Temperature dependence of the effects of some monohydric alcohols on the oxygen affinity of hemoglobin: Determination and analysis of thermodynamic parameters

We studied the effects of methanol, ethanol, iso-propanol, and n-propanol on the reaction of hemoglobin with oxygen at various temperatures. The analysis of the results in terms of the Monod-Wyman-Changeux model allowed determination of the overall contribution of the alcohols to the standard enthalpy and entropy differences between the T and R states of hemoglobin. A phenomenological approach allowed us to obtain separately the contributions related to the variations of the bulk dielectric constant of the solvent (bulk electrostatic contributions) and the contributions related to other effects (non-bulk-electrostatic contributions). The values of non-bulk-electrostatic contributions to ΔΔH and ΔΔS supported the suggestion that these contributions are mainly related to protein-solvent hydrophobic interactions.     

Effect of passage in culture on a clone of BALB/c 3T3 cells transformed by simian virus 40.

Most simian virus 40 (SV40)-transformed BALB/c 3T3 clones employed for biochemical studies have been used without regard to passage level. To determine whether virus-induced properties are stable as a function of passage, we have extensively characterized one transformed clone, FNE, which was isolated after SV40 infection BALB/c 3T3 cells in factor-free medium. From the initial testing at passage 5 and for at least 50 subsequent subcultures, the cells stably maintained many transformed growth properties, including high saturation density, morphology, colony formation on contact-inhibited monolayers, tumorigenicity, and synthesis of viral-specific RNA. However, other properties varied as a function of passage. There was a slight decrease in viral genome equivalents per cell from 1.1 copy/cell at passage 5 to 0.7 copies at passage 40. Initially, the cells were negative for all type C virus; however, cells carried at low density for 13 to 20 passages (65 to 100 generations) began to release an endogenous type C virus that then persisted in the culture. Spontaneous release of type C virus did not occur in control BALB/c 3T3 cells carried under identical culture conditions for 90 passages. When the cultures were releasing type C viruses they stained uniformly and brightly positive for SV40 tumor (T) antigen by immunofluorescence, whereas T antigen staining was variable at early passage. These experiments suggest that subtle but perhaps important differences in viral gene expression can occur as a function of passage; they also demonstrate the importance of evaluating the interactions between SV40 and endogenous type C viruses.     

Mechanisms of siderophore iron transport in enteric bacteria.

Uptake of 55Fe- and 3H-labeled siderophores and their chronic analogues have been studied in Salmonella typhimurium LT-2 and Escherichia coli K-12. In S. typhimurium LT-2, at least two different mechanisms for siderophore iron transport may be operative. Uptake of 55Fe- and 3H-labeled ferrichrome and kinetically inert lambda-cis-chromic [3H]deferriferrichrome by the S. typhimurium LT-2 enb7 mutant, which is defective in the production of its native siderophore, enterobactin, appears to occur by two concurrent mechanisms. The first mechanism is postulated to involve either rapid uptake of iron released from the ferric complex by cellular reduction without penetration of the complex or ligand or dissociation of the complex and simultaneous uptake of both ligand and iron coupled with simultaneous expulsion of the ligand. The second mechanism appears to consist of slower uptake of the intact ferric complex.     

The free energy folding penalty accompanying binding of intrinsically disordered α‐helical motifs

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes and preform critical roles in many cellular processes, most often through the association with globular proteins. Despite lacking a stable three‐dimensional structure by themselves, they may acquire a defined conformation upon binding globular targets. The most common type of secondary structure acquired by these binding motifs entails formation of an α‐helix. It has been hypothesized that such disorder‐to‐order transitions are associated with a significant free energy penalty due to IDP folding, which reduces the overall IDP‐target affinity. However, the exact magnitude of IDP folding penalty in α‐helical binding motifs has not been systematically estimated. Here, we report the folding penalty contributions for 30 IDPs undergoing folding‐upon‐binding and find that the average IDP folding penalty is +2.0 kcal/mol and ranges from 0.7 to 3.5 kcal/mol. We observe that the folding penalty scales approximately linearly with the change in IDP helicity upon binding, which provides a simple empirical way to estimate folding penalty. We analyze to what extent do pre‐structuring and target‐bound IDP dynamics (fuzziness) reduce the folding penalty and find that these effects combined, on average, reduce the folding cost by around half. Taken together, the presented analysis provides a quantitative basis for understanding the role of folding penalty in IDP‐target interactions and introduces a method estimate this quantity. Estimation and reduction of IDP folding penalty may prove useful in the rational design of helix‐stabilized inhibitors of IDP‐target interactions.StatementThe α‐helical binding motifs are ubiquitous among the intrinsically disordered proteins (IDPs). Upon binding their targets, they undergo a disorder‐to‐order transition, which is accompanied by a significant folding penalty whose magnitude is generally not known. Here, we use recently developed statistical‐thermodynamic model to estimate the folding penalties for 30 IDPs and clarify the roles of IDP pre‐folding and bound‐state dynamics in reducing the folding penalty.     

A new genus of Syllidae (Polychaeta) from Western Australia

During a study carried out on the subfamily Exogoninae (Syllidae) from Australia, several specimens of a new genus and species were found in samples of dead coral substrate from Western Australia. They have long palps, fused except for a terminal notch, long median and two short lateral antennae, a single pair of short tentacular cirri, and short dorsal cirri, somewhat longer than the parapodial lobes. These characters resemble those of the genus Exogone Örsted, 1845. However, all these appendages are articulated. The chaetae are very similar to those of several species of Syllis Lamarck, 1818, having coarse spines on the margin of compound chaetal blades and truncated dorsal simple chaetae. Furthermore, the pharynx begins in chaetiger 3, posterior to the peristomium, as in many species of the genus Syllis; this condition does not occur in any described species of Exogone. The new genus is provisionally proposed to belong to the subfamily Syllinae, although it has some characters typical of the Exogoninae. Examination under the SEM shows another peculiar feature, the nuchal organs are distinctly laterally located. Within the Syllinae, only Paratyposyllis Hartmann-Schröder, 1962 has a single pair of tentacular cirri, but in that genus, the palps are only basally fused.     

On preprocessing and antisymmetry in de novo peptide sequencing: improving efficiency and accuracy

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.     

Iron transport-mediated antagonism between plant growth-promoting and plant-deleterious Pseudomonas strains

Both plant growth-promoting Pseudomonas B10 and its yellow-green, fluorescent iron transport agent (siderophore) pseudobactin enhance potato growth and biologically control certain soil-borne fungal diseases in part by depriving specific root-colonizing endemic microorganisms including phytopathogens of iron(III), thus inhibiting their growth. The present study examines this mode of iron deprivation. The growth inhibition of certain bean-deleterious fluorescent pseudomonads by specific bean-beneficial fluorescent pseudomonads is due in part to the inability of susceptible strains to utilize siderophores from beneficial strains to transport iron(III). Conversely, deleterious strains which were able to utilize siderophores from beneficial strains were not inhibited. The ability of a given pseudomonad to utilize another pseudomonad's siderophore may depend upon its possessing a specific outer membrane receptor protein for that pseudomonad's ferric siderophore. Siderophore-mediated competition for iron in microbial systems appears to be a widespread phenomenon.