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At least 19 recordsLinked to original sources
PubMed2006

Mechanisms, pathways, and dynamics of excited-state energy flow in self-assembled wheel-and-spoke light-harvesting architectures.

Static and time-resolved optical measurements are reported for two cyclic hexameric porphyrin arrays and their self-assembled complexes with guest chromophores. The hexameric hosts contain zinc porphyrins and 0 or 3 free base (Fb) porphyrins (denoted Zn(6) or Zn(3)Fb(3), respectively). The guests are a tripyridyl arene (TP) and a dipyridyl-substituted free base porphyrin (DPFb), each of which coordinates to zinc porphyrins of a host via pyridyl-zinc dative bonding. Each architecture is designed to have an overall gradient of excited-state energies that affords excitation funneling within the host and ultimately to the guest. Collectively, the studies delineate the various pathways, mechanisms, and rate constants of energy flow among the weakly coupled constituents of the host-guest complexes. The pathways include downhill unidirectional energy transfer between adjacent chromophores, bidirectional energy migration between identical chromophores, and energy transfer between nonadjacent chromophores. The energy transfer to the lowest-energy chromophore(s) within the backbone of a hexameric host (Fb porphyrins in Zn(3)Fb(3) or pyridyl-coordinated zinc porphyrins in Zn(6)*TP and Zn(6)*DPFb) proceeds primarily via a through-bond mechanism; the transfer is rapid (approximately 40 ps depending on the array) and essentially quantitative (>or=98%). The energy transfer from a pyridyl-coordinated zinc porphyrin of the host to the Fb porphyrin guest in the Zn(6)*DPFb complex is almost exclusively Förster through-space in nature; this process is much slower ( approximately 1 ns) and has a lower yield (65%). These studies highlight the utility of cyclic architectures for efficient light harvesting and energy transfer to a designated trapping site.

Journal Article↗
PubMed1975

Effects of pH and thiols on the kinetics of yeast glyoxalase I. An evaluation of the random pathway mechanism.

The disproportionation of alpha-ketoaldehydes, catalyzed by yeast glyoxalase I, has been reported to involve a random pathway mechanism where one branch utilizes the hemimercaptal of glutathione and the alpha-ketoaldehyde in a one-substrate pathway, and the other branch utilizes first glutathione and then the alpha-ketoaldehyde in an ordered two-substrate pathway. The relative importance of the two pathways has been evaluated at 5 degrees in the pH range 3-7, using methylglyoxal and phenylglyoxal as representative aliphatic and aromatic alpha-ketoaldehydes, by comparing initial rates of hemimercaptal formation in the absence of enzyme with initial rates of product formation in the presence of high enzyme concentrations. If the enzyme is not added last, the initial rates of product formation are the same as the initial rates of adduct formation even under conditions where it could be shown that dehydration of the hydrated alpha-ketoaldehyde is not entirely rate determining. If the enzyme is added after hemimercaptal formation, there is a "burst" of product formation equivalent to the amount of hemimercaptal, followed by a slower reaction, consistent with the one-substrate pathway. Additional support for this pathway was obtained from a study of the effects of added thiol reagents on the "burst" kinetics. The broad specificity of yeast glyoxalase I for both aliphatic and aromatic alpha-ketoaldehydes, reflected in Vmax values which are insensitive to the nature of the alpha-ketoaldehyde drops abruptly if the side chain of the alpha-ketoaldehyde is sterically crowded. The hemimercaptal of tert-butylglyoxal has a Vmax 300-fold smaller than Vmax for methylglyoxal; 2,4,6-trimethylphenylglyoxal is essentially inactive as a substrate even though the closely related compound 2,4-dimethylphenylglyoxal is a normal substrate. Analysis of the Vmax and Km (or Ki) values of these alpha-ketoaldehydes suggests that sterically crowded side chains affect both enzyme-substrate formation and the catalytic reaction.

Binding Sites↗
PubMed2000

Cellular and molecular mediators in common pathway mechanisms of chronic renal disease progression.

Injury mechanisms activated by the hemodynamic adaptations to nephron loss are considered to represent a final common pathway that underlies the progressive nature of chronic renal disease. In this article, we review experimental evidence that the induction of cell adhesion molecule, cytokine and profibrotic growth factor gene expression and the resultant renal infiltration by inflammatory cells, especially macrophages, are important components of these common pathway mechanisms. Interventions aimed at inhibiting these mechanisms may offer new treatments for slowing or arresting the progression of chronic renal disease.

Animals↗
PubMed1999

A unique reaction in a common pathway: mechanism and function of chorismate synthase in the shikimate pathway.

Chorismate synthase, the seventh enzyme in the shikimate pathway, catalyzes the transformation of 5-enolpyruvylshikimate 3-phosphate to chorismate which is the last common precursor in the biosynthesis of numerous aromatic compounds in bacteria, fungi and plants. The enzyme has an absolute requirement for reduced FMN as a cofactor, although the 1,4-anti elimination of phosphate and the C(6proR)-hydrogen does not involve a net redox change. The role of the reduced FMN in catalysis has long been elusive. However, recent detailed kinetic and bioorganic approaches have fundamentally advanced our understanding of the mechanism of action, suggesting an initial electron transfer from tightly bound reduced flavin to the substrate, a process which results in C-O bond cleavage. Studies on chorismate synthases from bacteria, fungi and plants revealed that in these organisms the reduced FMN cofactor is made available in different ways to chorismate synthase: chorismate synthases in fungi--in contrast to those in bacteria and plants--carry a second enzymatic activity which enables them to reduce FMN at the expense of NADPH. Yet, as shown by the analysis of the corresponding genes, all chorismate synthases are derived from a common ancestor. However, several issues revolving around the origin of reduced FMN, as well as the possible regulation of the enzyme activity by means of the availability of reduced FMN, remain poorly understood. This review summarizes recent developments in the biochemical and genetic arena and identifies future aims in this field.

Catalysis↗
PubMed2003

Simulating the nucleation of water/ethanol and water/n-nonane mixtures: mutual enhancement and two-pathway mechanism.

A combination of the aggregation-volume-bias and configurational-bias Monte Carlo algorithms and the umbrella sampling technique was applied to investigate two different binary vapor-liquid nucleation systems: water/ethanol and water/n-nonane. The simulations are able to reproduce the different nonideal nucleation behavior observed experimentally for these two systems, i.e., the mutual enhancement of nucleation rates for water/ethanol mixtures and the two-pathway nucleation for water/n-nonane mixtures. Structural analysis provides microscopic explanations for the observed nucleation behavior. In particular, the simulations show a large and size-dependent surface enrichment of ethanol in the water/ethanol droplets, which confirms the previous experimental interpretation for this system. The immiscibility observed even for small water/n-nonane clusters causes the two-pathway nucleation mechanism.

Journal Article↗
PubMed1998

Signaling molecules derived from the cholesterol biosynthetic pathway: mechanisms of action and possible roles in human disease.

The association of high plasma cholesterol levels with the development of atherosclerosis is well known. The metabolic pathways that are regulated by cholesterol and the mechanisms involved are less well understood. Recent studies have identified not only cholesterol, but also oxysterols and isoprenoids, derived from the cholesterol biosynthetic pathway, as new signaling molecules. The transcriptional and post-transcriptional regulation of specific genes and metabolic pathways by these newly discovered signaling molecules may be important in the development of human disease and forms the topic of this review.

Abnormalities, Multiple↗
PubMed1995

Metastases: mechanisms, pathways, and cascades.

Metastases are the major cause of treatment failure in cancer patients. Sixty percent of patients with newly diagnosed solid tumors (excluding skin cancers other than melanoma) have clinically evident or microscopic metastases when the primary tumor is diagnosed [1]. Dissemination of malignant cells throughout the body and their survival to form secondary growths constitute a complicated process dependent on both host and tumor properties. This review outlines the mechanisms involved in the metastatic process, the pathways of tumor spread throughout the body, and the common routes used by various tumors.

Female↗
PubMed1994

The ubiquitin-mediated proteolytic pathway: mechanisms of action and cellular physiology.

Ubiquitin modification of many protein targets within cells plays important roles in a variety of biological processes. Among these are regulation of gene expression, regulation of cell cycle and division, involvement in the cellular stress response, modification of cell surface receptors, DNA repair, import of proteins into mitochondria, uptake of precursors of neurotransmitters into synaptosomes, biogenesis of peroxisomes, assembly of ribosomes, and programmed cell death. The mechanisms that underlie these complex processes are poorly understood. The best studied modification occurs in the ubiquitin-mediated proteolytic pathway. Recent experimental evidence indicates that the ubiquitin system is involved in the degradation of mitotic cyclins, oncoproteins and tumor suppressors, in the removal of abnormal and otherwise damaged proteins, and in processing of antigens restricted to class I MHC molecules. Degradation of a protein via the ubiquitin system involves two discrete steps. Initially, multiple ubiquitin molecules are covalently linked in an ATP-dependent mode to the protein substrate. The targeted protein is then degraded by a specific, energy-dependent and high molecular mass protease complex into peptides and free amino acids, and free and reutilizable ubiquitin is released. In addition, stable mono-ubiquitin adducts are also found in the cell, for example, those involving nucleosomal histones. Despite the considerable progress that has been made in elucidating the mode of action and roles of the ubiquitin system, many problems remain unsolved. For example, little is known on the signals that target proteins for degradation. While a few proteins are targeted for degradation following recognition of their N-terminal amino acid residue, the vast majority of cellular proteins are targeted by other signals. The identity of the native cellular substrates of the system is another important, yet unresolved problem: only a few proteins have been recognized so far as substrates of the system in vivo. The scope of this review is to discuss the mechanisms involved in ubiquitin activation, selection of substrates for conjugation, and degradation of ubiquitin-conjugated proteins in the cell-free system. In addition, we shall summarize what is currently known of the physiological roles of ubiquitin-mediated proteolysis in vivo.

Adenosine Triphosphate↗
PubMed2005

Platelet activation and the CD40/CD40 ligand pathway: mechanisms and implications for human disease.

The discovery that platelets express CD40 and the CD40 ligand has transformed these cells, once seen as exclusively involved in coagulation and thrombosis, into active players of immunity and inflammatory injury. Many of the broad and potent biological activities mediated through the CD40/CD40 pathway by immune and nonimmune cells are also exerted by activated platelets. This occurs either through the constitutive expression of CD40 on the platelet surface or the activation-induced expression of the CD40 ligand, which is membrane bound and released from the surface in a soluble form. The most prominent activities mediated by the platelet CD40/CD40 ligand pathway include inflammatory, immunoregulatory, and hemostatic functions, all of which contribute to the newly expanded view of platelets as key biological mediators involved in disease processes such as atherosclerosis, inflammatory bowel disease, and diabetes. Therefore, considering platelet CD40 and CD40 ligand as novel biological targets is justified and supported by animal studies. The clinical profit to be gained from blocking this molecular pair will be determined by results in humans with conditions in which the platelet CD40/CD40 ligand pathway is crucially involved in disease pathogenesis.

Animals↗
PubMed2006

Proteomic analysis of colorectal cancer reveals alterations in metabolic pathways: mechanism of tumorigenesis.

Colorectal cancer is the second leading killer cancer worldwide and presently the most common cancer among males in Singapore. The study aimed to detect changes of protein profiles associated with the process of colorectal tumorigenesis to identify specific protein markers for early colorectal cancer detection and diagnosis or as potential therapeutic targets. Seven pairs of colorectal cancer tissues and adjacent normal mucosa were examined by two-dimensional gel electrophoresis at basic pH range (pH 7-10). Intensity changes of 34 spots were detected with statistical significance. 16 of the 34 spots were identified by MALDI-TOF/TOF tandem mass spectrometry. Changes in protein expression levels revealed a significantly enhanced glycolytic pathway (Warburg effect), a decreased gluconeogenesis, a suppressed glucuronic acid pathway, and an impaired tricarboxylic acid cycle. Observed changes in protein abundance were verified by two-dimensional DIGE. These changes reveal an underlying mechanism of colorectal tumorigenesis in which the roles of impaired tricarboxylic acid cycle and the Warburg effect may be critical.

Case-Control Studies↗
PubMed1990

Proteolysis is a critical step in the physiological stop pathway: mechanisms involved in the blockade of axonal regeneration by mammalian astrocytes.

Regenerating axons of adult dorsal roots are stopped by reactive astrocytes at the PNS-CNS junction. While it has been suggested that the astrocytes might pose a physical barrier to axonal growth, based on ultrastructural comparisons of physically blocked and axo-glial endings, it was proposed that astrocytes in the root transitional zone block axonal growth by activating the physiological stop pathway within the growing axon tips. Part of the stop pathway involves the proteolytic breakdown and removal of neurofilaments as they enter the axon endings. Another component involves the establishment of anterograde-to-retrograde conversion for the removal of membranous elements from the axonal endings. Both of these components appear to be dependent upon the activation of proteases within the axon tips. Therefore, to further test our hypothesis we infused, by intrathecal catheterization, the region of the dorsal root transitional zone with the protease inhibitor leupeptin at a time when the majority of regenerating axons have terminated in the region. Ultrastructural analyses after leupeptin treatment revealed axo-glial endings distended by accumulations of neurofilaments and organelles, particularly tubulovesicular profiles. These observations further support the idea that astrocytes, like normal target cells, can activate the physiological stop pathway.

Animals↗
PubMed1994

The ubiquitin-mediated proteolytic pathway: mechanisms of recognition of the proteolytic substrate and involvement in the degradation of native cellular proteins.

Ubiquitin modification of a variety of protein targets within the cell plays important roles in many cellular processes. Among these are regulation of gene expression, regulation of cell cycle and division, involvement in the cellular stress response, modification of cell surface receptors, DNA repair, import of proteins into mitochondria, uptake of precursors into neurons, and biogenesis of mitochondria, ribosomes, and peroxisomes. The best studied modification occurs in the ubiquitin-mediated proteolytic pathway. Degradation of a protein via the ubiquitin system involves two discrete steps. Initially, multiple ubiquitin molecules are covalently linked in an ATP-dependent mode to the protein substrate. The targeted protein is then degraded by a specific and energy-dependent high molecular mass protease into free amino acids, and free and reutilizable ubiquitin is released. In addition, stable mono-ubiquitin adducts are also found in the cell, for example, those involving nucleosomal histones. Despite the considerable progress that has been made in elucidating the mode of action and roles of the ubiquitin system, many problems remain unsolved. For example, little is known on the signals that target proteins for degradation. Although mechanistic aspects of recognition via the N-terminal residue have been studied thoroughly, it is clear that the vast majority of cellular proteins are targeted by other signals. The identity of the native cellular substrates of the system is another important, yet unresolved, problem: only few proteins have been recognized so far as substrates of the system in vivo. The scope of this review is to discuss the mechanisms involved in ubiquitin activation, selection of substrates for conjugation, and degradation of ubiquitin-conjugated proteins in the cell-free system. In addition, we shall summarize what is currently known of the physiological roles of ubiquitin-mediated proteolysis in vivo.

Amino Acid Sequence↗
PubMed2006

Glucose utilization and the PI3-K pathway: mechanisms for cell survival in preimplantation embryos.

The maintenance of optimal glucose utilization during the preimplantation period is critical for embryo survival. A decrease in glucose transport during preimplantation development has been linked to the early steps of programmed cell death in these embryos. Decreased glucose transport is not thought to be simply a consequence of cell death, rather it is thought to be a trigger that can initiate the apoptotic cascade. Extensive apoptosis during the preimplantation period may manifest later in pregnancy as a malformation-- or miscarriage, if cell loss is excessive. Phosphatidylinositol 3-kinase (PI3-K) is a known regulator of a number of physiologic responses including cellular proliferation, growth, and survival as well as glucose metabolism. Studies performed in other cell systems have demonstrated that the PI3-K pathway plays a critical role in maintaining glucose transport and metabolism. This review will present the current evidence that suggests that PI3-K is vital for preimplantation embryo survival and development. In addition, data demonstrating that PI3-K activity is important for glucose metabolism during this early developmental period will be discussed.

Animals↗
PubMed2001

Acidic extracellular pH induces vascular endothelial growth factor (VEGF) in human glioblastoma cells via ERK1/2 MAPK signaling pathway: mechanism of low pH-induced VEGF.

Overexpression of vascular endothelial growth factor (VEGF) is associated with disease progression in human glioblastomas. We recently showed that VEGF promoter activity is inversely correlated with tumor extracellular pH (pH(o)) in vivo in the human glioma (U87 MG) xenografts. Here we show that substitution of the neutral culture medium (pH 7.3) with acidic pH medium (pH 6.6) up-regulates VEGF mRNA and protein production in human glioblastoma cells as reflected by Northern blot analysis and enzyme-linked immunosorbent assay. Functional analysis of the VEGF promoter reveals that the sequence between -961 bp and -683 bp upstream of the transcription start site is responsible for the transcriptional activation of the VEGF gene by acidic pH. This region contains the binding site for AP-1. Consequently, AP-1 luciferase reporter gene was activated by acidic pH. Gel-shift analysis confirmed that AP-1 DNA binding activity is induced under acidic pH. While investigating the upstream signaling pathways, we found that ERK1/2 MAPK is activated and translocates to the nucleus to activate Elk-1, and inhibition of the activation of ERK by specific inhibitors of MEK1 blocks the up-regulation of VEGF by low pH. Dominant negative forms of Ras and Raf abolished the activation of VEGF promoter by acidic pH. These results show that acidic pH activates Ras and the ERK1/2 MAPK pathway to enhance VEGF transcription via AP-1, leading to increased VEGF production.

Base Sequence↗