Lipid-lowering drugs

Although a change in life-style is often the method of first choice for lipid lowering, lipid-lowering drugs, in general, help to control elevated levels of different forms of lipids in patients with hyperlipidemia. While one group of drugs, statins, lowers cholesterol, the other group, fibrates, is known to take care of fatty acids and triglycerides. In addition, other drugs, such as ezetimibe, colesevelam, torcetrapib, avasimibe, implitapide, and niacin are also being considered to manage hyperlipidemia. As lipids are very critical for cardiovascular diseases, these drugs reduce fatal and nonfatal cardiovascular abnormalities in the general population. However, a number of recent studies indicate that apart from their lipidlowering activities, statins and fibrates exhibit multiple functions to modulate intracellular signaling pathways, inhibit inflammation, suppress the production of reactive oxygen species, and modulate T cell activity. Therefore, nowadays, these drugs are being considered as possible therapeutics for several forms of human disorders including cancer, autoimmunity, inflammation, and neurodegeneration. Here I discuss these applications in the light of newly discovered modes of action of these drugs. Received 5 September 2005; received after revision 29 December 2005; accepted 26 January 2006     

Biosynthesis of isoprenoids via the non-mevalonate pathway

The mevalonate pathway for the biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), is known in considerable detail. Only recently, the existence of a second mevalonate-independent pathway for the biosynthesis of IPP and DMAPP was detected in plants and certain eubacteria. Experiments with ¹³C and/or ²H-labelled precursors were crucial in the elucidation of this novel route. The pathway is essential in plants, many eubacteria and apicomplexan parasites, but not in archaea and animals. The genes, enzymes and intermediates of this pathway were rapidly unravelled over the past few years. Detailed knowledge about the mechanisms of this novel route may benefit the development of novel antibiotics, antimalarials and herbicides.Received 7 October 2003; received after revision 23 December 2003; accepted 21 January 2004     

Bacterial oligopeptide-binding proteins

This review focuses on bacterial oligopeptide-binding proteins, which form part of the oligopeptide transport system belonging to the ATP-binding cassette family of transporters. Depending on the bacterial species, these binding proteins (OppA) capture peptides ranging in size from 2 to 18 amino acids from the environment and pass them on to the other components of the oligopeptide transport system for internalisation. Bacteria have developed several strategies to produce these binding proteins, which are periplasmic in Gram^– bacteria and membrane-anchored in Gram⁺, with a higher stoichiometry (probably necessary for efficient transport) than the other components in the transport system. The expression of OppA-encoding genes is clearly modulated by external factors, especially nitrogen compounds, but the mechanisms of regulation are not always clear. The best-understood roles played by OppAs are internalisation of peptides for nutrition and recycling of muropeptides. It has, however, recently become clear that OppAs are also involved in sensing the external medium via specific or non-specific peptides.Received 10 February 2003; received after revision 9 April 2003; accepted 24 April 2003     

The link proteins

Aggregates of chondroitin-keratan sulfate proteoglycan (aggrecan) and hyaluronic acid (hyaluronan) are the major space-filling components of cartilage. A glycoprotein, link protein (LP; 40–48 kDa) stabilizes the aggregate by binding to both hyaluronic acid and aggrecan. In the absence of LP, aggregates are smaller (as estimated by rotary shadowing of electron micrographs) and less stable (they dissociate at pH 5) than they are in the presence of LP. The proteoglycan aggregate, including LP, is dissociated in the presence of chaotropes such as 4 M guanidine hydrochloride. On removal of the chaotrope, the complex will reassociate. This forms the basis of the isolation of LP from cartilage and has been described in detail elsewhere. Tryptic digestion of the proteoglycan aggregates results in a high molecular weight product that consists of hyaluronic acid to which is bound LP and the N-terminal globular domain of aggrecan (hyaluronic acid binding region; HABR) in a 11 stoichiometry. The amino acid sequences of LP and HABR are surprisingly similar. The amino acid sequence can be divided into three domains; an N-terminal domain that falls into the immunoglobulin super-family and two C-terminal domains that are similar to each other. The DNA structure echoes this similarity, in that the major domains are reflected in three separate exons in both LP and HABR. The two C-terminal domains are largely responsible for the association with HA and are related to two recently described hyaluronate-binding proteins, CD44 and TSG-6. A variety of approaches, including analysis of the forms of LP found in vivo, rotary shadowing and analysis of the sequence in the immunoglobulin-like domain, have shed considerable light on the structure-function relationships of LP. This review describes the structure and function of LP in detail, focusing on what can be inferred from the similarity of LP, HABR and related molecules such as immunoglobulins and lymphocyte HA-receptors.     

Resistant penicillin-binding proteins

Low-affinity penicillin-binding proteins (PBPs), which participate in the β-lactam resistance of several pathogenic bacteria, have different origins. Natural transformation and recombination events with DNA acquired from neighbouring intrinsically resistant organisms are responsible for the appearance of mosaic genes encoding two or three low-affinity PBPs in highly resistant strains of transformable microorganisms such as Neisseria and Streptococcus pneumoniae. Methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal strains possess the mecA determinant gene, which probably evolved within the Staphylococcus genus from a closely related and physiologically functional gene that was modified by point mutations. The expression of mecA is either inducible or constitutive. A stable high-level resistant phenotype requires the synthesis of a normally constituted peptidoglycan. Enterococci have a natural low susceptibility to β-lactams related to the presence of an intrinsic low-affinity PBP. Highly resistant enterococcal strains overexpress this PBP and/or reduce its affinity.     

S-Nitrosylation of proteins

The transfer of a nitric oxide group to cysteine sulfhydryls on proteins, known as S-nitrosylation, is increasingly becoming recognized as a ubiquitous regulatory reaction comparable to phosphorylation. It represents a form of redox modulation in diverse tissues, including the brain. An increasing number of proteins have been found to undergo S-nitrosylation in vivo. These proteins are called S-nitrosothiols, and may play an important role in many processes ranging from signal transduction, DNA repair, host defense, and blood pressure control to ion channel regulation and neurotransmission. This review focuses on the importance of the S-nitrosylation reaction and describes some recently identified S-nitrosothiols in various fields of research.     

From atoms to proteins

The investigation of biological macromolecules and the characteristics that determine their function has been of particular interest over the last decades. Here we overview some modern approaches for making the most of the 3-D protein structural information, with a distinctive emphasis on macromolecular crystallography and complementary techniques used to establish the structure-function relationship. A tight link between the biology of the cellular processes and the underlying chemistry of protein function governs the flow of the presented material. The reader will be lead through the basic principles of protein structure analysis and the means to capture the characteristics that portray the function. The techniques exploiting high-resolution data and allowing quantification of molecular motion and structure-activity relationship are given particular attention. Received 20 April 2007; accepted 20 April 2007     

Neurofilament proteins in neurodegenerative diseases

The function of neurofilaments, the major component in large myelinated neurons, is not well understood even though they were discovered as structures over 100 years ago. Recent studies have suggested that neuro-filaments are closely related to many neurodegenerative diseases, such as amyotrophic lateral sclerosis, Parkinson disease Alzheimer disease, and diabetes. Using in vitro assays, cultures and transgenic mice, these studies provided new insights into neurofilament function. The function of each subunit, the relationship of neurofilaments with other cytoskeletal elements and their clinical significance are topics of increasing attention.Received 22 June 2004; received after revision 4 August 2004; accepted 19 August 2004     

Crystallin proteins and amyloid fibrils

Improper protein folding (misfolding) can lead to the formation of disordered (amorphous) or ordered (amyloid fibril) aggregates. The major lens protein, α-crystallin, is a member of the small heat-shock protein (sHsp) family of intracellular molecular chaperone proteins that prevent protein aggregation. Whilst the chaperone activity of sHsps against amorphously aggregating proteins has been well studied, its action against fibril-forming proteins has received less attention despite the presence of sHsps in deposits found in fibril-associated diseases (e.g. Alzheimer’s and Parkinson’s). In this review, the literature on the interaction of αB-crystallin and other sHsps with fibril-forming proteins is summarized. In particular, the ability of sHsps to prevent fibril formation, their mechanisms of action and the possible in vivo consequences of such associations are discussed. Finally, the fibril-forming propensity of the crystallin proteins and its implications for cataract formation are described along with the potential use of fibrillar crystallin proteins as bionanomaterials. Received 13 June 2008; received after revision 29 July 2008; accepted 05 August 2008     

Structural genomics for membrane proteins

Structure-based drug discovery has proven useful in improving and shortening the drug development process. The approach of structural genomics to study a large number of targets in parallel has been commonly applied to protein families and even whole genomes. Paradoxically, although membrane proteins represent the largest type of drug targets, up to 70% today, determination of their structure has been modest compared to that of soluble proteins. Because membrane proteins are important for drug discovery an emphasis has been placed on developing technologies and methods to determine membrane protein structures. Several structural genomics initiatives have been established, focusing on the structural biology of membrane proteins. Received 31 May 2006; received after revision 5 July 2006; accepted 9 August 2006     

G proteins as drug targets

The structure and function of heterotrimeric G protein subunits is known in considerable detail. Upon stimulation of a heptahelical receptor by the appropriate agonists, the cognate G proteins undergo a cycle of activation and deactivation; the α-subunits and the βγ-dimers interact sequentially with several reaction partners (receptor, guanine nucleotides and effectors as well as regulatory proteins) by exposing appropriate binding sites. For most of these domains, low molecular weight ligands have been identified that either activate or inhibit signal transduction. These ligands include short peptides derived from receptors, G protein subunits and effectors, mastoparan and related insect venoms, modified guanine nucleotides, suramin analogues and amphiphilic cations. Because compounds that act on G proteins may be endowed with new forms of selectivity, we propose that G protein subunits may therefore be considered as potential drug targets. Received 18 September 1998; received after revision 6 November 1998; accepted 11 November 1998     

Lipid interactions with transmembrane proteins

Magnetic resonance results, principally from ²H-nuclear magnetic resonance, indicate that the mean lipid-chain ordering at the surface of transmembrane proteins is comparable to that in fluid lipid bilayers. Principally, it is the requirement for matching the hydrophobic lengths of lipid and protein that modulates the degree of chain ordering at the lipid-protein interface. The distribution of chain order parameters is, nonetheless, broader in the presence of integral proteins than in fluid lipid bilayers. The chain configurations of the phospholipids that are resolved in crystals of integral membrane proteins display considerable conformational heterogeneity. Chain C–C dihedral angles are, however, not restricted to the energetically allowable trans and gauche rotamers. This indicates that the chains of a given lipid do not have a unique configuration in protein crystals.     

Antimicrobial skin peptides and proteins

Human skin is permanently exposed to microorganisms, but rarely infected. One reason for this natural resistance might be the existence of a ‘chemical barrier’ consisting in constitutively and inducibly produced antimicrobial peptides and proteins (AMPs). Many of these AMPs can be induced in vitro by proinflammatory cytokines or bacteria. Apart from being expressed in vivo in inflammatory lesions, some AMPs are also focally expressed in skin in the absence of inflammation. This suggests that non-inflammatory stimuli of endogenous and/or exogenous origin can also stimulate AMP synthesis without inflammation. Such mediators might be ideal ‘immune stimulants’ to induce only the innate antimicrobial skin effector molecules without causing inflammation. Received 9 August 2005; received after revision 21 October 2005; accepted 16 November 2005     

Soluble proteins in insect chemical communication

Our understanding of the biochemical mechanisms that mediate chemoreception in insects has been greatly improved after the discovery of olfactory and taste receptor proteins. However, the presence of soluble polypeptides in high concentration around the dendrites of sensory neurons still poses unanswered questions. More than 2 decades after their discovery and despite the wealth of structural information available, the physiological function of odorant-binding proteins is not well understood. More recently, members of a second family of soluble polypeptides, the chemosensory proteins, were also discovered in the lymph of chemosensilla. Here we review the structural properties of both classes of soluble proteins, their affinity to small ligands, and their expression in the different parts of the insect body and subcellular localisation. Finally, we discuss current ideas and models of the role of such proteins in insect chemoreception. Received 27 December 2005; received after revision 6 March 2006; accepted 13 April 2006     

Large-scale production of functional membrane proteins

The preparation of sufficient amounts of high-quality samples is still the major bottleneck for the characterization of membrane proteins by in vitro approaches. The hydrophobic nature, the requirement for complicated transport and modification pathways, and the often observed negative effects on membrane properties are intrinsic features of membrane proteins that frequently cause significant problems in overexpression studies. Establishing efficient protocols for the production of functionally folded membrane proteins is therefore a challenging task, and numerous specific characteristics have to be considered. In addition, a variety of expression systems have been developed, and choice of appropriate techniques could strongly depend on the desired target membrane proteins as well as on their intended applications. The production of membrane proteins is a highly dynamic field and new or modified approaches are frequently emerging. The review will give an overview of currently established processes for the production of functionally folded membrane proteins.     

Hemolysins: Pore-forming proteins in invertebrates

Summary Invertebrates possess lytic molecules which lyse vertebrate erythrocytes. In all the species studied so far, hemolytic activity depends on proteins which possess a wide range of reactivity. It is generally calcium-dependent and heat-labile, although calcium-independent and heat-stable hemolysins have also been detected. The molecules interact with sugars or lipids which could represent the membrane receptors by which circular lesions on target membranes are produced.On the basis of some analogies with vertebrate lytic molecules it is conceivable that the hemolysins evolved from a common ancestral gene which also led to vertebrate pore-forming proteins.