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Several hyperbolically saturating empirical models, such as the Michaelis-Menten rate equation, Monod's relative population growth rate, competitive inhibition, and Langmuir's adsorption, are rederived from a simple queuing relation. The resulting derivations reveal and potentially explain the underlying structure and meaning of such empirical models. This view is proposed as a unifying heuristic.

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Bacterial chromosomes frequently contain arrays of contiguous genes that group according to related metabolic roles. We propose that clustering of genes for metabolically related functions confers thermodynamic advantage to the organism based upon our protein immobility model (PIM) of intracellular diffusion. This thermodynamic effect provides the selection force argument that is missing from previous models of gene clustering. The PIM posits that clustered genes produce local clusters of enzymes in bacteria owing to the co-linearity of transcription and translation, and to the relative immobility of large proteins released into the cytosol. We maintain that the resulting physical proximity of enzymes for related pathway steps minimizes the steady state level of reaction step intermediates and thus conserves the energy and material required for rapid growth and maintenance. Support for this idea comes from in silico experiments using the PIM applied to a model metabolic pathway A --> B --> C. The metabolites A, B, and C are small molecules that diffuse freely in a cytosol crowded with macromolecules, whereas the large enzyme molecules, E1 and E2, tend to remain in the vicinity of their point of release. Modeling E1 as a source of B from A, and E2 as a sink for B, numerical experiments suggest that the steady state concentration of B in the cytosol increases approximately in proportion to the square of the distance of the E1 and E2 separation. A further model prediction is that the steady state concentration of B is influenced by the geometric effects of the spatial location and orientation of E1 relative to E2. These results suggest that: (i) gene clustering reduces the energy and material costs of enzyme reactions linked by metabolic intermediates; (ii) gene clusters near ori, the origin of replication, utilize the geometric effect to conserve free energy by further reducing the steady state concentration of the intermediate; (iii) gene organization on a chromosome influences the organism's capacity to accelerate into steady state growth and is, in turn, influenced by the abundance and frequency of access to nutrients.

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Aneurysms of the left atrium are rare abnormalities. They can be congenital or acquired. Whereas a true congenital aneurysm presents as isolated pathology, inflammatory or degenerative processes involving the endocardium are associated with the acquired type. The clinical records of 2 patients with the diagnosis of left atrial aneurysm were reviewed, along with the surgical strategies, current literature, and patient outcomes. Because of the risk of life-threatening complications, surgery is recommended even in asymptomatic cases. Resection and mitral valvuloplasty should be the treatment of choice.

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Amino acid sequences for 11 acetohydroxy acid synthase (EC 4.1.3.18; AHS) polypeptides with experimentally established activity were chosen for computational comparisons to detect conserved local information associated with reaction specificity for each sequence. Windowed analysis by Pearson product moment cross-correlation of six amino acid sidechain properties revealed locally conserved segments common to all proteins with AHS activity. Seven information segments were detected in the same arrangement in sequences for the large subunit polypeptides of prokaryotes, and in the sequences for single polypeptides of eukaryotic AHS. The information segments were numbered 1-7 according to sequential position, and sequence features such as cofactor binding sites were defined for specific segments. Extension of the information segment analysis to seven other proteins of the pyruvate decarboxylase superfamily permitted use of the content and organization of information segments to recognize four classes of enzyme reaction specificity. Estimates of information entropy, based upon a state space defined by reaction specificity, directly reflected the known reaction complexity for all but one enzyme examined. Our data suggest that development of information-segment models for enzyme superfamilies may improve the accuracy of inferring protein activity from sequence.

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Equal Symbol Fourier Transforms (FTES), characterizing nucleotide periodicity, comprise components of 5-D vectors that define base-repeat properties of a genomic sequence. This report describes a conversion of the FTES signals to a common platform of Shannon information content to facilitate comparisons of periodic data with other measures of information for genes and genomes. The autocorrelation used to compute the discrete FTES formed the basis to define repeating bases in terms of conditional probabilities. We derived a vector equation to express the Shannon information content of a sequence in a way that preserves the distinct specificity of base repeat patterns characterized by FTES vectors. We suggest application of such information vectors to study the structure of information in genes, chromosomes, and genomes by chi(2) comparisons.

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Human cells contain four homologous Ras proteins, but it is unknown whether each of these Ras proteins participates in distinct signal transduction cascades or has different biological functions. To directly address these issues, we assessed the relative ability of constitutively active (G12V) versions of each of the four Ras homologs to activate the effector protein Raf-1 in vivo. In addition, we compared their relative abilities to induce transformed foci, enable anchorage-independent growth, and stimulate cell migration. We found a distinct hierarchy between the four Ras homologs in each of the parameters studied. The hierarchies were as follows: for Raf-1 activation, Ki-Ras 4B > Ki-Ras 4A >>> N-Ras > Ha-Ras; for focus formation, Ha-Ras >/= Ki-Ras 4A >>> N-Ras = Ki-Ras 4B; for anchorage-independent growth, Ki-Ras 4A >/= N-Ras >>> Ki-Ras 4B = Ha-Ras = no growth; and for cell migration, Ki-Ras 4B >>> Ha-Ras > N-Ras = Ki-Ras 4A = no migration. Our results indicate that the four Ras homologs significantly differ in their abilities to activate Raf-1 and induce distinctly different biological responses. These studies, in conjunction with our previous report that demonstrated that the Ras homologs can be differentially activated by upstream guanine nucleotide exchange factors (Jones, M. K., and Jackson, J. H. (1998) J. Biol. Chem. 273, 1782-1787), indicate that each of the four Ras proteins may qualitatively or quantitatively participate in distinct signaling cascades and have significantly different biological roles in vivo. Importantly, these studies also suggest for the first time that the distinct and likely cooperative biological functions of the Ki-ras-encoded Ki-Ras 4A and Ki-Ras 4B proteins may help explain why constitutively activating mutations of Ki-ras, but not N-ras or Ha-ras, are frequently detected in human carcinomas.

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The Rho family GTPases, Rac1 and Rac2, regulate a variety of cellular functions including cytoskeletal reorganization, the generation of reactive oxygen species, G1 cell cycle progression and, in concert with Ras, oncogenic transformation. Among the many putative protein targets identified for Rac (and/or Cdc42), the Ser/Thr kinase p21-activated kinase (PAK) is a prime candidate for mediating some of Rac's cellular effects. This report shows that Rac1 binds to and stimulates the kinase activity of PAK1 approximately 2- and 4-5-fold, respectively, better than Rac2. Mutational analysis was employed to determine the structural elements on Rac and PAK that are important for optimal binding and activation. The most notable difference between the highly homologous Rac isomers is the composition of their C-terminal polybasic domains. Mutation of these six basic residues in Rac1 to neutral amino acids dramatically decreased the ability of Rac1 to bind PAK1 and almost completely abolished its ability to stimulate PAK activity. Moreover, replacing the highly charged polybasic domain of Rac1 with the less charged domain of Rac2 (and vice versa) completely reversed the PAK binding/activation properties of the two Rac isomers. Thus, polybasic domain differences account for the disparate abilities of Rac1 and Rac2 to activate PAK. PAK proteins also contain a basic region, consisting of three contiguous lysine residues (Lys66-Lys67-Lys68), which lies outside of the previously identified Cdc42/Rac-binding domain. Mutation of these Lys residues to neutral residues decreased PAK binding to activated Rac1 and Rac2 (but not Cdc42) and greatly reduced PAK1 activation by Rac1, Rac2, and Cdc42 proteins in vivo. In contrast, mutation of lysines 66-68 to basic Arg residues did not decrease (and in some cases enhanced) the ability of Rac1, Rac2, and Cdc42 to bind and activate PAK1. Our studies suggest that the polybasic domain of Rac is a novel effector domain that may allow the two Rac isomers to activate different effector proteins. In addition, our results indicate that a basic region in PAK is required for PAK activation and that binding of Rac/Cdc42 to PAK is not sufficient for kinase activation.

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Human cells contain four homologous Ras proteins, but it is unknown whether these homologues have different biological functions. As a first step in determining if Ras homologues might participate in distinct signaling cascades, we assessed whether a given Ras guanine nucleotide exchange factor could selectively activate a single Ras homologue in vivo. We found that Ras-GRF/Cdc25Mm activates Ha-Ras, but does not activate N-Ras or K-Ras 4B, protein in vivo. Moreover, our results suggested that residues within the C-terminal hypervariable domains of Ras proteins may dictate, at least in part, the specificity of Ras-GRF/CDC25Mm for Ha-Ras protein. Our studies represent the first biochemical evidence that a Ras GEF can selectively activate a single Ras homologue in vivo. Selective activation of a single Ras homologue by Ras-GRF/Cdc25Mm or other Ras guanine nucleotide exchange factors could potentially enable each of the Ras homologues to participate in different signal transduction pathways.

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Human tissues which are chronically infiltrated with inflammatory leukocytes are more likely to develop malignancies than non-inflamed tissues, however the mechanism(s) by which leukocytes contribute to carcinogenesis is unknown. Stimulated human leukocytes release superoxide anion and hydrogen peroxide which, in the presence of iron, can be converted into the potent oxidant, hydroxyl radical (.OH). Previous studies have shown that leukocyte-derived .OH (or a .OH-like species) can cause DNA damage, however a relationship between leukocyte-induced DNA damage and carcinogenesis has not been established. The present report demonstrates that leukocyte-derived .OH-induced DNA damage can cause K-ras oncogene activation, and suggests that there may be a characteristic pattern of .OH-induced K-ras oncogene activation. Since activation of the K-ras oncogene is believed to play a crucial role in the pathogenesis of many human malignancies, .OH-induced K-ras oncogene activation could be an important mechanism by which human leukocytes contribute to carcinogenesis.

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The channeling behavior of acetohydroxy acid synthases I and III (EC 4.1.3.18; AHAS) was studied by computer simulation of activities over a wide range of concentrations for the substrates pyruvate and 2-ketobutyrate. The ratios of reaction rates for both channels and three-dimensional plots of single-channel reaction rates versus substrate concentrations were introduced to compare the substrate channeling properties of the isozymes. Substrate ranges were identified in which AHAS I and III operated both channels, and in which they used only one. Kinetic constants were varied to simulate whether and how AHAS might be made channel-specific. Our study suggests that AHAS might be made channel-specific for acetolactate but not for acetohydroxybutyrate. We postulate specific physiological roles for AHAS I and III to support cell growth under conditions that vary the levels and balance of substrates.

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Previous studies have shown that posttranslational modifications are required for both oncogenic K-ras 4B protein membrane binding and transforming activity. In addition, Hancock et al. [Hancock, J. F., Patterson, H. & Marshall, C. J. (1990) Cell 63, 133-139] found that a polylysine domain contained at the C terminus of K-ras 4B was also absolutely essential for K-ras 4B membrane binding but, surprisingly, neither the polylysine domain nor membrane binding was required for transforming activity. We have performed similar studies, but our results are distinctly different. Our studies indicate that the polylysine domain is crucial for K-ras 4B transforming activity. Moreover, we demonstrate that although the polylysine domain increases K-ras 4B membrane binding, significant amounts of membrane binding can occur in the absence of this domain. Finally, while our studies are consistent with the notion that membrane binding is required for K-ras 4B transforming activity, we show that membrane binding, in and of itself, is not sufficient for efficient K-ras 4B transforming activity.

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