Folding kinetics of phage 434 Cro protein

Folding kinetics for phage 434 Cro protein are examined and compared with those reported for lambda(6-85), the N-terminal domain of the repressor of phage lambda. The two proteins have similar all-helical structures consisting of five helices but different stabilities. In contrast to lambda(6-85), sharp and distinct aromatic (1)H NMR signals without exchange broadening characterize the native and urea-denatured 434 Cro forms at equilibrium at 20 degrees C, indicating slow interconversion on the NMR time scale. Stopped-flow fluorescence data using the single 434 Cro tryptophan indicate strongly urea-dependent refolding rates and smaller urea dependencies of the unfolding rates, suggesting a native-like transition state ensemble. Refolding rates are slower and unfolding rates considerably faster at pH 4 than at pH 6. This accounts for the lower stability of 434 Cro at pH 4 and suggests the existence of pH-dependent, possibly salt bridge interactions that are more stabilizing at pH 6. At <2 M urea, decreased folding amplitudes and nonlinear urea dependencies that are apparent at pH 6 indicate deviation from two-state behavior and suggest the formation of an early folding intermediate. The folding behavior of 434 Cro and why it folds 2 orders of magnitude slower than lambda(6-85) are rationalized in terms of the lower intrinsic helix stabilities and putative charge interactions in 434 Cro.     

Contribution of cell surface hydrophobicity protein 1 (Csh1p) to virulence of hydrophobic Candida albicans serotype A cells

The CSH1 gene product is the first protein implicated to affect the phenotype of cell surface hydrophobicity in Candida albicans. Ablation of expression of CSH1 resulted in a 75% loss of the cell surface hydrophobicity (CSH) phenotype. When the C. albicans csh1 knockout derivative was cultured from frozen stocks, it had reacquired CSH levels similar to the parent strain and isogenic reintegrant in the absence of Csh1p re-expression through an unknown mechanism. Prior to reacquisition of CSH, the knockout was less adherent to fibronectin than the parent. Comparison of the csh1 knockout and CSH1 reintegrant in a hematogenous dissemination model allows analysis of Csh1p contribution to virulence using matched strains with similar levels of CSH. No statistical significance between the knockout and reintegrant was found in virulence based on median day of survival, although a reproducible delay in onset of lethal infection for the knockout was observed. A modest difference in mucosal colonization in a vaginal infection model was also observed between the knockout and reintegrant. The present study demonstrates that Csh1p contributes to virulence of C. albicans in mice, but other gene products also contribute to the CSH phenotype and virulence.     

Biochemical analysis of point mutations in the 5'-3' exonuclease of DNA polymerase I of Streptococcus pneumoniae. Functional and structural implications

To define the active site of the 5'-3' exonucleolytic domain of the Streptococcus pneumoniae DNA polymerase I (Spn pol I), we have constructed His-tagged Spn pol I fusion protein and introduced mutations at residues Asp(10), Glu(88), and Glu(114), which are conserved among all prokaryotic and eukaryotic 5' nucleases. The mutations, but not the fusion to the C-terminal end of the wild-type, reduced the exonuclease activity. The residual exonuclease activity of the mutant proteins has been kinetically studied, together with potential alterations in metal binding at the active site. Comparison of the catalytic rate and dissociation constant of the D10G, E114G, and E88K mutants and the control fusion protein support: (i) a critical function of Asp(10) in the catalytic event, (ii) a role of Glu(114) in the exonucleolytic reaction, being secondarily involved in both catalysis and DNA binding, and (iii) a nonessential function of Glu(88) for the exonuclease activity of Spn pol I. Moreover, the pattern of metal activation of the mutant proteins indicates that none of the three residues is a metal-ligand at the active site. These findings and those previously obtained with D190A mutant of Spn pol I are discussed in relation to structural and mutational data for related 5' nucleases.     

Biochemical basis for the dominant inheritance of hypermethioninemia associated with the R264H mutation of the MAT1A gene. A monomeric methionine adenosyltransferase with tripolyphosphatase activity

Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (AdoMet), the main alkylating agent in living cells. Additionally, in the liver, MAT is also responsible for up to 50% of methionine catabolism. Humans with mutations in the gene MAT1A, the gene that encodes the catalytic subunit of MAT I and III, have decreased MAT activity in liver, which results in a persistent hypermethioninemia without homocystinuria. The hypermethioninemic phenotype associated with these mutations is inherited as an autosomal recessive trait. The only exception is the dominant mild hypermethioninemia associated with a G-A transition at nucleotide 791 of exon VII. This change yields a MAT1A-encoded subunit in which arginine 264 is replaced by histidine. Our results indicate that in the homologous rat enzyme, replacement of the equivalent arginine 265 by histidine (R265H) results in a monomeric MAT with only 0.37% of the AdoMet synthetic activity. However the tripolyphosphatase activity is similar to that found in the wild type (WT) MAT and is inhibited by PP(i). Our in vivo studies demonstrate that the R265H MAT I/III mutant associates with the WT subunit resulting in a dimeric R265H-WT MAT unable to synthesize AdoMet. Tripolyphosphatase activity is maintained in the hybrid MAT, but is not stimulated by methionine and ATP, indicating a deficient binding of the substrates. Our data indicate that the active site for tripolyphosphatase activity is functionally active in the monomeric R265H MAT I/III mutant. Moreover, our results provide a molecular mechanism that might explain the dominant inheritance of the hypermethioninemia associated with the R264H mutation of human MAT I/III.     

Characterization of Scale Abnormalities in Pinfish, Lagodon rhomboides, from Biscayne Bay, Florida

Correlations between marine habitat degradation and the prevalence of abnormalities and diseases in populations can provide a starting point for understanding the effects of changes in environmental conditions on marine organisms. The present study characterized the features of scale disorientation (SD), a common morphological anomaly encountered in pinfish, Lagodon rhomboides, in Biscayne Bay, Florida (U.S.A.). Scale disorientation consisted of discrete patches of scales rotated dorsally or ventrally away from the normal scale position without any projection of the scales outwards from the body surface. The direction of scale growth within the patches varied from normal to a minor misalignment to a complete reversal of direction. The severity of SD, defined as the percentage of body surface area affected, varied from 1 to 34% with a mean of 9.3%. Affected fish monitored in the laboratory demonstrated a proportional growth of SD areas such that the percentage of body surface affected did not change as the fish grew. Scale disorientation was more prevalent in the northern region of the bay, an area known to be more contaminated. Scales from SD areas exhibited significantly abnormal morphology with larger average focus diameter, smaller size, more elongate shape and fewer radii relative to normal scales. Experimental removal of scales demonstrated that normal scales regrew in normal orientation and morphology while those from SD areas regrew in abnormal orientations and morphologies. Experiments in which fish were exposed to acute and chronic injuries indicated that these physical traumas were insufficient to directly induce formation of scale disorientations typical of those seen in the wild. Observations of pinfish in the laboratory revealed that SD areas can appear spontaneously in normal juvenile and adult fish. These new SD areas developed relatively rapidly, did not require prior scale loss and remained stable in size after first appearance. Although the etiology of SD remains unknown, the significant difference in prevalence of this syndrome between regions of Biscayne Bay having different levels of sediment contaminants suggests that environmental factors may be important in development of SD.     

Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins

Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine–aspartate domain–containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.     

Agricultural development and maize diversity in Mexico

Mexico is within the center of origin of Zea mays and has among the highest levels of maize genetic diversity in the world. This diversity is traced to factors at the regional and farm levels. Loss of crop genetic diversity has been related to economic and agricultural development, although opposed views of this exist for the Mexican case. Agricultural development appears to be affecting virtually all types of farms in Mexico. A case study in Chiapas suggests that the adoption of some improved varieties has enhanced genetic diversity in maize, but one improved type competes with landraces in the most favorable land. The adoption of this improved type is associated with greater access to capital and with lower risk.The research for this project was carried out with the support of the UC/MEXUS program of the University of California and CONACYT. We wish to acknowledge the advice and assistance provided by Esteban Betanzos of the Chiapas office of the Instituto Nacional de Investigaciones Forestales y Agropecuarios, Efraim Hernandez of the Colegio de Postgraduados at Chapingo, Robert Tripp of the Centro Internacional de Mejoramiento de Maiz y Trigo, and to Manuel Parra of the Centro de Investigaciones Ecologicas del Sureste in San Cristobal de las Casas. The authors wish to thank J. Edward Taylor, Andraes Buerkert, Aaron Zazueta, and Daniel Mountjoy for their useful comments on an earlier draft.     

Gold Nanostar Synthesis with a Silver Seed Mediated Growth Method

The physical, chemical and optical properties of nano-scale colloids depend on their material composition, size and shape ^1-5. There is a great interest in using nano-colloids for photo-thermal ablation, drug delivery and many other biomedical applications ⁶. Gold is particularly used because of its low toxicity ^7-9. A property of metal nano-colloids is that they can have a strong surface plasmon resonance ¹⁰. The peak of the surface plasmon resonance mode depends on the structure and composition of the metal nano-colloids. Since the surface plasmon resonance mode is stimulated with light there is a need to have the peak absorbance in the near infrared where biological tissue transmissivity is maximal ^{11, 12}.We present a method to synthesize star shaped colloidal gold, also known as star shaped nanoparticles ^13-15 or nanostars ¹⁶. This method is based on a solution containing silver seeds that are used as the nucleating agent for anisotropic growth of gold colloids ^17-22. Scanning electron microscopy (SEM) analysis of the resulting gold colloid showed that 70 % of the nanostructures were nanostars. The other 30 % of the particles were amorphous clusters of decahedra and rhomboids. The absorbance peak of the nanostars was detected to be in the near infrared (840 nm). Thus, our method produces gold nanostars suitable for biomedical applications, particularly for photo-thermal ablation.