid-like proteinase activity on fibrillar procollagens, in a substrate-specific manner. Here, we performed a detailed quantitative study of the binding of PCPE-1 and of its minimal active fragment (CUB1-CUB2) to three regions of the procollagen III molecule: the triple helix, the C-telopeptide, and the C-propeptide. Contrary to results described elsewhere, we found the PCPE-1-binding sites to be located exclusively in the C-propeptide region. In addition, binding and enhancing activities were found to be independent of the glycosylation state of the C-propeptide. These data exclude previously proposed mechanisms for the action of PCPEs and also suggest new mechanisms to explain how these proteins can stimulate BMP-1/tolloid-like proteinases by up to 20-fold.     

CD1 mediated T cell recognition of glycolipids

Specialized subsets of T lymphocytes can distinguish the carbohydrate portions of microbial and self-glycolipids when they are presented by proteins in the CD1 family of antigen presenting molecules. Recent immunochemical and structural analyses indicate that the chemical composition of the presented carbohydrate, together with its precise orientation above the CD1 binding groove, determines if a particular T cell is activated. More recently, however, it has been shown that the lipid backbone of the glycolipid, buried inside the CD1 protein, also can have an impact on T cell activation. While glycolipid recognition is a relatively new category of T cell specificity, the powerful combination of microbial antigen discovery and structural biochemistry has provided great insight into the mechanism of carbohydrate recognition.     

Adipose Triglyceride Lipase (ATGL) and Hormone-Sensitive Lipase (HSL) Deficiencies Affect Expression of Lipolytic Activities in Mouse Adipose Tissues

Adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) are key enzymes involved in intracellular degradation of triacylglycerols. It was the aim of this study to elucidate how the deficiency in one of these proteins affects the residual lipolytic proteome in adipose tissue. For this purpose, we compared the lipase patters of brown and white adipose tissue from ATGL (−/−) and HSL (−/−) mice using differential activity-based gel electrophoresis. This method is based on activity-recognition probes possessing the same substrate analogous structure but carrying different fluorophores for specific detection of the enzyme patterns of two different tissues in one electrophoresis gel. We found that ATGL-deficiency in brown adipose tissue had a profound effect on the expression levels of other lipolytic and esterolytic enzymes in this tissue, whereas HSL-deficiency hardly showed any effect in brown adipose tissue. Neither ATGL- nor HSL-deficiency greatly influenced the lipase patterns in white adipose tissue. Enzyme activities of mouse tissues on acylglycerol substrates were analyzed as well, showing that ATGL-and HSL-deficiencies can be compensated for at least in part by other enzymes. The proteins that responded to ATGL-deficiency in brown adipose tissue were overexpressed and their activities on acylglycerols were analyzed. Among these enzymes, Es1, Es10, and Es31-like represent lipase candidates as they catalyze the hydrolysis of long-chain acylglycerols.Excess lipids are stored as intracellular triacylglycerol and steryl ester deposits in animals, plant seeds, and fungi. In mammals adipose tissue is the body''s largest storage organ for triacylglycerols (TAG)¹ as the primary source of energy during periods of starvation and increased energy demand. Two types of adipose tissue, namely brown (BAT) and white (WAT) adipose tissue exist in mammals, localizing to anatomically distinct areas. BAT and WAT differ in almost all their structural and functional features. Whereas BAT develops prenatally, WAT is subject to maturation postnatally. The different appearance of brown and white adipose tissue is caused by differences in lipid content and the abundance of mitochondria in the constituent adipocytes. Brown fat cells contain several small multilocular lipid droplets and a high number of large mitochondria with numerous cristae. In addition, BAT is highly vascularized and highly innervated by the sympathetic nervous system. In contrast, white adipocytes, usually contain one major unilocular lipid droplet that fills most of the cytoplasm leaving space for only few mitochondria (1–3). WAT accumulates excess energy as triacylglycerols, whereas BAT dissipates energy through adaptive thermogenesis. The thermogenic activity of BAT is caused by the expression of one protein unique in brown adipocytes, the uncoupling protein 1 (UCP1). This polypeptide is a facultative proton transporter and localizes to the inner mitochondrial membrane. It generates heat instead of ATP by uncoupling oxidation in the respiratory chain (3).Lipolysis in WAT is the catabolic process responsible for the release of free fatty acids from triacylglycerol (4, 5). The balance of lipid storage and mobilization is tightly regulated to ensure whole body energy homeostasis. The mobilization of triacylglycerol stores by activation of lipolytic enzymes is specifically stimulated by hormones and chemical agents. In addition, a number of specific physiological conditions owing to exercise, aging, and nutritional status (feeding, fasting) also regulate degradation of TAGs (6). Impairment of lipolysis in adipocytes may be associated with clinical symptoms including obesity, insulin resistance, diabetes mellitus, and dyslipidaemia. All these conditions seem to have a common substrate called lipotoxicity (7–10).The sequential hydrolysis of triacylglycerols in adipocytes producing FFAs is catalyzed by a cascade of lipolytic enzymes, with different substrate preferences (11). The committed enzyme catalyzing the first step of TAG hydrolysis is ATGL, which was identified in three different laboratories in 2004 (12–14). Its activity appears to be largely dependent on association with CGI-58 (14, 15). HSL exhibits a much broader substrate spectrum, with preference for diacylglycerols as well as cholesteryl and retinyl esters (16, 17). In the final step of lipolysis, monoacylglycerol lipase (MGL) degrades MAG thereby generating free fatty acid and glycerol (18). ATGL is the major TAG lipase in adipose tissue. Expression in other tissues is rather low. Currently it cannot be excluded, that other lipases also exist that are important for lipid catabolism (19). Recent functional proteomic screens in various mouse tissues led to the identification of enzyme candidates that are currently subject to functional characterization (unpublished data).The intracellular degradation of triacylglycerols is catalyzed by a cascade of lipolytic enzymes. There appears to be an overlap of substrate preferences as well as a redundancy of lipases to ensure a proper function of this important catabolic process if individual lipase activities are reduced or entirely absent. This study aimed at identifying the effects of ATGL and HSL-deficiency on the expression of other lipolytic enzymes in adipose tissue. For this purpose, we compared the lipolytic proteomes of BAT and WAT from ATGL (−/−) and HSL (−/−) mice with the enzyme patterns of wt tissues using differential activity-based gel electrophoresis (DABGE) (20). This method is based on activity-recognition probes containing same substrate analogous structures but carrying different fluorophores for specific detection of the individual enzyme patterns of two different tissues. These inhibitors react with the nucleophilic serine in the active center of lipolytic enzymes thereby generating covalent bound lipid-protein complexes, which can be separated by gel electrophoresis. We found, that ATGL-deficiency in BAT had a profound effect on the expression levels of other lipolytic and esterolytic enzymes in this tissue, whereas HSL-deficiency hardly showed any effect in BAT. Neither ATGL- nor HSL-deficiency greatly influenced the lipase patterns in WAT. ATGL-deficiency led to a significant but not total reduction in the TAG hydrolyzing activity of adipose tissues. Obviously, there must be (an)other enzyme(s) compensating for the hydrolytic capacity of ATGL. Three proteins that responded to ATGL-deficiency in BAT were overexpressed and their activities on acylglycerols were analyzed. Among these proteins, Es1, Es10, and Es31-like emerged as novel lipase candidates in these studies.     

Post-stroke depression: mechanisms, translation and therapy

The interaction between depression and stroke is highly complex. Post-stroke depression (PSD) is among the most frequent neuropsychiatric consequences of stroke. Depression also negatively impacts stroke outcome with increased morbidity, mortality and poorer functional recovery. Antidepressants such as the commonly prescribed selective serotonin reuptake inhibitors improve stroke outcome, an effect that may extend far beyond depression, e.g., to motor recovery. The main biological theory of PSD is the amine hypothesis. Conceivably, ischaemic lesions interrupt the projections ascending from midbrain and brainstem, leading to a decreased bioavailability of the biogenic amines--serotonin (5HT), dopamine (DA) and norepinephrine (NE). Acetylcholine would also be involved. So far, preclinical and translational research on PSD is largely lacking. The implementation and characterization of suitable animal models is clearly a major prerequisite for deeper insights into the biological basis of post-stroke mood disturbances. Equally importantly, experimental models may also pave the way for the discovery of novel therapeutic targets. If we cannot prevent stroke, we shall try to limit its long-term consequences. This review therefore presents animal models of PSD and summarizes potential underlying mechanisms including genomic signatures, neurotransmitter and neurotrophin signalling, hippocampal neurogenesis, cellular plasticity in the ischaemic lesion, secondary degenerative changes, activation of the hypothalamo-pituitary-adrenal (HPA) axis and neuroinflammation. As stroke is a disease of the elderly, great clinical benefit may especially accrue from deciphering and targeting basic mechanisms underlying PSD in aged animals.