bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyamine biosynthetic enzymes as drug targets in parasitic protozoa
Authors: Heby O. , Roberts S.C. , Ullman B.
Published: June 2004

Molecular, biochemical and genetic characterization of ornithine decarboxylase, S-adenosylmethionine decarboxylase and spermidine synthase establishes that these polyamine-biosynthetic enzymes are essential for growth and survival of the agents that cause African sleeping sickness, Chagas' disease, leishmaniasis and malaria. These enzymes exhibit features that differ significantly between the parasites and the human host. Therefore it is conceivable that exploitation of such differences can lead to the design of new inhibitors that will selectively kill the parasites while exerting minimal, or at least tolerable, effects on the parasite-infected patient.
Effect of age on susceptibility to post-traumatic infection in the elderly
Authors: Butcher S.K. , Killampalli V. , Chahal H. , Kaya Alpar E. , Lord J.M.
Published: June 2004

Previous work has demonstrated an age-related decline in neutrophil function, including a decline in phagocytic capacity, with age in healthy individuals. This decline in function may contribute to increased susceptibility to bacterial infections in the elderly population. The present study has investigated the effects of age on susceptibility to infection and neutrophil function in elderly humans following mild trauma. Specifically, we have measured neutrophil function in 44 patients, all of whom had no significant co-morbidity, were over 65 years old (mean age 82.5 years) and had sustained a fractured neck of femur. We obtained neutrophils and examined the process of microbial engulfment by phagocytosis and the bactericidal mechanism of superoxide production. In the 5-week period after trauma, almost half of the elderly trauma patients succumbed to bacterial or fungal infection, with a predominance of chest and urinary tract infections. When examining neutrophil function, a decline in superoxide production was observed in neutrophils from the elderly trauma group at the time of hip fracture when compared with those from healthy elderly controls, and this was maintained 5 weeks after trauma. This was accompanied by an age-related reduction in phagocytic function during this period. We propose that trauma and an age-related decline in neutrophil function combine to decrease the immune response to bacteria in the elderly.
Critique of the demographic evidence for ‘late-life non-senescence’
Authors: de Grey A.D.N.J.
Published: June 2004

Although the Gompertz formula accurately describes observed mortality distributions over most of their extent, their ‘tail’ is much longer than that of a Gompertz curve fitted to the whole data set. A simple candidate explanation is that the longest-lived subset of any population will necessarily be enriched in individuals that age more slowly than the average of that population. However, some investigators have suggested that, instead, individuals actually cease to senesce after a certain age. Here, using a new approach to determining the best-fit degree of heterogeneity in the Gompertz slope parameter, it is shown that observed distributions can in fact be fit quite accurately by purely ‘heterogeneous Gompertz’ curves. Either explanation may therefore be correct.
Skeletal muscles of aged male mice fail to adapt following contractile activity
Authors: Vasilaki A. , Iwanejko L.M , McArdle F. , Broome C.S. , Jackson M.J. , McArdle A.
Published: June 2004

Skeletal muscle adapts rapidly following exercise by the increased production of heat-shock proteins (HSPs). The aim of this study was to examine the ability of muscle from adult and aged mice to produce HSPs following non-damaging exercise. Adult and aged B6XSJL mice were anaesthetized and their hind limbs were subjected to isometric contractions. At different time points, muscles were analysed for HSP production by Western and Northern blotting and by electrophoretic mobility-shift assay. HSP protein and mRNA levels in muscles from adult mice increased significantly following exercise. This was not evident in muscles of aged mice. In contrast, binding of the transcription factor heat-shock factor 1 (HSF1) was not grossly altered in muscles of aged mice compared with adult mice. The data suggest that the inability of muscles of aged mice to produce HSPs appears to be due to alterations during gene transcription.
Proteasomal interactors control activities as diverse as the cell cycle and glutaminergic neurotransmission
Authors: Rezvani K. , Mee M. , Dawson S. , McIlhinney J. , Fujita J. , Mayer R.J.
Published: June 2004

The six regulatory non-redundant ATPases in the base of the 19 S regulator of the 26 S proteasome belong to the AAA superfamily of ATPases. Yeast two-hybrid genetic screens, biochemical analyses and cell biological studies have identified and characterized new interactors of the human S6 (rpt3) and S8 (rpt6) ATPases of the 19 S regulator of the 26 S proteasome. The S6 ATPase interacts with gankyrin. This protein is found in purified human 26 S proteasomes and in a smaller complex(es) containing CDK4 and free S6 ATPase. Gankyrin overexpression causes the phosphorylation of the retinoblastoma protein (pRb) and the release of E2F transcription factor to trigger the expression of DNA synthesis genes. Gankyrin is oncogenic in nude mice and is overexpressed in hepatocellular carcinoma cells (HCCs). The S8 ATPase interacts with members of the large Homer-3 protein family. There are three Homer genes; the Homer 1 and 2 gene products control trafficking and calcium-store-related functions of metabotropic glutamate receptors (e.g. mGluR1α). Homer-3A11 by binding to the S8 ATPase brings mGluR1α to the 26 S proteasome for degradation. The degradation of mGluR1α is blocked by proteasomal inhibitors and by overexpression of the N-terminus of Homer which binds to the receptor. The S8 ATPase and mGluR1α are co-localized in Purkinje dendrites in rat cerebellum. The data are discussed in terms of the regulation of the cell cycle and glutaminergic receptor functions by the 26 S proteasome.
The ubiquitin proteolytic system and pathogenesis of human diseases: a novel platform for mechanism-based drug targeting
Authors: Ciechanover A.
Published: June 2004

Until the early 1980s, protein degradation was a neglected research area, and scientists were mostly busy deciphering the genetic code and its translation to the proteome. Destruction of cellular proteins was thought to be a scavenger, non-specific and dead-end process. Although it was known that proteins do turn over, the large extent and high specificity of the process, whereby distinct proteins have half-lives that range from a few minutes to several days, was not appreciated. The discovery of the lysosome by Christian de Duve did not change this view significantly, as it was clear that this organelle is involved mostly in the degradation of extracellular proteins, and their proteases cannot be substrate-specific. The discovery of the complex cascade of the ubiquitin pathway revolutionized the field. It is clear now that degradation of cellular proteins via the ubiquitin system is a highly complex, temporally controlled and tightly regulated process that plays major roles in a variety of basic pathways and processes during cell life and death, and in health and disease. The system is involved in targeting many cellular proteins, among them cell cycle regulators, growth- and differentiation-controlling factors, transcriptional activators, cell-surface receptors and ion channels, endoplasmic reticulum proteins, antigenic proteins destined for presentation on class I MHC molecules, and abnormal/misfolded proteins. Consequently, it is involved in regulating many basic cellular processes, such as cell cycle and division, growth and differentiation, signal transduction and transcription, modulation of the secretory and endocytic pathways, the immune and inflammatory responses, and quality control. With the multitude of substrates targeted and the numerous processes involved, it is not surprising that aberrations in the pathway have been implicated in the pathogenesis of many diseases, with certain malignancies and neurodegenerative disorders being ranked among them.
Antibiotic glycosyltransferases
Authors: Walsh C.T. , Losey H.C. , Freel Meyers C.L.
Published: June 2004

In the biosynthesis of several classes of antibiotics, sugars are attached to aglycone scaffolds by antibiotic-specific glycosyltransferases in the latter stages of the pathways. Two glycosylation pathways will be examined: the glycopeptide antibiotics of the vancomycin class and the aminocoumarin antibiotics of the novobiocin class. An oxidatively cross-linked heptapeptide scaffold is sequentially glucosylated and vancosaminylated by GtfE and GtfD, respectively, in vancomycin maturation, while in chloroeremomycin assembly the same heptapeptide is glucosylated by GtfB, then epivancosaminylated at two distinct sites by GtfA and GtfC. The specificity and mechanism of these glycosyltransferases will be discussed. In novobiocin biosynthesis, three enzymes (NovM, NovP and NovN) are thought to act sequentially to transfer an l-noviose moiety to the novobiocic acid aglycone (NovM), followed by 4´-hydroxyl methylation (NovP) and 3´-hydroxyl carbamoylation to produce the mature antibiotic structure, targeting the GyrB subunit of DNA gyrase. Initial characterization of NovM and NovP will be discussed.
What can structure tell us about in vivo function? The case of aminoglycoside-resistance genes
Authors: Vetting M. , Roderick S.L. , Hegde S. , Magnet S. , Blanchard J.S.
Published: June 2004

Resistance to antibiotics used in the treatment of bacterial infections is an expanding clinical problem. Aminoglycosides, one of the oldest classes of natural product antibiotics, exert their bactericidal effect as the result of inhibiting bacterial protein synthesis by binding to the acceptor site of the 30 S ribosomal subunit. The most common mechanism of clinical resistance to aminoglycosides results from the expression of enzymes that covalently modify the aminoglycoside. We will discuss the enzymology and structure of two representative chromosomally encoded aminoglycoside N-acetyltransferases, Mycobacterium tuberculosis AAC(2´)-Ic and Salmonella enterica AAC(6´)-Iy, and speculate about their possible physiological function and substrates.
Structural insights into the evolution of the pantothenate-biosynthesis pathway
Authors: Lobley C.M.C. , Schmitzberger F. , Kilkenny M.L. , Whitney H. , Ottenhof H.H. , Chakauya E. , Webb M.E. , Birch L.M. , Tuck K.L. , Abell C. , Smith A.G. , Blundell T.L.
Published: June 2004

Pantothenate is synthesized in bacteria, fungi and plants, and as vitamin B5 is a dietary requirement in animals. The three-dimensional structures of the four Escherichia coli enzymes involved in the production of pantothenate have been determined. We describe the use of comparative analyses of the sequences and structures to identify distant homologues of the four enzymes in an attempt to understand the evolution of the pathway. We conclude that it is likely to have evolved via a patchwork mechanism, whereby the individual enzymes were recruited separately.
United at last: the tuberous sclerosis complex gene products connect the phosphoinositide 3-kinase/Akt pathway to mammalian target of rapamycin (mTOR) signalling
Authors: Manning B.D. , Cantley L.C.
Published: June 2004

The molecular interplay between the phosphoinositide 3-kinase (PI3K) pathway and mammalian target of rapamycin (mTOR) signalling in the control of cell growth and proliferation has been the subject of much interest and debate amongst cell biologists. A recent escalation of research in this area has come from the discovery of the tuberous sclerosis complex gene products, tuberin and hamartin, as central regulators of mTOR activation. The PI3K effector Akt/protein kinase B has been found to directly phosphorylate tuberin and is thereby thought to activate mTOR through inhibition of the tuberin–hamartin complex. The many recent studies aimed at defining the molecular nature of this revamped PI3K/Akt/mTOR pathway are reviewed here. The collective data discussed have laid the groundwork for important new insights into the many cancers caused by aberrant PI3K activation and the clinically challenging tuberous sclerosis complex disease and have suggested a possible means of treatment for both.
Tuberous sclerosis complex (TSC) gene involvement in sporadic tumours
Authors: Knowles M.A. , Hornigold N. , Pitt E.
Published: June 2004

In tuberous sclerosis patients, inactivation of the tuberous sclerosis complex tumour-suppressor genes TSC1 and TSC2 contributes to the development of a wide range of hamartomatous lesions. These patients do not, however, show an increased risk of the common adult solid cancers. Recent evidence that the TSC genes play a role in the phosphoinositide 3-kinase pathway, a pathway whose dysregulation is implicated in a wide range of human malignancies, raises the possibility that their inactivation could contribute to the development of some sporadic cancers. To date the only evidence for this comes from the finding of mutations of TSC1 in bladder cancer. The mutation spectrum of TSC1 in bladder cancer and functional evidence from TSC1-gene-replacement studies in bladder tumour cells will be presented. The literature on genetic changes in several other sporadic epithelial cancers reveals relatively common deletions in the region of the TSC genes. In ovarian and gall bladder carcinoma and non-small-cell carcinoma of the lung, deletions in both 16p13 and 9q34 are found at significant frequency. Mutation analyses in such tumours are now merited.
Similarity-based approaches to virtual screening
Authors: Willett P.
Published: June 2004

Current similarity measures for virtual screening are based on the use of molecular fingerprints and the Tanimoto coefficient. This paper describes two ways in which one can increase the effectiveness of similarity-based virtual screening: using similarity coefficients other than the Tanimoto coefficient for the comparison of molecular fingerprints; and using a graph-theoretic similarity measure based on the largest substructure common to a pair of molecules.
Human carboxylesterase 1: from drug metabolism to drug discovery
Authors: Redinbo M.R. , Bencharit S. , Potter P.M.
Published: June 2004

Human carboxylesterase 1 (hCE1) is a serine esterase involved in both drug metabolism and activation, as well as other biological processes. hCE1 catalyses the hydrolysis of heroin and cocaine, and the transesterification of cocaine in the presence of ethanol to the toxic metabolite cocaethylene. We have determined the crystal structures of hCE1 in complex with either the cocaine analogue homatropine or the heroin analogue naloxone. These are the first structures of a human carboxylesterase, and they provide details about narcotic metabolism in humans. hCE1's active site contains rigid and flexible pockets, explaining the enzyme's ability to act both specifically and promiscuously. hCE1 has also been reported to contain cholesteryl ester hydrolase, fatty acyl-CoA hydrolase and acyl-CoA:cholesterol acyltransferase activities, and thus appears to be involved in cholesterol metabolism. Since the enzyme may be useful as a treatment for cocaine overdose, and may afford protection against chemical weapons like Sarin, Soman and VX gas, hCE1 could serve as both a drug and a drug target. Selective hCE1 inhibitors targeted to several sites on the enzyme may also pave the way for novel clinical tools to manage cholesterol homoeostasis in humans.
Role of adapters in Toll-like receptor signalling
Authors: Akira S. , Yamamoto M. , Takeda K.
Published: June 2004

Toll-like receptors (TLRs) play a critical role in the detection of invading pathogens within the body and the subsequent immune response. Individual TLRs recognize distinct microbial components. The TLRs are a type 1 transmembrane receptor that possess an extracellular leucine-rich repeat domain and cytoplasmic domain homologous with that of the interleukin 1 receptor (IL-1R) family. Upon stimulation, TLR recruits the IL-1R-associated kinase (IRAK) via the adapter MyD88, ultimately leading to the activation of nuclear factor-κB. Cytokine production in response to all TLR ligands is completely abolished in MyD88-deficient cells, indicating that MyD88 is an essential signalling molecule shared among members of the IL-1R/Toll family. However, several novel adaptor molecules have recently been identified. Evidence is now accumulating showing that differential utilization of these adaptors may activate overlapping as well as distinct signalling pathways, and ultimately give rise to distinct biological effects exerted by individual TLR family members.
The role of MyD88-like adapters in Toll-like receptor signal transduction
Authors: O'Neill L.A.J.
Published: June 2004

Signal-transduction pathways activated by Toll-like receptors (TLRs) have been the subject of intense investigation because of the key role played by TLRs in the recognition and elimination of microbes. Signalling is initiated by a domain termed the Toll/interleukin-1 (IL-1) receptor (TIR) domain that occurs on the cytosolic face of TLRs. This recruits, via homotypic interactions, adapter proteins that contain TIR domains. Three such adapter proteins have been discovered to date, and have been named MyD88, Mal [MyD88 adapter-like; also known as TIRAP (TIR domain-containing adapter protein)] and Trif (TIR-domain-containing adapter inducing interferon-β). Differences are emerging between TLRs in terms of which adapter is recruited by which TLR. This may lead to specificities in TLR signalling, with pathways being triggered that are specific for the elimination of the invading microbe. However, signals that separate Mal from MyD88 have yet to emerge, although biochemical differences between the two proteins imply that each will have a specific function.
Toll and Toll-like receptors in Drosophila
Authors: Bilak H. , Tauszig-Delamasure S. , Imler J.-L.
Published: June 2004

The Drosophila Toll receptor controls the immune response to Gram-positive bacteria and fungi by activating a signalling pathway partially conserved throughout evolution. The Drosophila genome encodes eight additional Toll-related receptors, most of which appear to carry out developmental rather than immune functions. One exception may be Toll-9, which shares structural and functional similarities with mammalian TLRs.
Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism
Authors: Allers T. , Ngo H.-P.
Published: June 2004

Homologous recombination is a fundamental cellular process that rearranges genes both within and between chromosomes, promotes repair of damaged DNA and underpins replication. Much of our understanding of recombination stems from pioneering studies of bacterial and eukaryotic systems such as Escherichia coli and Saccharomyces cerevisiae. Since most archaeal species are extremophilic and difficult to cultivate, current knowledge of recombination in the Archaea is confined largely to comparative genomics and biochemistry. A clear view of what we can learn will not emerge until genetic and molecular systems have been established. We are developing such systems using Haloferax volcanii as a model organism, as it can be cultivated in the laboratory with ease and offers great potential for establishing tractable and informative genetic systems.
Immunoglobulin-binding domains: Protein L from Peptostreptococcus magnus
Authors: Housden N.G. , Harrison S. , Roberts S.E. , Beckingham J.A. , Graille M. , Stura E. , Gore M.G.
Published: June 2004

Protein L is a multidomain cell-wall protein isolated from Peptostreptococcus magnus. It belongs to a group of proteins that contain repeated domains that are able to bind to Igs without stimulating an immune response, the most characterized of this group being Protein A (Staphylococcus aureus) and Protein G (Streptococcus). Both of these proteins bind predominantly to the interface of CH2-CH3 heavy chains, while Protein L binds exclusively to the VL domain of the κ-chain. The function of these proteins in vivo is not clear but it is thought that they enable the bacteria to evade the host's immune system. Two binding sites for κ-chain on a single Ig-binding domain from Protein L have recently been reported and we give evidence that one site has a 25–55-fold higher affinity for κ-chain than the second site.
Implications of enzyme kinetics
Authors: McDonald A.G.
Published: June 2004

Of the many examples of oscillatory kinetic behaviour known, several are briefly reviewed, including those of glycolysis, the peroxidase–oxidase reaction and oscillations in cellular calcium concentration. It is shown that simple mathematical models employing allosteric rate laws are sufficient to explain the instability of the steady state and the appearance of sustained oscillations. The cAMP-signalling systems of cellular slime moulds and the dynamics of intracellular calcium oscillations illustrate the importance of such oscillophores to inter- and intra-cellular communication and differentiation.
Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
Authors: Shoolingin-Jordan P.M. , Al-Dbass A. , McNeill L.A. , Sarwar M. , Butler D.
Published: June 2004

Porphobilinogen deaminase mutants that cause acute intermittent porphyria have been investigated as recombinant proteins expressed in Escherichia coli, yielding important insight into the mechanism of dipyrromethane cofactor assembly and tetrapyrrole chain polymerization. A mutation that affects a key catalytic residue, D99G, results in an inactive holo-protein that exists as a complex with two substrate molecules covalently bound to the dipyrromethane cofactor arising from the reaction between the apo-protein and pre-uroporphyrinogen. The R149Q mutant is also devoid of catalytic activity but the mutant protein is unable to assemble the dipyrromethane cofactor from pre-uroporphyrinogen and persists as an unstable, heat-labile apo-protein. The mutant, R173Q, has very low activity and, like R149Q, also exhibits largely as an apo-protein. The inability to reconstitute either R149Q or R173Q with exogenous pre-uroporphyrinogen confirms the importance of these two arginine residues for dipyrromethane cofactor assembly. In contrast, the mutant R167Q exists as a holo-enzyme but the catalytic cycle is severely compromised, leading to the accumulation of stable enzyme–substrate intermediates from the catalytic cycle.
Introduction to mannan-binding lectin
Authors: Kilpatrick D.C.
Published: June 2004

Mannan-binding lectin (MBL) was first discovered as a plasma opsonin for baker's yeast and was independently characterized biochemically. It belongs to the small subfamily of collectins: C-type lectins possessing a collagen-like domain. MBL is synthesized by the liver and secreted into the bloodstream. It is believed to be an important component of innate immunity, acting as an ante-antibody and/or as a disease modifier. It is thought to influence disorders as diverse as meningococcal disease, rheumatoid arthritis, cystic fibrosis and recurrent miscarriage. Lack of MBL may be most relevant in the context of a co-existing secondary immune deficiency. Replacement therapy, first carried out 30 years ago with unfractionated plasma, appears promising. The development of a recombinant product should permit the extension of MBL therapy to randomized clinical trials of sufficient size to provide clear evidence about the physiological significance of this intriguing glycoprotein.
Anti-microbial activities of mannose-binding lectin
Authors: Jack D.L. , Turner M.W.
Published: June 2004

Mannose-binding lectin (MBL; also known as mannan-binding lectin) is involved in first-line defence by binding to bacteria, viruses, protozoa and helminths through a pattern-recognition mode of detection and then initiating a range of host responses. Currently, we have been unable to extrapolate from what we know of the biochemistry of MBL binding to predict accurately the interaction of MBL with individual micro-organisms; even subtle surface alterations have been shown to have an extensive impact on MBL-mediated recognition of pathogens. MBL has a major protective effect through activation of the complement system via MBL-associated serine proteases (MASPs). This can cause the lysis of Gram-negative bacteria and also opsonize a wide spectrum of potential pathogens for phagocytosis. MBL may also influence phagocytosis in the absence of complement activation through an interaction with one or more collectin receptors. This may also be the basis for a direct effect of the protein on inflammatory responses. MBL can alter the function of microbial structures, such as gp120 of HIV, to prevent infection. The protein may also interact with the components of other cascade systems such as the clotting system, which will have a role in microbial pathogenesis. An understanding of these basic mechanisms will be vital if we are to use purified or recombinant MBL in therapeutic applications.
Recombinant mannan-binding lectin (MBL) for therapy
Authors: Jensenius J.C. , Jensen P.H. , McGuire K. , Larsen J.L. , Thiel S.
Published: June 2004

Mannan-binding lectin (MBL) is a plasma protein involved in the innate immune response. It binds to a number of micro-organisms and promotes killing of these through complement activation either directly or through opsonization. Clinical evidence indicates that in a variety of situations genetically determined low MBL levels are associated with increased susceptibility to infections. Infusions of plasma-derived MBL into MBL-deficient individuals was found to be safe in preliminary trials, but we considered that sufficient production and product safety could only be achieved through synthesis of recombinant MBL. A transfected human cell line produces MBL showing the same biological activity as plasma-derived MBL, and an essentially identical profile on MS. The production has been scaled up and clinical trials will start this year.
Infusion of plasma-derived mannan-binding lectin (MBL) into MBL-deficient humans
Authors: Valdimarsson H.
Published: June 2004

Our first experience of mannan-binding lectin (MBL)-replacement therapy was with a patient experiencing recurrent erythema multiforme associated with reactivation of herpes simplex virus; his erythematous eruptions could be controlled with infusions of fresh frozen plasma containing MBL, but not with plasma lacking MBL. Some years later, we treated a young girl with recurrent, debilitating infections with purified MBL; this was also followed by a dramatic clinical improvement. We have now carried out a phase I clinical trial on 20 MBL-deficient, but healthy, adult volunteers. The MBL was prepared by the State Serum Institute in Copenhagen, Denmark, from blood donor plasma. Each volunteer received a total of 18 mg of MBL in three 6-mg doses given intravenously once a week over 3 weeks. The volunteers were monitored closely after each infusion and no adverse clinical or laboratory effects were observed. Laboratory parameters included C-reactive protein, various complement components, and antibodies to MBL, HIV and hepatitis viruses. C3a (the anaphylotoxin derived from complement component C3) was monitored for signs of complement activation, but no significant infusion-associated fluctuations were observed. Serum levels of MBL after each 6-mg infusion ranged between 1200 and 2500 ng/ml. The half-life of the infused MBL was about 70 h, or 3 days. It was concluded that infusion of purified MBL manufactured by the Danish State Serum Institute is a safe procedure. However, adults may have to be given 6 mg or more at least twice weekly to maintain protective plasma MBL levels in MBL-deficient individuals.
Mannan-binding lectin (MBL) serum levels and post-operative infections
Authors: Siassi M. , Hohenberger W. , Riese J.
Published: June 2004

Mannan-binding lectin (MBL) is a central component of the innate immune system. Here we investigated the role of MBL in surgical patients during the peri-operative phase. Basal and post-operative (days 1–3 post-surgery) serum samples were obtained prospectively from 156 patients undergoing major elective gastrointestinal surgery for malignant disease. In contrast to procalcitonin (a typical acute-phase protein), there was no significant difference in serum MBL between pre- and post-operative samples (P=0.62). Nevertheless, patients who developed post-operative infections showed significantly lower pre- and post-operative MBL levels than those who did not (P=0.013 and P=0.005, respectively). There was no significant difference in pre-operative procalcitonin between the two groups (P=0.56). We conclude (i) that serum MBL levels did not respond immediately to surgical trauma, and (ii) that lower MBL levels were associated with an increased occurrence of post-operative infections. Studies on larger patient groups are necessary, however, to assess the value of MBL measurements in identifying patients at risk of post-operative complications.
Consensus statement on the future of mannan-binding lectin (MBL)-replacement therapy
Authors: Kilpatrick D.C.
Published: June 2004

Prepared by David C. Kilpatrick on behalf of the speakers and delegates. There follows a consensus statement on the future of mannan-binding lectin replacement therapy to ‘wrap up’ this series of articles.
Expression of BPI (bactericidal/permeability-increasing protein) in human mucosal epithelia
Authors: Levy O. , Canny G. , Serhan C.N. , Colgan S.P.
Published: June 2004

Among the antimicrobial proteins and peptides of humans is the cationic 55 kDa bactericidal/permeability-increasing protein (BPI), which possesses antibacterial, endotoxin-neutalizing and opsonic activity against Gram-negative bacteria. Although identified originally as an abundant constituent of neutrophil granules, we have recently identified functional expression of BPI by human mucosal epithelia. BPI expression was markedly up-regulated by exposure of epithelia to lipoxins, endogenous anti-inflammatory eicosanoids that are generated in vivo in the context of aspirin treatment (aspirin-triggered lipoxins). Epithelial BPI was found to be surface expressed and fully functional, as measured by antibacterial activity against Salmonella typhimurium as well as lipopolysaccharide (LPS; endotoxin)-neutralizing activity. These results suggest a role for BPI as an effector of epithelial antibacterial activity and as a modulator of epithelial responses to LPS. Both BPI and the lipoxins are currently the subject of intensive biopharmaceutical development, raising the possibility that therapeutic use of BPI or modulation of epithelial BPI expression may be a useful adjunctive therapy for conditions in which epithelial inflammation is associated with Gram-negative infections and/or endotoxin.
Comparative analysis of the PLUNC (palate, lung and nasal epithelium clone) protein families
Authors: Bingle C.D. , Craven C.J.
Published: June 2004

PLUNC (palate, lung and nasal epithelium clone) is a small, secreted protein that is expressed in the oropharynx and upper airways of humans, mice and rats. We have described a family of at least 14 PLUNC genes localized on chromosome 20 (in humans), 2 (in mice) or 3 (in rats). These rapidly evolving proteins are structurally related to lipopolysaccharide-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI). In the present analysis we comment on the comparative aspects of this protein family, which may function to protect epithelial surfaces from pathogenic micro-organisms.
Regulation of the exocytotic machinery by cAMP-dependent protein kinase: implications for presynaptic plasticity
Authors: Evans G.J.O. , Morgan A.
Published: June 2004

For over a decade, the enhancement of regulated exocytosis by cAMP-dependent protein kinase (PKA) has remained unexplained at the molecular level. The fact that this phenomenon has been observed in such a wide variety of secretory cell types, from pancreatic β-cells to neurons, suggests that it is an important and fundamental mechanism. Extensive analysis of the phosphorylation of exocytotic proteins has yielded few substrates of PKA in vitro, and fewer still have had physiological effects attributed to their phosphorylation. Here we review two proteins that do fulfil these criteria: the synaptic vesicle proteins cysteine string protein (CSP) and Snapin. Phosphorylation of these proteins by PKA produces changes in their respective protein–protein interactions, and has been attributed to modulation of the vesicle priming (Snapin) and vesicle fusion (CSP) stages of exocytosis. We also discuss how the function of CSP and Snapin phosphorylation might fit into an interesting aspect of the PKA-dependent enhancement of exocytosis: presynaptic plasticity in the brain.
Neuronal calcium sensor-1: a multifunctional regulator of secretion
Authors: Hilfiker S.
Published: June 2004

Ca2+ ions play a crucial role not only as the trigger for neurotransmitter release, but also in other aspects of brain function, such as short-term and long-term modulation of synaptic efficacy, which may underlie certain forms of learning and memory. The actions of Ca2+ are mediated by Ca2+-binding proteins, including a group of proteins known as neuronal calcium sensor (NCS) proteins. The NCS family includes NCS-1, visinin-like proteins, recoverins, guanylate cyclase-activating proteins and potassium channel-interacting proteins. Some members of this family, such as recoverin and guanylate cyclase-activating protein, are only expressed in photoreceptor cells and have been implicated in the control of visual transduction pathways, while the functional roles of the other members are largely unknown. NCS-1 was originally identified in Drosophila in a screen for neuronal hyperexcitability mutants. NCS-1 is an N-terminally myristoylated protein that contains four EF-hand motifs, three of which are able to bind Ca2+ in the submicromolar range. Overexpression of NCS-1 has been shown to enhance evoked neurotransmitter release, paired-pulse facilitation and exocytosis in several neuronal and neuroendocrine cell types. Recent experiments suggest that NCS-1 interacts directly with phosphatidylinositol 4-hydroxykinase in yeast as well as mammalian cells, suggesting that it may enhance neuronal secretion by modulating cellular trafficking steps in a phosphoinositide-dependent manner. In contrast, an involvement of NCS-1 in the expression and regulation of voltage-gated Ca2+ channels and K+ channels has also been proposed, which may be attributed, at least in part, to the effects of NCS-1 on vesicular trafficking pathways. The present review describes current knowledge about the cellular functions and molecular mechanisms by which NCS-1 may regulate neurotransmitter release.
Early events in the trafficking of N-methyl-d-aspartate (NMDA) receptors
Authors: Wenthold R.J. , Sans N. , Standley S. , Prybylowski K. , Petralia R.S.
Published: June 2004

The N-methyl-d-aspartate (NMDA) receptor plays a central role at excitatory synapses where it has been implicated in multiple functions associated with synaptic plasticity. While this receptor has been intensely studied with respect to its physiology and pharmacology, its cell-biological properties, such as subunit assembly, post-translational processing and trafficking in neurons, are only beginning to be addressed. Critical to many of the functions of the NMDA receptor are the multiple proteins with which it interacts. While these interactions have been most thoroughly studied with respect to the receptor at the synapse, the same proteins may also interact with the receptor much earlier in its biosynthetic pathway and play important roles in receptor trafficking from the endoplasmic reticulum to the synapse.
General considerations for proteolytic cascades
Authors: Amour A. , Bird M. , Chaudry L. , Deadman J. , Hayes D. , Kay C.
Published: June 2004

Proteases are involved in the regulation of a wide variety of essential physiological processes, often by participating in a highly orchestrated sequence of events termed a ‘proteolytic cascade’. Four major proteolytic cascades with disease relevance are candidates for therapeutic intervention, namely caspase-mediated apoptosis, blood coagulation, the matrix metalloproteinase cascade and the complement cascade. Understanding the various steps involved in the functioning of a cascade is key to deciding possible points of intervention for the design of potential drug molecules. This brief review illustrates some of the common features of proteolytic cascades using the blood coagulation pathway as an example.
Matrix metalloprotease inhibitors: design from structure
Authors: Borkakoti N.
Published: June 2004

The zinc- and calcium-dependent family of proteins called the MMPs (matrix metalloproteases) are collectively responsible for the degradation of the extracellular matrix. The enzymes are synthesized as zymogens, and under physiological conditions are selectively regulated by endogenous inhibitors. An imbalance between the active enzymes and their natural inhibitors leads to the accelerated destruction of connective tissue associated with the pathology of diseases such as arthritis, cancer, multiple sclerosis and cardiovascular diseases. The potential for using specific enzyme inhibitors as therapeutic agents to redress this balance has led to intensive research focused on the design, synthesis and molecular deciphering of low-molecular-mass inhibitors of this family of proteins. The design of early MMP inhibitors was based on the scissile site sequence of peptide substrates, with moieties customized to chelate the critical zinc ion at the enzymes' active site. These initial efforts were supported by X-ray and NMR data on MMP complexes, exploiting sequence and structural differences in the principal specificity pocket of the enzymes, leading to subtype-selective MMP inhibitors. This review will provide a critical appraisal of the design principles that have been utilized in generating molecules that inhibit MMPs, and explore issues relevant to obtaining clinical efficacy of MMP inhibitor-based therapies.
Improved RNA cleavage by LNAzyme derivatives of DNAzymes
Authors: Vester B. , Lundberg L.B. , Sørensen M.D. , Babu B.R. , Douthwaite S. , Wengel J.
Published: June 2004

Specific cleavage of RNA is catalysed by short oligodeoxynucleotides termed DNAzymes. DNAzymes consist of two binding arms that hybridize to a predetermined RNA sequence and a catalytic core that cleaves a phosphodiester bond held between the binding arms. DNAzymes are exemplified by the well-studied 10-23 DNAzyme, which compared with protein ribonucleases is highly specific, albeit slow. Here we report a significant improvement in cleavage kinetics, while maintaining specificity, by incorporation of LNA (locked nucleic acid) and α-l-LNA nucleotides into the binding arms of 10-23 DNAzyme. DNAzymes modified in this way (LNAzymes) enhance cleavage of a phosphodiester bond presented in a short RNA substrate as well as in longer and highly structured substrates, and efficient cleavage is maintained from single- to multiple-turnover conditions. Analysis of the cleavage reaction indicates that substrate hybridization is boosted by the presence of the locked residues within the LNAzymes, while no apparent change occurs in the catalytic strand-scission step.
Semi-synthetic DNA–protein conjugates: novel tools in analytics and nanobiotechnology
Authors: Niemeyer C.M.
Published: June 2004

This article reports on the syntheses, characterization and applications of semi-synthetic conjugates composed of nucleic acids, proteins and inorganic nanoparticles. For example, self-assembled oligomeric networks consisting of streptavidin and double-stranded DNA are applicable as reagents in immunoassays, model systems for ion-switchable nanoparticle networks as well as nanometer-scaled ‘soft material’ standards for scanning probe microscopy. Covalent conjugates of single-stranded DNA and streptavidin are utilized as biomolecular adapters for the immobilization of biotinylated macromolecules at solid substrates via nucleic acid hybridization. This ‘DNA-directed immobilization’ allows for reversible and site-selective functionalization of solid substrates with metal and semiconductor nanoparticles or, vice versa, for the DNA-directed functionalization of gold nanoparticles with proteins, such as immunoglobulins and enzymes. This approach is applicable for the detection of chip-immobilized antigens. Moreover, covalent DNA–protein conjugates allow for their selective positioning along single-stranded nucleic acids, and thus for the construction of nanometre-scale assemblies composed of proteins and/or nanoclusters. Examples include the fabrication of functional biometallic nanostructures from gold nanoparticles and antibodies, applicable as diagnostic tools in bioanalytics.
Membrane cholesterol and the regulation of signal transduction
Authors: Fielding C.J. , Fielding P.E.
Published: June 2004

The plasma membrane of mammalian cells consists of microdomains differing in lipid and protein composition. Two distinct classes of cholesterol/sphingolipid microdomain (caveolae and lipid rafts) are assembly points for transmembrane signalling complexes. Recent evidence suggests that transient changes in cholesterol content may be important in regulating signal transduction.
The genes and proteins of atherogenic lipoprotein production
Authors: Shoulders C.C. , Naoumova R.P.
Published: June 2004

Dietary fat provides a major source of nutrition, but may in excess lead to obesity, insulin resistance, high blood cholesterol levels and atherosclerosis. Here we report molecular events that co-ordinate whole-body lipid homoeostasis from insects to humans, viewed in the context of rare and common genetic disorders of apolipoprotein B-containing lipoprotein production.
Chylomicron metabolism
Authors: Redgrave T.G.
Published: June 2004

Chylomicrons are the ‘orphans’ of the lipoprotein family. Difficulty of measurement has impeded understanding of their metabolism. Plasma concentrations of chylomicrons and chylomicron remnants give no insight into the magnitude of substrate flux through these pathways. A defect in clearance of chylomicron remnants is probably an indication of a more generalized defect in lipoprotein metabolism. Accumulating evidence supports a relationship between abnormalities in the clearance from plasma of chylomicron remnants and accelerated progression of atherosclerosis. Methods using stable isotopes in appropriately formulated emulsions are providing valuable new information.
LXR (liver X receptor) and HNF-4 (hepatocyte nuclear factor-4): key regulators in reverse cholesterol transport
Authors: Crestani M. , De Fabiani E. , Caruso D. , Mitro N. , Gilardi F. , Vigil Chacon A.B. , Patelli R. , Godio C. , Galli G.
Published: June 2004

Cholesterol homoeostasis is the result of the fine tuning between intake and disposal of this molecule. High levels of cholesterol in the blood are detrimental as they may lead to excessive accumulation in vessel walls, a condition predisposing to the development of atherosclerotic lesions. Cholesterol is removed from the vessel wall and transported to the liver through a process called reverse cholesterol transport. Nuclear receptors are among the most important transcription factors regulating genes involved in different steps of reverse cholesterol transport. Here, we discuss the role of the nuclear receptors LXR (liver X receptor) and HNF-4α (hepatocyte nuclear factor-4α) in different steps of reverse cholesterol transport. LXR controls the transcription of crucial genes in cholesterol efflux from macrophages and its transport to the liver, such as ABCA1 (ATP binding cassette A1), CYP27A1 (sterol 27-hydroxylase), CLA-1 (scavenger receptor type B1) and apolipoprotein E. Some oxysterols present in oxidized low-density lipoproteins and proinflammatory cytokines modulate the activity of LXR by antagonizing the effect of activators of this receptor, thus contributing to cholesterol accumulation in macrophages. Bile acid synthesis, which represents the final step of reverse cholesterol transport, is transcriptionally regulated by several nuclear receptors at the level of the liver-specific cytochrome P450 cholesterol 7α-hydroxylase (CYP7A1), the rate-limiting enzyme of this metabolic pathway. Bile acids returning to the liver through the enterohepatic circulation down-regulate CYP7A1 transcription via the bile acid sensors farnesoid X receptor and HNF-4α. Based on this evidence, these nuclear receptors are candidate targets of new drugs for the treatment and prevention of atherosclerotic disease.
Chylomicron-remnant-like particles modify production of vasoactive mediators by endothelial cells
Authors: Evans M. , Berhane Y. , Botham K.M. , Elliott J. , Wheeler-Jones C.P.D.
Published: June 2004

Endothelial-cell dysfunction is a critical initiating event in the pathogenesis of atherosclerosis. Although there is evidence to suggest that chylomicron remnants (CMRs), lipoproteins derived from the diet, influence endothelial-cell function to generate a pro-atherogenic phenotype, the mechanisms involved remain undefined. We have examined the effects of CMR-like particles (CMR-LPs) on human endothelial-cell function, focusing on the cyclo-oxygenase (COX) and nitric oxide synthase (NOS) pathways. CMR-LPs strongly enhanced the expression of the inducible cyclo-oxygenase COX-2 and increased prostacyclin synthesis in a biphasic manner. Studies with the COX-2-selective inhibitor NS-398 confirmed the COX-2 dependency of the later increase in prostanoid production. Pre-incubation with CMR-LPs reduced basal and thrombin-stimulated cGMP generation, whereas expression of endothelial NOS was not modified by remnant treatment.
B-cell antigen receptor activates transcription factors NFAT (nuclear factor of activated T-cells) and NF-κB (nuclear factor κB) via a mechanism that involves diacylglycerol
Authors: Antony P. , Petro J.B. , Carlesso G. , Shinners N.P. , Lowe J. , Khan W.N.
Published: June 2004

Engagement of the B-cell antigen receptor (BCR) induces the activation of various transcription factors, including NFAT (nuclear factor of activated T-cells) and NF-κB (nuclear factor κB), which participate in long-term biological responses such as proliferation, survival and differentiation of B-lymphocytes. We addressed the biochemical basis of this process using the DT40 chicken B-cell lymphoma. We discovered that Bruton's tyrosine kinase (BTK) and phospholipase C-γ2 (PLC-γ2) are required to activate NFAT and NF-κB, and to produce the lipid second messenger diacylglycerol in response to BCR cross-linking. Therefore the functional integrity of the BTK/PLC-γ2/diacylglycerol signalling axis is crucial for BCR-directed activation of both transcription factors NFAT and NF-κB.
Caveolins and membrane cholesterol
Authors: Ikonen E. , Heino S. , Lusa S.
Published: June 2004

Caveolae (small plasma membrane invaginations) and their coat proteins, caveolins, have attracted the attention of researchers in diverse fields, including cell biology, cardiovascular and cancer research. The tight association between caveolin and cholesterol governs the biochemical behaviour of caveolae and is emerging as an important characteristic in a number of processes assigned to these multifunctional organelles. In this review, selected aspects of the caveolin–cholesterol association and its potential functional implications are discussed.