Three originally distinct concepts – lipid rafts, detergent-resistant membranes (DRMs) and liquid-ordered (lo) lipid phases – are often confused in current literature; many researchers have assumed that all three names refer to the same chemico-biological entity. In fact, theoretical and experimental findings provide strong evidence against identifying DRMs with rafts and lo domains. Because much of what we think we know about lipid rafts is based on their unjustified identification as DRMs, functional domains in biological membranes might differ markedly from the generally accepted picture.
The reasons why the standards of evaluating Western medicine are not suitable for testing traditional Chinese medicine (TCM) are explicit in the therapeutic objective and principles of TCM. TCM aims to correct maladjustments and restore the self-regulatory ability of the body, and not to antagonize specific pathogenetic targets. Maladjustments in a disease can be classified into several ‘patterns’ according to TCM theory. Multiple diseases might share one ‘pattern’ and be treated by the same herbal formula whereas one disease might display several different ‘patterns’ and be treated by multiple formulae. These principles are supported by evidence that multi-system changes in one pattern can be modulated by a herbal formula. The approaches used in systems biology and pharmacogenetics are similar to the practices of TCM. I propose that a combined approach using specific parameters associated with modern medicine, the general condition of individuals, as outlined by TCM, and pattern stratification of diseases should be employed to re-evaluate herbal formulae.
Forkhead box, class O (FoxO) transcription factors are inhibited by insulin-induced FoxO phosphorylation. Recently, acetylation of FoxO factors by calcium response element-binding (CREB)-binding protein (CBP) and/or p300 has been identified as a novel regulatory pathway, although the exact consequences of acetylation remain unclear. We propose that binding of CBP/p300 to FoxO factors is essential for FoxO-mediated transcription. CBP and p300 act as FoxO cofactors by weakening histone–DNA interactions. Acetylation of FoxO factors, however, attenuates FoxO-mediated transcriptional activity by disrupting the interaction between FoxO factors and target DNA. Therefore, acetylation shifts the function of FoxO from cell-cycle arrest and protection against oxidative stress towards cell death.
LxxLL motifs participate in many protein–protein interactions associated with different aspects of transcriptional regulation. These motifs are present in many transcription factors and cofactors, mediating interactions that can activate or repress transcription. Several recently reported 3D structures of protein–LxxLL motif complexes and an intriguing novel interaction implicated in leukaemia have further highlighted the diversity and regulatory importance of this seemingly simple motif.
The current view of the cytoplasm as a ‘bustling and well-organized metropolitan city’ raises the issue of how physicochemical forces control the macromolecular interactions and transport of metabolites and energy in the cell. Motivated by studies on bacterial osmosensors, we argue that charged cytoplasmic macromolecules are stabilized electrostatically by their ionic atmospheres. The high cytoplasmic crowding (25–50% of cell volume) shapes the remaining cell volume (50–75%) into transient networks of electrolyte pathways and pools. The predicted ‘semi-conductivity’ of the electrolyte pathways guides the flow of biochemical ions throughout the cytoplasm. This metabolic and signaling current is powered by variable electrochemical gradients between the pools. The electrochemical gradients are brought about by cellular biochemical reactions and by extracellular stimuli. The cellular metabolism is thus vectorial not only across the membrane but also throughout the cytoplasm.
The recent identification of genes encoding a novel family of soluble aromatic prenyltransferases from species and the structural characterization of one of these proteins are challenging discoveries in the biochemistry of natural compounds. In addition to their notable physiological role in the biosynthesis of aminocoumarin antibiotics, these enzymes represent an advanced tool for exploring novel isoprenoid substitutions in aromatic compounds and are expected to foster the emerging pharmacological applications of prenylated flavonoids.
The vascular system is rich in G-protein-coupled receptors (GPCRs), particularly Class 1 GPCRs, which are activated by an eclectic range of chemical entities including peptides. These chemical messengers can function in blood vessels as directly acting vasoconstrictors, directly acting vasodilators or indirectly acting vasodilators. During the past ten years >50 receptors previously designated as ‘orphan receptors’ have been paired with their cognate ligands. New transmitter systems are emerging with some displaying potent activity in the vascular system, including the vasoconstrictors apelin, motilin, neuromedin U, sphingosine-1-phosphate and urotensin-II, and the vasodilators ghrelin and nociceptin. All Class 2 GPCRs are activated by peptides. Those displaying vasoactivity all function as directly acting vasodilators and include adrenomedullin and the emerging urocortin transmitters. Hypertension can persist despite treatment with combinations of blood-pressure-lowering drugs. Thus, it is likely that further as yet undiscovered transmitter systems will provide new targets for novel therapies or diagnosis.
Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture?
Guanine (G)-rich DNA sequences can adopt stable G-quadruplex structures by G-tetrad hydrogen-bonding and hydrophobic stacking. Recently, it has been shown that a DNA sequence forms an aptamer (termed ) and adopts a novel dimeric quadruplex folding topology in K solution. This aptamer exhibits anti-HIV1 integrase activity in the nanomolar range . A docking-based model of the -integrase complex positions the DNA aptamer within a channel of the tetrameric integrase. This mutual fitting blocks several catalytic amino acid residues that are essential for integrase function, and accounts for the anti-HIV1 activity of the aptamer.
The existence of intramembrane receptor–receptor interactions for heptaspanning membrane receptors is now fully accepted, but a model considering dimers as the basic unit that binds to two ligand molecules is lacking. Here, we propose a two-state-dimer model in which the ligand-induced conformational changes from one component of the dimer are communicated to the other. Our model predicts cooperativity in binding, which is relevant because the other current models fail to address this phenomenon satisfactorily. Our two-state-dimer model also predicts the variety of responses elicited by full or partial agonists, neutral antagonists and inverse agonists. This model can aid our understanding of the operation of heptaspanning receptors and receptor channels, and, potentially, be important for improving the treatment of cardiovascular, neurological and neuropsychyatric diseases.