Evolution of protein function, from a structural perspective

The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.

Receptor-mediated and enzyme-dependent targeting of cytotoxic anticancer drugs

This review is a survey of various approaches to targeting cytotoxic anticancer drugs to tumors primarily through biomolecules expressed by cancer cells or associated vasculature and stroma. These include monoclonal antibody immunoconjugates; enzyme prodrug therapies, such as antibody-directed enzyme prodrug therapy, gene-directed enzyme prodrug therapy, and bacterial-directed enzyme prodrug therapy; and metabolism-based therapies that seek to exploit increased tumor expression of, e.g., proteases, low-density lipoprotein receptors, hormones, and adhesion molecules. Following a discussion of factors that positively and negatively affect drug delivery to solid tumors, we concentrate on a mechanistic understanding of selective drug release or generation at the tumor site.

Antioxidants and exercise

Muscular exercise results in an increased production of radicals and other forms of reactive oxygen species. Further more, growing evidence implicates cytotoxic ROS as an underlying cause in exercise-induced disturbances in muscle redox status that could result in muscle fatigue or injury. Muscle cells contain complex cellular defense mechanisms to minimize the risk for oxidative injury. Two major classes of endogenous protective mechanisms work together to reduce the harmful effects of oxidants in the cell: (1) enzymatic and (2) nonenzymatic antioxidants. Key antioxidant enzymes include superoxide dismutase, glutathione peroxidase, and catalase. These enzymes are responsible for removing superoxide radicals, hydrogen peroxide or organic hydroperoxides, and hydrogen peroxide, respectively. Important nonenzymatic antioxidants include vitamins E and C, beta-carotene, GSH, uric acid, ubiquinone, and bilirubin. Vitamin E, beta-carotene, and ubiquinone are located in lipid regions of the cell, whereas uric acid, GSH, and bilirubin are in aqueous compartments of the cell. Although numerous animal experiments have demonstrated that the addition of antioxidants can improve muscular performance, to date, limited evidence shows that dietary supplementation with antioxidants improves human performance. This is an important area for future research.

Symposium overview: Characterization of xenobiotic metabolizing enzyme function using heterologous expression systems

Genetically modified cell lines can be very useful models for assessing the toxicologic effects of modulation of expression of individual gene products in comparison to their isogenic parental control cell lines. This symposium begins with an overview of general issues related to development and utilization of model systems created by transfection of cell lines to induce elevated expression of metabolic enzymes of toxicologic relevance. Selected studies that illustrate the heterologous expression rationale and various approaches to transgenic-cell model construction are represented. Results to date with cells engineered to express specific transfected genes are discussed, with emphasis on the effects of expression of selected phase I or phase II enzymes on cellular sensitivity to several toxic end-points. The individual sections highlight the utility of these model cell lines for examining the role of enzyme catalysis and function in metabolism of biologically active xenobiotic or endobiotic compounds of interest in toxicology. Both activating and detoxifying enzymes are discussed, with principal emphasis on the latter. This symposium includes talks on transfected cells that express aldehyde dehydrogenases, superoxide dismutase, UDP-glycosyltransferases, glutathione transferases, and cytochrome P450 isozymes. In addition to the general toxicologic utility and advantages of these genetically engineered cell lines, this overview emphasizes their particular contributions to the insights obtained to date with the specific model cell lines.

Adaptive responses in Chlamydomonas reinhardtii

The photosynthetic single cellular alga Chlamydomonas reinhardtii has been used as a model organism to examine in detail the physiological, biochemical and molecular processes of photosynthesis, flagella synthesis and movement, mineral stress, interactions between nucleus, chloroplasts and mitochondria and other processes. In this review we summarize part of the current knowledge on adaptive responses in C. reinhardtii when it is exposed to oxidative stress and to changes in light intensity, concentration of minerals, herbicides and metals. The individual responses are linked in order to understand the response of the cell, which is continuously subjected to fluctuations, as a whole.

The development of microfabricated biocatalytic fuel cells

The production of electricity by biocatalytic fuel cells has been feasible for almost two decades and can produce electric power at a practical level. These fuel cells use immobilized microorganisms or enzymes as catalysts, and glucose as a fuel. A microfabricated enzyme battery has recently been made that is designed to function as a power supply for microsurgery robots or artificial organs.

The CATH Database provides insights into protein structure/function relationships

We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.

Why do antimicrobial agents become ineffectual?

Antibiotic resistance has evolved over the past 50 years from a merely microbiological curiosity to a serious medical problem in hospitals all over the world. Resistance has been reported in almost all species of gram-positive and -negative bacteria to various classes of antibiotics including recently developed ones. Bacteria acquire resistance by reducing permeability and intracellular accumulation, by alteration of targets of antibiotic action, and by enzymatic modification of antibiotics. Inappropriate use of an antibiotic selects resistant strains much more frequently. Once resistant bacteria has emerged, the resistance can be transferred to other bacteria by various mechanisms, resulting in multiresistant strains. MRSA is one of the typical multiresistant nosocomial pathogens. A study of the PFGE pattern of endonuclease-digested chromosomal DNA showed that MRSA of a few clones were disseminated among newborns in the NICU of a Japanese hospital. In this regard, it is important to choose appropriate antibiotics and then after some time, to change to other classes to reduce the selection of resistant strains. Since the development of epoch-making new antibiotics is not expected in the near future, it has become very important to use existing antibiotics prudently based on mechanisms of antibiotic action and bacterial resistance. Control of nosocomial infection is also very important to reduce further spread of resistant bacteria.

Porphyrias

The porphyrias are a heterogeneous group of metabolic disorders caused by genetic defects of the enzymes involved in heme biosynthesis. The diseases are characterized by excessive accumulation and excretion of porphyrin or porphyrin precursors. The disorders have been classified as cutaneous, hepatic, or neuropsychiatric according to the organ system involved. This review describes the enzymes of the heme biosynthetic pathway along with the clinical features and management of the porphyrias.

[Vitamin K: biochemistry, function, and deficiency. Review]

Vitamin K is a cofactor for the synthesis of blood coagulation Factors II, VII, IX and X, and inhibitors such as Protein C and S and bone matrix protein. Its active form is a coenzyme in the glutamic acid carboxylation. Vitamin K-dependent factors form enzymatic complexes with calcium and membrane phospholipids. The insufficiency of gamma glutamic carboxylation impairs the hemostatic function. Hereditary deficiencies, antibiotics and oral anticoagulants, decrease the capacity of complex formation giving way to hemorrhage or thrombosis, or bone mass disturbances which are easily treated with administration of Vitamin K. The main causes of Vitamin K deficiency are lack of hepatic storage in newborns, liver insufficiency, malabsorption, dietetic deficiency, therapy with the antibiotics and coumarin administration. For the study of Vitamin K there are methods to measure the Vit K dependent proteins and as well methods to measure specifically the quinonas.

Effect of hypoxia on the activity and binding of glycolytic and associated enzymes in sea scorpion tissues

The effect of hypoxia on the levels of glycogen, glucose and lactate as well as the activities and binding of glycolytic and associated enzymes to subcellular structures was studied in brain, liver and white muscle of the teleost fish, Scorpaena porcus. Hypoxia exposure decreased glucose levels in liver from 2.53 to 1.70 mumol/g wet weight and in muscle led to its increase from 3.64 to 25.1 mumol/g wet weight. Maximal activities of several enzymes in brain were increased by hypoxia: hexokinase by 23%, phosphoglucoisomerase by 47% and phosphofructokinase (PFK) by 56%. However, activities of other enzymes in brain as well as enzymes in liver and white muscle were largely unchanged or decreased during experimental hypoxia. Glycolytic enzymes in all three tissues were partitioned between soluble and particulate-bound forms. In several cases, the percentage of bound enzymes was reduced during hypoxia; bound aldolase in brain was reduced from 36.4 to 30.3% whereas glucose-6-phosphate dehydrogenase fell from 55.7 to 28.7% bound. In muscle PFK was reduced from 57.4 to 41.7% bound. Oppositely, the proportion of bound aldolase and triosephosphate isomerase increased in hypoxic muscle. Phosphoglucomutase did not appear to occur in a bound form in liver and bound phosphoglucomutase disappeared in muscle during hypoxia exposure. Anoxia exposure also led to the disappearance of bound fructose-1,6-bisphosphatase in liver, whereas a bound fraction of this enzyme appeared in white muscle of anoxic animals. The possible function of reversible binding of glycolytic enzymes to subcellular structures as a regulatory mechanism of carbohydrate metabolism is discussed.

Plasma lipoproteins support prothrombinase and other procoagulant enzymatic complexes

The prothrombinase complex (factor [F]Xa, FVa, calcium ions, and lipid membrane) converts prothrombin to thrombin (FIIa). To determine whether plasma lipoproteins could provide a physiologically relevant surface, we determined the rates of FIIa production by using purified human coagulation factors, and isolated fasting plasma lipoproteins from healthy donors. In the presence of 5 nmol/L FVa, 5 nmol/L FXa, and 1.4 micromol/L prothrombin, physiological levels of very low density lipoprotein (VLDL) (0.45 to 0.9 mmol/L triglyceride, or 100 to 200 micromol/L phospholipid) yielded rates of 2 to 8 nmol Flla x L(-1) x s(-1) in a donor-dependent manner. Low density lipoprotein (LDL) and high density lipoprotein (HDL) also supported prothrombinase but at much lower rates (< or =1.0 nmol FIIa x L(-1) x s[-1]). For comparison, VLDL at 2 mmol/L triglyceride yielded approximately 50% the activity of 2X10(8) thrombin-activated platelets per milliliter. Although the FIIa production rate was slower on VLDL than on synthetic phosphatidylcholine/phosphatidylsenne vesicles (approximately 50 nmol FIIa x L(-1) x s[-1]), the prothrombin Km values were similar, 0.8 and 0.5 micromol/L, respectively. Extracted VLDL lipids supported rates approaching those of phosphatidylcholine/phosphatidylserine vesicles, indicating the importance of the intact VLDL conformation. However, the presence of VLDL-associated, factor-specific inhibitors was ruled out by titration experiments, suggesting a key role for lipid organization. VLDL also supported FIIa generation in an assay system comprising 0.1 nmol/L FVIIa; 0.55 nmol/L tissue factor; physiological levels of FV, FVIII, FIX, and FX; and prothrombin (3 nmol/L FIIa x L(-1) x s[-1]). These results indicate that isolated human VLDL can support all the components of the extrinsic coagulation pathway, yielding physiologically relevant rates of thrombin generation in a donor-dependent manner. This support is dependent on the intact lipoprotein structure and does not appear to be regulated by specific VLDL-associated inhibitors. Further studies are needed to determine the extent of this activity in vivo.

Xenobiotic metabolizing enzymes of the kidney

The kidney possesses most of the common xenobiotic metabolizing enzymes, and is thus able to make an important contribution to the body's metabolism of drugs and foreign compounds. An overview of the renal localization, catalytic activity, developmental regulation, induction, and sex and species differences for the key enzymes involved in phase I and phase II of xenobiotic metabolism is presented. In general, the catalytic activities of the various renal enzymes are lower than those of the liver, although there are exceptions, such as the enzymes involved in the processing of glutathione conjugates to their mercapturic acids. Xenobiotic metabolizing enzymes are not evenly distributed along the nephron; cytochromes P-450 and those enzymes involved in the conjugation of glutathione, glucuronic acid, or sulfate are primarily localized in the proximal tubules. However, some isozymes of cytochrome(s) P-450 and glutathione S-transferases are selectively localized in cells of the thick ascending limb and distal tubules, whereas prostaglandin H synthase is concentrated in the collecting ducts in the medulla. Thus, the proximal tubule, the principal site of xenobiotic biotransformation, is particularly susceptible to chemical insult, and the localization of prostaglandin synthase in the inner medulla and papilla may be a contributary factor to the toxicity produced by chemicals in this part of the nephron. Many of the enzymes discussed, in addition to metabolizing foreign compounds, have important endogenous functions in the kidney, such as the regulation of salt and water balance and the synthesis of vitamin D.

How does Helicobacter pylori cause mucosal damage? Direct mechanisms

Helicobacter pylori-associated gastritis is characterized by an abundant inflammatory response and gastric epithelial cell injury. Adherence of H. pylori to gastric epithelial cells seems to be required for bacterial colonization of the gastric mucosa. Attachment of the bacterium to polarized gastric epithelial cells causes damage to microvilli and stimulates actin polymerization, which is associated with adherence pedestal formation. Studies suggest that H. pylori directly contributes to the injury of gastric epithelial cells by the elaboration of cytotoxic factors. The first toxin identified from H. pylori strains, known as vacuolating cytotoxin, induces vacuole formation in eukaryotic cells. Elaborated enzymes by H. pylori may also contribute directly to epithelial cell injury. Ammonia produced through urease activity may be toxic to gastric epithelial cells. H. pylori protease and lipase degrade gastric mucus and disrupt the phospholipid-rich layer at the apical epithelial cell surface, allowing for cell injury from back diffusion of gastric acid. This cell injury may lead to cell death, believed to result from induction of apoptosis. There are sufficient data to suggest that H. pylori, through direct pathogenic mechanisms, contributes significantly to the gastric mucosal injury associated with this infection, and may enhance the susceptibility of gastric epithelial cells to carcinogenic conversion.

Mechanisms of signaling and related enzymes

Most enzymes involved in cell signaling, such as protein kinases, protein phosphatases, GTPases, and nucleotide cyclases catalyze nucleophilic substitutions at phosphorus. When possible, the mechanisms of such enzymes are most clearly described quantitatively in terms of how associative or dissociative they are. The mechanisms of cell signaling enzymes range from < or = 8% associative (cAMP-dependent protein kinase) to approximately 50% associative (G protein Gi alpha 1). Their catalytic powers range from 10(5.7) (p21ras) to 10(11.7) (lambda Ser-Thr protein phosphatase), usually comparable in magnitude with those of nonsignaling enzymes of the same mechanistic class. Exceptions are G proteins, which are 10(3)- to 10(5)-fold poorer catalysts than F1 and myosin ATPases. The lower catalytic powers of G proteins may be ascribed to the absence of general base catalysis, and additionally in the case of p21ras, to the absence of a catalytic Arg residue, which interacts with the transition state. From kinetic studies of mutant and metal ion substituted enzymes, the catalytic powers of cell signaling and related enzymes can be rationalized quantitatively by factors contributed by metal ion catalysis (> or = 10(5), general acid catalysis (approximately 10(3 +/- 1)), general base catalysis (approximately 10(3 +/- 1)), and transition-state stabilization by cationic and hydrogen bond donating residues (approximately 10(3 +/- 1)).

Enzyme adaptations of human skeletal muscle during bicycle short-sprint training and detraining

The effect of sprint training and detraining on supramaximal performances was studied in relation to muscle enzyme adaptations in eight students trained four times a week for 9 weeks on a cycle ergometer. The subjects were tested for peak oxygen uptake (VO2peak), maximal aerobic power (MAP) and maximal short-term power output (Wmax) before and after training and after 7 weeks of detraining. During these periods, biopsies were taken from vastus lateralis muscle for the determination of creatine kinase (CK), adenylate kinase (AK), glycogen phosphorylase (PHOS), hexokinase (HK), phosphofructokinase (PFK), lactate dehydrogenase (LDH) and its isozymes, 3-hydroxy-acyl-CoA dehydrogenase (HAD) and citrate synthase (CS) activities. Training induced large improvements in Wmax (28%) with slight increases (3%) in VO2peak (P < 0.10). This was associated with a greater glycolytic potential as shown by higher activities for PHOS (9%), PFK (17%) and LDH (31%) after training, without changes in CK and oxidative markers (CS and HAD). Detraining induced significant decreases in VO2peak (4%), MAP (5%) and oxidative markers (10-16%), while Wmax and the anaerobic potential were maintained at a high level. This suggests a high level in supramaximal power output as a result of a muscle glycogenolytic and glycolytic adaptation. A long interruption in training has negligible effects on short-sprint ability and muscle anaerobic potential. On the other hand, a persistent training stimulus is required to maintain high aerobic capacity and muscle oxidative potential. This may contribute to a rapid return to competitive fitness for sprinters and power athletes.

Age-related changes in the blood-brain barrier

Aging of the cerebral microcirculation results in significant alteration in the blood-brain barrier (BBB). The barrier function appears to remain intact in older animals, although it may be more susceptible to disruption by external factors (hypertension) and drugs (haloperidol). While overall transport processes do not change with age, aging animals and humans have altered BBB function of select carrier mediated transport systems including the transport of choline, glucose, butyrate and triiodothyronine. These age-related changes are the result of either alteration in the carrier molecules or the physiochemical properties of the cerebral microvessels. At the present time, it is not known whether changes in the BBB contribute to the age-related neurodegenerative diseases or are merely epiphenomena of aging.

Altered muscle energy metabolism in post-absorptive patients with chronic renal failure

Skeletal muscle biopsies were performed on 12 healthy sedentary subjects and on 22 non-dyalized chronic renal failure patients (CRF) on a free diet and after overnight fasting. Parathormone, glucagon and insulin were determined at the same time of biopsies. CRF patients showed significantly low ATP and creatine phosphate levels. Regarding enzyme activities, a high hexokinase Vmax was found, while the pyruvate kinase activity was lower than in the control group. For the tricarboxylic acid cycle, citrate synthase, succinate dehydrogenase and malate dehydrogenase activities were higher; total NADH cytochrome c reductase activity was also high, while cytochrome oxidase activity was slightly lower. Both alanine aminotransferase and aspartate aminotransferase activities were considerably high in comparison with the control group. In conclusion, our study revealed a hypermetabolic TCA cycle, but impaired oxidative phosphorylation, which partly explained the reduced ATP concentration. Excessive protein intake and hormonal derangements may play a role in these metabolic changes.

Enzyme adaptation along a heterothermic tissue: the visceral retia mirabilia of the bluefin tuna

We measured enzyme activities along a heterothermic tissue, the visceral retia mirabilia of the bluefin tuna, to test current theories of enzyme temperature adaptation. The heterothermic tissue model is ideal for the study of fundamental temperature adaptation because it eliminates confounding effects of whole animal acclimation. Enzymes were measured at six positions along the rete at four temperatures (15, 20, 25, and 30 degrees C). Five enzymes (aspartate aminotransferase, citrate synthase, glucose-6-phosphate dehydrogenase, glutamate dehydrogenase, and pyruvate kinase) exhibited a significant positive compensatory effect, with activity at the cold end of the rete 1.2-3.1 times higher than at the warm end. Two enzymes (alanine aminotransferase and lactate dehydrogenase) exhibited no significant compensation. On the basis of activation energies of enzymes along the rete, differences in activity were due to differences in enzyme concentration and not isozymes or enzyme modification. Analysis of the compensatory responses of the enzymes in light of their thermal sensitivities leads us to conclude that the pentose phosphate shunt is especially enhanced at the cold end of the rete.

A possible role for enzymes in tumour-cell invasion

The complex molecular and cellular processes of metastatic invasion as well as the anti-invasion possibilities are summarized. Invasion by neoplastic cells is a major obstacle to successful cancer therapy. Enzymes such as hyaluronidase, sialyltransferase, urokinase-type plasminogen activator, plasmin, matrix metalloproteinases, and others, play central roles in the catabolism of extracellular matrix macromolecules. However, this process can be opposed by inhibitors of these enzymes. Both invasion (promoters) and anti-invasion factors (suppressors) need further investigation, to clarify the role of these factors in the aetiology and possibly in the treatment and prognosis of metastatic cancer.

Lessons for joint destruction from animal models

There is growing evidence that tumor necrosis factor-alpha is involved in onset of arthritis, whereas the cartilage destructive process is mainly interleukin-1 driven. Moreover, direct generation of interleukin-1 may occur in the absence of tumor necrosis factor action. This is shown in various arthritis models using neutralizing antibodies, receptor antagonists, and soluble receptors, and similar proof has been provided in cytokine-targeted transgenic and knockout mice. Further evidence for local impact of interleukin-1 is obtained from gene transfer of interleukin-1 receptor agonist to joint tissues, whereas these experiments also underline the therapeutic applicability of this approach. In addition to tumor necrosis factor-alpha and interleukin-1 action, the destructive process appears to be under the control of mediators such as interleukin-6 and -10. Marked cartilage protection can be achieved with additional treatment with interleukin-4 and -10. These modulatory studies also underline the potential uncoupling of inflammatory and destructive processes. Although T cells may drive arthritic processes, it is clear that fibroblasts can cause major destruction in the absence of T cells. Insight in pivotal enzymes primarily involved in cartilage destruction is still limited.